Note: the module "R" cannot be unloaded because it was not loaded. WARNING: ignoring environment value of R_HOME R Under development (unstable) (2026-07-04 r90207) -- "Unsuffered Consequences" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > (cargs <- commandArgs(trailingOnly=TRUE)) [1] "/scratch/th798/data.table-revdeps/2026-07-06/deps.csv" [2] "1314" [3] "/scratch/th798/data.table-revdeps/2026-07-06/data.table_release_1.18.4.tar.gz" [4] "/scratch/th798/data.table-revdeps/2026-07-06/data.table_master_1.18.99.8c4291395093bf68a53853c867ac62cbc138e6fe.tar.gz" > if(length(cargs)==0){ + ## before running interactively, make sure to start emacs/R with + ## environment defined in /scratch/...check_one.sh, particularly + ## R_LIBS_USER=/tmp/... otherwise we get error when installing + ## data.table. + base <- "/scratch/th798/data.table-revdeps/*" + cargs <- c( + Sys.glob(file.path(base,"deps.csv")), + "9", + Sys.glob(file.path(base, "data.table_release_*tar.gz")), + Sys.glob(file.path(base, "data.table_master_*tar.gz")) + ) + } > names(cargs) <- c("deps.csv", "task.str", "release", "master") > dput(cargs) c(deps.csv = "/scratch/th798/data.table-revdeps/2026-07-06/deps.csv", task.str = "1314", release = "/scratch/th798/data.table-revdeps/2026-07-06/data.table_release_1.18.4.tar.gz", master = "/scratch/th798/data.table-revdeps/2026-07-06/data.table_master_1.18.99.8c4291395093bf68a53853c867ac62cbc138e6fe.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/29939837/R-devel/1314" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache Failed with error: 'there is no package called 'R.cache'' > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (deps.row <- deps.df[task.id,]) Package task.id Version 1314 restatapi 1314 0.25.0 > (rev.dep <- deps.row$Package) [1] "restatapi" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/29939837/R-devel/1314/library" [2] "/projects/genomic-ml/R/R-devel/library" > local.CRAN <- "/projects/genomic-ml/CRAN" > cran.url <- paste0("file://", local.CRAN) > #this should be in ~/.Rprofile too. > options(repos=c(CRAN=cran.url)) > print(Sys.time()) [1] "2026-07-06 11:01:09 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/29939837/R-devel/1314/library' (as 'lib' is unspecified) also installing the dependencies 'fs', 'R6', 'rappdirs', 'base64enc', 'cachem', 'fastmap', 'lifecycle', 'memoise', 'mime', 'sass', 'digest', 'cli', 'rlang', 'evaluate', 'highr', 'xfun', 'yaml', 'bslib', 'fontawesome', 'htmltools', 'jquerylib', 'jsonlite', 'tinytex', 'rjson', 'xml2', 'chron', 'knitr', 'rmarkdown', 'tinytest', 'remotes' * installing *source* package 'fs' ... ** this is package 'fs' version '2.1.0' ** package 'fs' successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/home/th798/.conda/envs/emacs1/include Using PKG_LIBS=-L/home/th798/.conda/envs/emacs1/lib -luv -lrt -ldl ** libs using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dir.cc -o dir.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c error.cc -o error.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c file.cc -o file.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fs.cc -o fs.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c getmode.cc -o getmode.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c id.cc -o id.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.cc -o init.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c link.cc -o link.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c path.cc -o path.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.cc -o utils.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c unix/getmode.cc -o unix/getmode.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bsd/setmode.c -o bsd/setmode.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bsd/strmode.c -o bsd/strmode.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bsd/reallocarray.c -o bsd/reallocarray.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o fs.so dir.o error.o file.o fs.o getmode.o id.o init.o link.o path.o utils.o unix/getmode.o bsd/setmode.o bsd/strmode.o bsd/reallocarray.o -L/home/th798/.conda/envs/emacs1/lib -luv -lrt -ldl installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-fs/00new/fs/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fs) * installing *source* package 'R6' ... ** this is package 'R6' version '2.6.1' ** package 'R6' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (R6) * installing *source* package 'rappdirs' ... ** this is package 'rappdirs' version '0.3.4' ** package 'rappdirs' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c win-path.c -o win-path.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o rappdirs.so init.o win-path.o installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-rappdirs/00new/rappdirs/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rappdirs) * installing *source* package 'base64enc' ... ** this is package 'base64enc' version '0.1-6' ** package 'base64enc' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c base64.c -o base64.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dummy.c -o dummy.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uriencode.c -o uriencode.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utf8.c -o utf8.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o base64enc.so base64.o dummy.o uriencode.o utf8.o installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-base64enc/00new/base64enc/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (base64enc) * installing *source* package 'fastmap' ... ** this is package 'fastmap' version '1.2.0' ** package 'fastmap' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilib/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -DR_NO_REMAP -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmap.cpp -o fastmap.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Ilib/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o fastmap.so fastmap.o init.o installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-fastmap/00new/fastmap/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fastmap) * installing *source* package 'mime' ... ** this is package 'mime' version '0.13' ** package 'mime' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rawmatch.c -o rawmatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o mime.so init.o rawmatch.o installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-mime/00new/mime/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mime) * installing *source* package 'digest' ... ** this is package 'digest' version '0.6.39' ** package 'digest' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c SpookyV2.cpp -o SpookyV2.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c aes.c -o aes.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c blake3.c -o blake3.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c blake3_dispatch.c -o blake3_dispatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c blake3_portable.c -o blake3_portable.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c crc32.c -o crc32.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c crc32c.cpp -o crc32c.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c crc32c_portable.cpp -o crc32c_portable.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c digest.c -o digest.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c digest2int.c -o digest2int.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c md5.c -o md5.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c pmurhash.c -o pmurhash.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c raes.c -o raes.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c sha1.c -o sha1.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c sha2.c -o sha2.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c sha256.c -o sha256.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c spooky_serialize.cpp -o spooky_serialize.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xxhash.c -o xxhash.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o digest.so SpookyV2.o aes.o blake3.o blake3_dispatch.o blake3_portable.o crc32.o crc32c.o crc32c_portable.o digest.o digest2int.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o spooky_serialize.o xxhash.o installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-digest/00new/digest/libs ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (digest) * installing *source* package 'cli' ... ** this is package 'cli' version '3.6.6' ** package 'cli' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ansi.c -o ansi.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cleancall.c -o cleancall.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c diff.c -o diff.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c errors.c -o errors.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c glue.c -o glue.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c inst.c -o inst.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c keypress-unix.c -o keypress-unix.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c keypress-win.c -o keypress-win.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c keypress.c -o keypress.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c md5.c -o md5.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c progress-altrep.c -o progress-altrep.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c progress.c -o progress.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c sha1.c -o sha1.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c sha256.c -o sha256.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c thread.c -o thread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c tty.c -o tty.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utf8.c -o utf8.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.c -o utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vt.c -o vt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vtparse.c -o vtparse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vtparse_table.c -o vtparse_table.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c win-utf8.c -o win-utf8.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c winfiles.c -o winfiles.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xxhash.c -o xxhash.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xxhash2.c -o xxhash2.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o cli.so ansi.o cleancall.o diff.o errors.o glue.o init.o inst.o keypress-unix.o keypress-win.o keypress.o md5.o progress-altrep.o progress.o sha1.o sha256.o thread.o tty.o utf8.o utils.o vt.o vtparse.o vtparse_table.o win-utf8.o winfiles.o xxhash.o xxhash2.o -lpthread installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-cli/00new/cli/libs ** R ** exec ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cli) * installing *source* package 'rlang' ... ** this is package 'rlang' version '1.2.0' ** package 'rlang' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I./rlang/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c capture.c -o capture.o touch internal.c /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I./rlang/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c internal.c -o internal.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I./rlang/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rlang.c -o rlang.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I./rlang/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c version.c -o version.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o rlang.so capture.o internal.o rlang.o version.o installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-rlang/00new/rlang/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rlang) * installing *source* package 'evaluate' ... ** this is package 'evaluate' version '1.0.5' ** package 'evaluate' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (evaluate) * installing *source* package 'xfun' ... ** this is package 'xfun' version '0.57' ** package 'xfun' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c base64.c -o base64.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rand_lcg.c -o rand_lcg.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o xfun.so base64.o init.o rand_lcg.o installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-xfun/00new/xfun/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (xfun) * installing *source* package 'yaml' ... ** this is package 'yaml' version '2.3.12' ** package 'yaml' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c api.c -o api.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dumper.c -o dumper.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c emitter.c -o emitter.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c implicit.c -o implicit.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c loader.c -o loader.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c parser.c -o parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c r_emit.c -o r_emit.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c r_ext.c -o r_ext.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c r_parse.c -o r_parse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c reader.c -o reader.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c scanner.c -o scanner.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c writer.c -o writer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o yaml.so api.o dumper.o emitter.o implicit.o loader.o parser.o r_emit.o r_ext.o r_parse.o reader.o scanner.o writer.o installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-yaml/00new/yaml/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (yaml) * installing *source* package 'jsonlite' ... ** this is package 'jsonlite' version '2.0.0' ** package 'jsonlite' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c base64.c -o base64.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c collapse_array.c -o collapse_array.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c collapse_object.c -o collapse_object.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c collapse_pretty.c -o collapse_pretty.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c escape_chars.c -o escape_chars.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c integer64_to_na.c -o integer64_to_na.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c is_datelist.c -o is_datelist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c is_recordlist.c -o is_recordlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c is_scalarlist.c -o is_scalarlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c modp_numtoa.c -o modp_numtoa.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c null_to_na.c -o null_to_na.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c num_to_char.c -o num_to_char.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c parse.c -o parse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c prettify.c -o prettify.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c push_parser.c -o push_parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c r-base64.c -o r-base64.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c register.c -o register.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c row_collapse.c -o row_collapse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c transpose_list.c -o transpose_list.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c validate.c -o validate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c yajl/yajl.c -o yajl/yajl.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c yajl/yajl_buf.c -o yajl/yajl_buf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c yajl/yajl_encode.c -o yajl/yajl_encode.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c yajl/yajl_gen.c -o yajl/yajl_gen.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c yajl/yajl_lex.c -o yajl/yajl_lex.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c yajl/yajl_parser.c -o yajl/yajl_parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c yajl/yajl_tree.c -o yajl/yajl_tree.o ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-jsonlite/00new/jsonlite/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for 'asJSON' with signature '"AsIs"': no definition for class "AsIs" in method for 'asJSON' with signature '"ITime"': no definition for class "ITime" in method for 'asJSON' with signature '"hms"': no definition for class "hms" in method for 'asJSON' with signature '"json"': no definition for class "json" in method for 'asJSON' with signature '"integer64"': no definition for class "integer64" in method for 'asJSON' with signature '"pairlist"': no definition for class "pairlist" in method for 'asJSON' with signature '"blob"': no definition for class "blob" in method for 'asJSON' with signature '"scalar"': no definition for class "scalar" in method for 'asJSON' with signature '"sf"': no definition for class "sf" in method for 'asJSON' with signature '"sfc"': no definition for class "sfc" in method for 'asJSON' with signature '"vctrs_vctr"': no definition for class "vctrs_vctr" ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (jsonlite) * installing *source* package 'rjson' ... ** this is package 'rjson' version '0.2.23' ** package 'rjson' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dump.cpp -o dump.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c parser.c -o parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c register.c -o register.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o rjson.so dump.o parser.o register.o installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-rjson/00new/rjson/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rjson) * installing *source* package 'chron' ... ** this is package 'chron' version '2.3-62' ** package 'chron' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c chron_strs.c -o chron_strs.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c unpaste.c -o unpaste.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o chron.so chron_strs.o init.o unpaste.o installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-chron/00new/chron/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (chron) * installing *source* package 'tinytest' ... ** this is package 'tinytest' version '1.4.3' ** package 'tinytest' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tinytest) * installing *source* package 'remotes' ... ** this is package 'remotes' version '2.5.0' ** package 'remotes' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (remotes) * installing *source* package 'cachem' ... ** this is package 'cachem' version '1.1.0' ** package 'cachem' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cache.c -o cache.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o cachem.so cache.o init.o installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-cachem/00new/cachem/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cachem) * installing *source* package 'lifecycle' ... ** this is package 'lifecycle' version '1.0.5' ** package 'lifecycle' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (lifecycle) * installing *source* package 'highr' ... ** this is package 'highr' version '0.12' ** package 'highr' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (highr) * installing *source* package 'htmltools' ... ** this is package 'htmltools' version '0.5.9' ** package 'htmltools' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c template.c -o template.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o htmltools.so init.o template.o installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-htmltools/00new/htmltools/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (htmltools) * installing *source* package 'tinytex' ... ** this is package 'tinytex' version '0.59' ** package 'tinytex' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tinytex) * installing *source* package 'xml2' ... ** this is package 'xml2' version '1.5.2' ** package 'xml2' successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include Using PKG_LIBS=-L/home/th798/.conda/envs/emacs1/lib -lxml2 -L/home/th798/.conda/envs/emacs1/lib -lz -L/home/th798/.conda/envs/emacs1/lib -llzma -lpthread -L/home/th798/.conda/envs/emacs1/lib -L/home/th798/.conda/envs/emacs1/lib -licui18n -licuuc -licudata -lm -ldl ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c connection.cpp -o connection.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xml2_doc.cpp -o xml2_doc.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xml2_init.c -o xml2_init.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xml2_namespace.cpp -o xml2_namespace.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xml2_node.cpp -o xml2_node.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xml2_output.cpp -o xml2_output.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xml2_schema.cpp -o xml2_schema.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xml2_url.cpp -o xml2_url.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xml2_xpath.cpp -o xml2_xpath.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o xml2.so connection.o init.o xml2_doc.o xml2_init.o xml2_namespace.o xml2_node.o xml2_output.o xml2_schema.o xml2_url.o xml2_xpath.o -L/home/th798/.conda/envs/emacs1/lib -lxml2 -L/home/th798/.conda/envs/emacs1/lib -lz -L/home/th798/.conda/envs/emacs1/lib -llzma -lpthread -L/home/th798/.conda/envs/emacs1/lib -L/home/th798/.conda/envs/emacs1/lib -licui18n -licuuc -licudata -lm -ldl installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-xml2/00new/xml2/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (xml2) * installing *source* package 'memoise' ... ** this is package 'memoise' version '2.0.1' ** package 'memoise' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (memoise) * installing *source* package 'sass' ... ** this is package 'sass' version '0.4.10' ** package 'sass' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I./libsass/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c compile.c -o compile.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I./libsass/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.cpp -o init.o MAKEFLAGS= CC="/packages/gcc/12.2.0-nnbserq/bin/gcc" CFLAGS="-I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include " CXX="/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20" AR="ar" LDFLAGS="-L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64" make -C libsass make[1]: Entering directory '/tmp/th798/29939837/Rtmp9Ag2vb/R.INSTALLaa76515d347de/sass/src/libsass' /packages/gcc/12.2.0-nnbserq/bin/gcc -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -I ./include -fPIC -c -o src/cencode.o src/cencode.c /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast.o src/ast.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_values.o src/ast_values.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_supports.o src/ast_supports.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_sel_cmp.o src/ast_sel_cmp.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_sel_unify.o src/ast_sel_unify.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_sel_super.o src/ast_sel_super.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_sel_weave.o src/ast_sel_weave.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_selectors.o src/ast_selectors.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/context.o src/context.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/constants.o src/constants.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_utils.o src/fn_utils.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_miscs.o src/fn_miscs.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_maps.o src/fn_maps.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_lists.o src/fn_lists.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_colors.o src/fn_colors.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_numbers.o src/fn_numbers.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_strings.o src/fn_strings.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_selectors.o src/fn_selectors.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/color_maps.o src/color_maps.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/environment.o src/environment.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_fwd_decl.o src/ast_fwd_decl.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/bind.o src/bind.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o 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-I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/memory/shared_ptr.o src/memory/shared_ptr.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/utf8_string.o src/utf8_string.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/base64vlq.o src/base64vlq.cpp mkdir lib ar rcvs lib/libsass.a src/cencode.o src/ast.o src/ast_values.o src/ast_supports.o src/ast_sel_cmp.o src/ast_sel_unify.o src/ast_sel_super.o src/ast_sel_weave.o src/ast_selectors.o src/context.o src/constants.o src/fn_utils.o src/fn_miscs.o src/fn_maps.o src/fn_lists.o src/fn_colors.o src/fn_numbers.o src/fn_strings.o src/fn_selectors.o src/color_maps.o src/environment.o src/ast_fwd_decl.o src/bind.o src/file.o src/util.o src/util_string.o src/json.o src/units.o src/values.o src/plugins.o src/source.o src/position.o src/lexer.o src/parser.o src/parser_selectors.o src/prelexer.o src/eval.o src/eval_selectors.o src/expand.o src/listize.o src/cssize.o src/extender.o src/extension.o src/stylesheet.o src/output.o src/inspect.o src/emitter.o src/check_nesting.o src/remove_placeholders.o src/sass.o src/sass_values.o src/sass_context.o src/sass_functions.o src/sass2scss.o src/backtrace.o src/operators.o src/ast2c.o src/c2ast.o src/to_value.o src/source_map.o src/error_handling.o src/memory/allocator.o src/memory/shared_ptr.o src/utf8_string.o src/base64vlq.o a - src/cencode.o a - src/ast.o a - src/ast_values.o a - src/ast_supports.o a - src/ast_sel_cmp.o a - src/ast_sel_unify.o a - src/ast_sel_super.o a - src/ast_sel_weave.o a - src/ast_selectors.o a - src/context.o a - src/constants.o a - src/fn_utils.o a - src/fn_miscs.o a - src/fn_maps.o a - src/fn_lists.o a - src/fn_colors.o a - src/fn_numbers.o a - src/fn_strings.o a - src/fn_selectors.o a - src/color_maps.o a - src/environment.o a - src/ast_fwd_decl.o a - src/bind.o a - src/file.o a - src/util.o a - src/util_string.o a - src/json.o a - src/units.o a - src/values.o a - src/plugins.o a - src/source.o a - src/position.o a - src/lexer.o a - src/parser.o a - src/parser_selectors.o a - src/prelexer.o a - src/eval.o a - src/eval_selectors.o a - src/expand.o a - src/listize.o a - src/cssize.o a - src/extender.o a - src/extension.o a - src/stylesheet.o a - src/output.o a - src/inspect.o a - src/emitter.o a - src/check_nesting.o a - src/remove_placeholders.o a - src/sass.o a - src/sass_values.o a - src/sass_context.o a - src/sass_functions.o a - src/sass2scss.o a - src/backtrace.o a - src/operators.o a - src/ast2c.o a - src/c2ast.o a - src/to_value.o a - src/source_map.o a - src/error_handling.o a - src/memory/allocator.o a - src/memory/shared_ptr.o a - src/utf8_string.o a - src/base64vlq.o make[1]: Leaving directory '/tmp/th798/29939837/Rtmp9Ag2vb/R.INSTALLaa76515d347de/sass/src/libsass' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o sass.so compile.o init.o ./libsass/lib/libsass.a rm -f libsass/lib/libsass.a installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-sass/00new/sass/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sass) * installing *source* package 'fontawesome' ... ** this is package 'fontawesome' version '0.5.3' ** package 'fontawesome' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fontawesome) * installing *source* package 'jquerylib' ... ** this is package 'jquerylib' version '0.1.4' ** package 'jquerylib' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (jquerylib) * installing *source* package 'knitr' ... ** this is package 'knitr' version '1.51' ** package 'knitr' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (knitr) * installing *source* package 'restatapi' ... ** this is package 'restatapi' version '0.25.0' ** package 'restatapi' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (restatapi) * installing *source* package 'bslib' ... ** this is package 'bslib' version '0.10.0' ** package 'bslib' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bslib) * installing *source* package 'rmarkdown' ... ** this is package 'rmarkdown' version '2.31' ** package 'rmarkdown' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rmarkdown) > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 261.891 24.261 294.765 > print(Sys.time()) [1] "2026-07-06 11:06:03 MST" > (pkg_Version.tar.gz <- paste0(rev.dep,"_", deps.row[,"Version"], ".tar.gz")) [1] "restatapi_0.25.0.tar.gz" > (pkg.tar.gz <- file.path(local.CRAN, "src", "contrib", pkg_Version.tar.gz)) [1] "/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz" > (rev.dep.release.tar.gz <- normalizePath(pkg.tar.gz, mustWork=TRUE)) [1] "/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz" > pkg.Rcheck <- paste0(rev.dep, ".Rcheck") > > proj.dir <- "~/genomic-ml/data.table-revdeps" > source(file.path(proj.dir, "myStatus.R")) > Rvers <- gsub("[()]", "", gsub(" ", "_", R.version[["version.string"]])) > dir.create(Rvers, showWarnings=FALSE) > Rcheck.list <- list() > for(dt.version.short in c("release", "master")){ + dt.tar.gz <- cargs[[dt.version.short]] + dt.version <- gsub(".tar.gz|/.*?_", "", dt.tar.gz) + print(Sys.time()) + install.packages(dt.tar.gz, repos=NULL) + print(Sys.time()) + check.cmd <- get_check_cmd(rev.dep.release.tar.gz) + system(check.cmd) + print(Sys.time()) + dest.Rcheck <- file.path( + Rvers, + paste0(dt.version, ".Rcheck")) + unlink(dest.Rcheck, recursive=TRUE) + file.rename(pkg.Rcheck, dest.Rcheck) + Rcheck.list[[dt.version]] <- file.path(dest.Rcheck, "00check.log") + } [1] "2026-07-06 11:06:03 MST" Installing package into '/tmp/th798/29939837/R-devel/1314/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.18.4' ** package 'data.table' successfully unpacked and MD5 sums checked ** using staged installation zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c assign.c -o assign.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c between.c -o between.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bmerge.c -o bmerge.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c chmatch.c -o chmatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cj.c -o cj.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c coalesce.c -o coalesce.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dogroups.c -o dogroups.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmean.c -o fastmean.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fcast.c -o fcast.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fifelse.c -o fifelse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fmelt.c -o fmelt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c forder.c -o forder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frank.c -o frank.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fread.c -o fread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c freadR.c -o freadR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c froll.c -o froll.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollR.c -o frollR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frolladaptive.c -o frolladaptive.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollapply.c -o frollapply.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fsort.c -o fsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwrite.c -o fwrite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwriteR.c -o fwriteR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c gsumm.c -o gsumm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c hash.c -o hash.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c idatetime.c -o idatetime.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ijoin.c -o ijoin.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c inrange.c -o inrange.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c mergelist.c -o mergelist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nafill.c -o nafill.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c negate.c -o negate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nqrecreateindices.c -o nqrecreateindices.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c openmp-utils.c -o openmp-utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c programming.c -o programming.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c quickselect.c -o quickselect.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rbindlist.c -o rbindlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c reorder.c -o reorder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shellsort.c -o shellsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shift.c -o shift.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c snprintf.c -o snprintf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c subset.c -o subset.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c transpose.c -o transpose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c types.c -o types.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uniqlist.c -o uniqlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.c -o utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vecseq.c -o vecseq.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wrappers.c -o wrappers.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o hash.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fvisibility=hidden -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fvisibility=hidden -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-data.table/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) [1] "2026-07-06 11:06:28 MST" * using log directory '/tmp/th798/29939837/R-devel/1314/restatapi.Rcheck' * using R Under development (unstable) (2026-07-04 r90207) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * current time: 2026-07-06 18:06:29 UTC * checking for file 'restatapi/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'restatapi' version '0.25.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'restatapi' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'tinytest.R' OK * checking PDF version of manual ... OK * DONE Status: OK [1] "2026-07-06 11:11:42 MST" [1] "2026-07-06 11:11:42 MST" Installing package into '/tmp/th798/29939837/R-devel/1314/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.18.99' ** using staged installation zlib 1.2.13 is available ok * checking if OpenMP works with CFLAGS='' LIBS=''... no * checking if OpenMP works with CFLAGS='$(SHLIB_OPENMP_CFLAGS)' LIBS='$(SHLIB_OPENMP_CFLAGS)'... yes ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c assign.c -o assign.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c between.c -o between.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bmerge.c -o bmerge.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c chmatch.c -o chmatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cj.c -o cj.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c coalesce.c -o coalesce.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c deleterows.c -o deleterows.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dogroups.c -o dogroups.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmean.c -o fastmean.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fcast.c -o fcast.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fifelse.c -o fifelse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fmelt.c -o fmelt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c forder.c -o forder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frank.c -o frank.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fread.c -o fread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c freadR.c -o freadR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c froll.c -o froll.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollR.c -o frollR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frolladaptive.c -o frolladaptive.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollapply.c -o frollapply.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fsort.c -o fsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwrite.c -o fwrite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwriteR.c -o fwriteR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c gsumm.c -o gsumm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c hash.c -o hash.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c idatetime.c -o idatetime.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ijoin.c -o ijoin.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c inrange.c -o inrange.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c mergelist.c -o mergelist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nafill.c -o nafill.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c negate.c -o negate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nqrecreateindices.c -o nqrecreateindices.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c openmp-utils.c -o openmp-utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c programming.c -o programming.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c quickselect.c -o quickselect.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rbindlist.c -o rbindlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c reorder.c -o reorder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shellsort.c -o shellsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shift.c -o shift.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c snprintf.c -o snprintf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c subset.c -o subset.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c transpose.c -o transpose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c types.c -o types.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uniqlist.c -o uniqlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.c -o utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vecseq.c -o vecseq.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wrappers.c -o wrappers.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o deleterows.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o hash.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fvisibility=hidden -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fvisibility=hidden -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz installing to /tmp/th798/29939837/R-devel/1314/library/00LOCK-data.table/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) [1] "2026-07-06 11:12:09 MST" * using log directory '/tmp/th798/29939837/R-devel/1314/restatapi.Rcheck' * using R Under development (unstable) (2026-07-04 r90207) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * current time: 2026-07-06 18:12:09 UTC * checking for file 'restatapi/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'restatapi' version '0.25.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'restatapi' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'tinytest.R' OK * checking PDF version of manual ... OK * DONE Status: OK [1] "2026-07-06 11:20:39 MST" > system(paste(c("diff -u", Rcheck.list), collapse=" ")) --- R_Under_development_unstable_2026-07-04_r90207/release_1.18.4.Rcheck/00check.log 2026-07-06 11:11:42.698160424 -0700 +++ R_Under_development_unstable_2026-07-04_r90207/master_1.18.99.8c4291395093bf68a53853c867ac62cbc138e6fe.Rcheck/00check.log 2026-07-06 11:20:39.149556329 -0700 @@ -6,7 +6,7 @@ GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII -* current time: 2026-07-06 18:06:29 UTC +* current time: 2026-07-06 18:12:09 UTC * checking for file 'restatapi/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'restatapi' version '0.25.0' > library(data.table, lib.loc=R.home("library")) Attaching package: 'data.table' The following object is masked from 'package:base': %notin% > (sig.diff.dt <- myDiff(Rvers)) Key: Empty data.table (0 rows and 3 cols): checking,master,release > > ## If there are significant differences, use git bisect to find when > ## they started. > if(nrow(sig.diff.dt)){ + dt.git <- file.path(task.dir, "data.table.git") + unlink(dt.git, recursive=TRUE, force=TRUE) + system(paste("cd ~/R/data.table && git fetch --tags")) + system(paste("git clone ~/R/data.table", dt.git)) + release.tag <- gsub(".tar.gz|.*_", "", cargs[["release"]]) + rev.parse.cmd <- paste( + "cd", dt.git, "&& git rev-parse master") + master.sha <- system(rev.parse.cmd, intern=TRUE) + merge.base.cmd <- paste( + "cd", dt.git, "&& git merge-base master", release.tag) + merge.base.sha <- system(merge.base.cmd, intern=TRUE) + old.sha <- merge.base.sha + run_R <- file.path(proj.dir, "install_dt_then_check_dep.R") + sig.diff.dt[, first.bad.commit := NA_character_] + sig.diff.dt[, comments := NA_character_] + for(diff.i in 1:nrow(sig.diff.dt)){ + sig.diff.row <- sig.diff.dt[diff.i] + bisect.cmd <- paste( + "cd", dt.git, "&&", + "git bisect start &&", + "git bisect old", old.sha, "&&", + "git bisect new master &&", + "git bisect run", + R.home('bin/Rscript'), + run_R, + shQuote(sig.diff.row$checking), + sig.diff.row$release, + rev.dep.release.tar.gz, + release.tag) + print(bisect.cmd) + bisect.out <- system(bisect.cmd, intern=TRUE) + cat(bisect.out,sep="\n") + if(is.null(attr(bisect.out,"status"))){ + first.bad.sha <- nc::capture_all_str( + bisect.out, + sha="[0-9a-f]+", + " is the first new commit")$sha + parent.cmd <- paste( + "cd ~/R/data.table && git log --pretty=%P -n 1", + first.bad.sha) + parent.sha <- system(parent.cmd, intern=TRUE) + sig.diff.dt[diff.i, first.bad.commit := first.bad.sha] + parent.msg <- paste0("parent=", parent.sha) + this.comment <- if(parent.sha==old.sha){ + paste(parent.msg, "same as git bisect old") + }else if(first.bad.sha==master.sha){ + paste("same as git bisect new=master,", parent.msg) + }else{ + parent.msg + } + sig.diff.dt[diff.i, comments := this.comment] + } + } + ## add CRAN column. + sig.diff.dt[, CRAN := { + flavor <- get_flavor(Rvers) + details <- data.table(flavor=unique(flavor))[, { + base <- "https://www.r-project.org/nosvn/R.check/" + u <- paste0(base, flavor, "/", rev.dep, "-00check.txt") + check.txt <- tempfile() + tryCatch({ + download.file(u, check.txt, quiet=TRUE) + }, error=function(e){ + NULL + }) + check.lines <- if(file.exists(check.txt)){ + readLines(check.txt,encoding="UTF-8") + }else{ + "" + } + repl.lines <- gsub("[\u2018\u2019]", "'", check.lines) + ##gsub("[‘’]", "'", check.lines) does not work with LC_ALL=C. + myStatus(line.vec=repl.lines) + }, by=flavor] + select.dt <- data.table(flavor, checking) + details[select.dt, msg, on=.(flavor, checking)] + }] + dir.create(file.path(job.dir, Rvers)) + diffs.csv <- file.path(job.dir, Rvers, "significant_differences.csv") + data.table::fwrite(sig.diff.dt, diffs.csv) + print(sig.diff.dt) + } > WARNING: ignoring environment value of R_HOME R version 4.6.1 (2026-06-24) -- "Happy Hop" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > (cargs <- commandArgs(trailingOnly=TRUE)) [1] "/scratch/th798/data.table-revdeps/2026-07-06/deps.csv" [2] "1314" [3] "/scratch/th798/data.table-revdeps/2026-07-06/data.table_release_1.18.4.tar.gz" [4] "/scratch/th798/data.table-revdeps/2026-07-06/data.table_master_1.18.99.8c4291395093bf68a53853c867ac62cbc138e6fe.tar.gz" > if(length(cargs)==0){ + ## before running interactively, make sure to start emacs/R with + ## environment defined in /scratch/...check_one.sh, particularly + ## R_LIBS_USER=/tmp/... otherwise we get error when installing + ## data.table. + base <- "/scratch/th798/data.table-revdeps/*" + cargs <- c( + Sys.glob(file.path(base,"deps.csv")), + "9", + Sys.glob(file.path(base, "data.table_release_*tar.gz")), + Sys.glob(file.path(base, "data.table_master_*tar.gz")) + ) + } > names(cargs) <- c("deps.csv", "task.str", "release", "master") > dput(cargs) c(deps.csv = "/scratch/th798/data.table-revdeps/2026-07-06/deps.csv", task.str = "1314", release = "/scratch/th798/data.table-revdeps/2026-07-06/data.table_release_1.18.4.tar.gz", master = "/scratch/th798/data.table-revdeps/2026-07-06/data.table_master_1.18.99.8c4291395093bf68a53853c867ac62cbc138e6fe.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/29939837/R-release/1314" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache Failed with error: 'there is no package called 'R.cache'' > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (deps.row <- deps.df[task.id,]) Package task.id Version 1314 restatapi 1314 0.25.0 > (rev.dep <- deps.row$Package) [1] "restatapi" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/29939837/R-release/1314/library" [2] "/projects/genomic-ml/R/R-release/library" > local.CRAN <- "/projects/genomic-ml/CRAN" > cran.url <- paste0("file://", local.CRAN) > #this should be in ~/.Rprofile too. > options(repos=c(CRAN=cran.url)) > print(Sys.time()) [1] "2026-07-06 11:20:45 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/29939837/R-release/1314/library' (as 'lib' is unspecified) also installing the dependencies 'fs', 'R6', 'rappdirs', 'base64enc', 'cachem', 'fastmap', 'lifecycle', 'memoise', 'mime', 'sass', 'digest', 'cli', 'rlang', 'evaluate', 'highr', 'xfun', 'yaml', 'bslib', 'fontawesome', 'htmltools', 'jquerylib', 'jsonlite', 'tinytex', 'rjson', 'xml2', 'chron', 'knitr', 'rmarkdown', 'tinytest', 'remotes' * installing *source* package 'fs' ... ** this is package 'fs' version '2.1.0' ** package 'fs' successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/home/th798/.conda/envs/emacs1/include Using PKG_LIBS=-L/home/th798/.conda/envs/emacs1/lib -luv -lrt -ldl ** libs using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dir.cc -o dir.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c error.cc -o error.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c file.cc -o file.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fs.cc -o fs.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c getmode.cc -o getmode.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c id.cc -o id.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.cc -o init.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c link.cc -o link.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c path.cc -o path.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.cc -o utils.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c unix/getmode.cc -o unix/getmode.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bsd/setmode.c -o bsd/setmode.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bsd/strmode.c -o bsd/strmode.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bsd/reallocarray.c -o bsd/reallocarray.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o fs.so dir.o error.o file.o fs.o getmode.o id.o init.o link.o path.o utils.o unix/getmode.o bsd/setmode.o bsd/strmode.o bsd/reallocarray.o -L/home/th798/.conda/envs/emacs1/lib -luv -lrt -ldl installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-fs/00new/fs/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fs) * installing *source* package 'R6' ... ** this is package 'R6' version '2.6.1' ** package 'R6' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (R6) * installing *source* package 'rappdirs' ... ** this is package 'rappdirs' version '0.3.4' ** package 'rappdirs' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c win-path.c -o win-path.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o rappdirs.so init.o win-path.o installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-rappdirs/00new/rappdirs/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rappdirs) * installing *source* package 'base64enc' ... ** this is package 'base64enc' version '0.1-6' ** package 'base64enc' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c base64.c -o base64.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dummy.c -o dummy.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uriencode.c -o uriencode.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utf8.c -o utf8.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o base64enc.so base64.o dummy.o uriencode.o utf8.o installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-base64enc/00new/base64enc/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (base64enc) * installing *source* package 'fastmap' ... ** this is package 'fastmap' version '1.2.0' ** package 'fastmap' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -Ilib/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -DR_NO_REMAP -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmap.cpp -o fastmap.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Ilib/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o fastmap.so fastmap.o init.o installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-fastmap/00new/fastmap/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fastmap) * installing *source* package 'mime' ... ** this is package 'mime' version '0.13' ** package 'mime' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rawmatch.c -o rawmatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o mime.so init.o rawmatch.o installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-mime/00new/mime/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mime) * installing *source* package 'digest' ... ** this is package 'digest' version '0.6.39' ** package 'digest' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c SpookyV2.cpp -o SpookyV2.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c aes.c -o aes.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c blake3.c -o blake3.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c blake3_dispatch.c -o blake3_dispatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c blake3_portable.c -o blake3_portable.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c crc32.c -o crc32.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c crc32c.cpp -o crc32c.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c crc32c_portable.cpp -o crc32c_portable.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c digest.c -o digest.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c digest2int.c -o digest2int.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c md5.c -o md5.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c pmurhash.c -o pmurhash.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c raes.c -o raes.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c sha1.c -o sha1.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c sha2.c -o sha2.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c sha256.c -o sha256.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c spooky_serialize.cpp -o spooky_serialize.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xxhash.c -o xxhash.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o digest.so SpookyV2.o aes.o blake3.o blake3_dispatch.o blake3_portable.o crc32.o crc32c.o crc32c_portable.o digest.o digest2int.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o spooky_serialize.o xxhash.o installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-digest/00new/digest/libs ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (digest) * installing *source* package 'cli' ... ** this is package 'cli' version '3.6.6' ** package 'cli' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ansi.c -o ansi.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cleancall.c -o cleancall.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c diff.c -o diff.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c errors.c -o errors.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c glue.c -o glue.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c inst.c -o inst.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c keypress-unix.c -o keypress-unix.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c keypress-win.c -o keypress-win.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c keypress.c -o keypress.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c md5.c -o md5.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c progress-altrep.c -o progress-altrep.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c progress.c -o progress.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c sha1.c -o sha1.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c sha256.c -o sha256.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c thread.c -o thread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c tty.c -o tty.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utf8.c -o utf8.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.c -o utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vt.c -o vt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vtparse.c -o vtparse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vtparse_table.c -o vtparse_table.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c win-utf8.c -o win-utf8.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c winfiles.c -o winfiles.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xxhash.c -o xxhash.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xxhash2.c -o xxhash2.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o cli.so ansi.o cleancall.o diff.o errors.o glue.o init.o inst.o keypress-unix.o keypress-win.o keypress.o md5.o progress-altrep.o progress.o sha1.o sha256.o thread.o tty.o utf8.o utils.o vt.o vtparse.o vtparse_table.o win-utf8.o winfiles.o xxhash.o xxhash2.o -lpthread installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-cli/00new/cli/libs ** R ** exec ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cli) * installing *source* package 'rlang' ... ** this is package 'rlang' version '1.2.0' ** package 'rlang' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I./rlang/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c capture.c -o capture.o touch internal.c /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I./rlang/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c internal.c -o internal.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I./rlang/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rlang.c -o rlang.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I./rlang/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c version.c -o version.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o rlang.so capture.o internal.o rlang.o version.o installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-rlang/00new/rlang/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rlang) * installing *source* package 'evaluate' ... ** this is package 'evaluate' version '1.0.5' ** package 'evaluate' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (evaluate) * installing *source* package 'xfun' ... ** this is package 'xfun' version '0.57' ** package 'xfun' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c base64.c -o base64.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rand_lcg.c -o rand_lcg.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o xfun.so base64.o init.o rand_lcg.o installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-xfun/00new/xfun/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (xfun) * installing *source* package 'yaml' ... ** this is package 'yaml' version '2.3.12' ** package 'yaml' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c api.c -o api.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dumper.c -o dumper.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c emitter.c -o emitter.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c implicit.c -o implicit.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c loader.c -o loader.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c parser.c -o parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c r_emit.c -o r_emit.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c r_ext.c -o r_ext.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c r_parse.c -o r_parse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c reader.c -o reader.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c scanner.c -o scanner.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c writer.c -o writer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o yaml.so api.o dumper.o emitter.o implicit.o loader.o parser.o r_emit.o r_ext.o r_parse.o reader.o scanner.o writer.o installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-yaml/00new/yaml/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (yaml) * installing *source* package 'jsonlite' ... ** this is package 'jsonlite' version '2.0.0' ** package 'jsonlite' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c base64.c -o base64.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c collapse_array.c -o collapse_array.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c collapse_object.c -o collapse_object.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c collapse_pretty.c -o collapse_pretty.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c escape_chars.c -o escape_chars.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c integer64_to_na.c -o integer64_to_na.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c is_datelist.c -o is_datelist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c is_recordlist.c -o is_recordlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c is_scalarlist.c -o is_scalarlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c modp_numtoa.c -o modp_numtoa.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c null_to_na.c -o null_to_na.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c num_to_char.c -o num_to_char.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c parse.c -o parse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c prettify.c -o prettify.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c push_parser.c -o push_parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c r-base64.c -o r-base64.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c register.c -o register.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c row_collapse.c -o row_collapse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c transpose_list.c -o transpose_list.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c validate.c -o validate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c yajl/yajl.c -o yajl/yajl.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c yajl/yajl_buf.c -o yajl/yajl_buf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c yajl/yajl_encode.c -o yajl/yajl_encode.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c yajl/yajl_gen.c -o yajl/yajl_gen.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c yajl/yajl_lex.c -o yajl/yajl_lex.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c yajl/yajl_parser.c -o yajl/yajl_parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -Iyajl/api -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c yajl/yajl_tree.c -o yajl/yajl_tree.o ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-jsonlite/00new/jsonlite/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for 'asJSON' with signature '"AsIs"': no definition for class "AsIs" in method for 'asJSON' with signature '"ITime"': no definition for class "ITime" in method for 'asJSON' with signature '"hms"': no definition for class "hms" in method for 'asJSON' with signature '"json"': no definition for class "json" in method for 'asJSON' with signature '"integer64"': no definition for class "integer64" in method for 'asJSON' with signature '"pairlist"': no definition for class "pairlist" in method for 'asJSON' with signature '"blob"': no definition for class "blob" in method for 'asJSON' with signature '"scalar"': no definition for class "scalar" in method for 'asJSON' with signature '"sf"': no definition for class "sf" in method for 'asJSON' with signature '"sfc"': no definition for class "sfc" in method for 'asJSON' with signature '"vctrs_vctr"': no definition for class "vctrs_vctr" ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (jsonlite) * installing *source* package 'rjson' ... ** this is package 'rjson' version '0.2.23' ** package 'rjson' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dump.cpp -o dump.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c parser.c -o parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c register.c -o register.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o rjson.so dump.o parser.o register.o installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-rjson/00new/rjson/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rjson) * installing *source* package 'chron' ... ** this is package 'chron' version '2.3-62' ** package 'chron' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c chron_strs.c -o chron_strs.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c unpaste.c -o unpaste.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o chron.so chron_strs.o init.o unpaste.o installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-chron/00new/chron/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (chron) * installing *source* package 'tinytest' ... ** this is package 'tinytest' version '1.4.3' ** package 'tinytest' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tinytest) * installing *source* package 'remotes' ... ** this is package 'remotes' version '2.5.0' ** package 'remotes' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (remotes) * installing *source* package 'cachem' ... ** this is package 'cachem' version '1.1.0' ** package 'cachem' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cache.c -o cache.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o cachem.so cache.o init.o installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-cachem/00new/cachem/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (cachem) * installing *source* package 'lifecycle' ... ** this is package 'lifecycle' version '1.0.5' ** package 'lifecycle' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (lifecycle) * installing *source* package 'highr' ... ** this is package 'highr' version '0.12' ** package 'highr' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (highr) * installing *source* package 'htmltools' ... ** this is package 'htmltools' version '0.5.9' ** package 'htmltools' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c template.c -o template.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o htmltools.so init.o template.o installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-htmltools/00new/htmltools/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (htmltools) * installing *source* package 'tinytex' ... ** this is package 'tinytex' version '0.59' ** package 'tinytex' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tinytex) * installing *source* package 'xml2' ... ** this is package 'xml2' version '1.5.2' ** package 'xml2' successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include Using PKG_LIBS=-L/home/th798/.conda/envs/emacs1/lib -lxml2 -L/home/th798/.conda/envs/emacs1/lib -lz -L/home/th798/.conda/envs/emacs1/lib -llzma -lpthread -L/home/th798/.conda/envs/emacs1/lib -L/home/th798/.conda/envs/emacs1/lib -licui18n -licuuc -licudata -lm -ldl ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c connection.cpp -o connection.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xml2_doc.cpp -o xml2_doc.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xml2_init.c -o xml2_init.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xml2_namespace.cpp -o xml2_namespace.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xml2_node.cpp -o xml2_node.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xml2_output.cpp -o xml2_output.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xml2_schema.cpp -o xml2_schema.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xml2_url.cpp -o xml2_url.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/include -I/home/th798/.conda/envs/emacs1/include/libxml2 -I/home/th798/.conda/envs/emacs1/include -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -DSTRICT_R_HEADERS -DR_NO_REMAP -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c xml2_xpath.cpp -o xml2_xpath.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o xml2.so connection.o init.o xml2_doc.o xml2_init.o xml2_namespace.o xml2_node.o xml2_output.o xml2_schema.o xml2_url.o xml2_xpath.o -L/home/th798/.conda/envs/emacs1/lib -lxml2 -L/home/th798/.conda/envs/emacs1/lib -lz -L/home/th798/.conda/envs/emacs1/lib -llzma -lpthread -L/home/th798/.conda/envs/emacs1/lib -L/home/th798/.conda/envs/emacs1/lib -licui18n -licuuc -licudata -lm -ldl installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-xml2/00new/xml2/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (xml2) * installing *source* package 'memoise' ... ** this is package 'memoise' version '2.0.1' ** package 'memoise' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (memoise) * installing *source* package 'sass' ... ** this is package 'sass' version '0.4.10' ** package 'sass' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I./libsass/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c compile.c -o compile.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-release/include" -DNDEBUG -I./libsass/include -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.cpp -o init.o MAKEFLAGS= CC="/packages/gcc/12.2.0-nnbserq/bin/gcc" CFLAGS="-I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include " CXX="/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20" AR="ar" LDFLAGS="-L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64" make -C libsass make[1]: Entering directory '/tmp/th798/29939837/RtmpHmAesS/R.INSTALLb37df1a4e4a3e/sass/src/libsass' /packages/gcc/12.2.0-nnbserq/bin/gcc -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -I ./include -fPIC -c -o src/cencode.o src/cencode.c /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast.o src/ast.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_values.o src/ast_values.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_supports.o src/ast_supports.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_sel_cmp.o src/ast_sel_cmp.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_sel_unify.o src/ast_sel_unify.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_sel_super.o src/ast_sel_super.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_sel_weave.o src/ast_sel_weave.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_selectors.o src/ast_selectors.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/context.o src/context.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/constants.o src/constants.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_utils.o src/fn_utils.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_miscs.o src/fn_miscs.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_maps.o src/fn_maps.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_lists.o src/fn_lists.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_colors.o src/fn_colors.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_numbers.o src/fn_numbers.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_strings.o src/fn_strings.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 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-I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/sass_context.o src/sass_context.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/sass_functions.o src/sass_functions.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/sass2scss.o src/sass2scss.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ 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src/ast2c.o src/ast2c.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/c2ast.o src/c2ast.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/to_value.o src/to_value.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/source_map.o src/source_map.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/error_handling.o src/error_handling.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/memory/allocator.o src/memory/allocator.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/memory/shared_ptr.o src/memory/shared_ptr.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/utf8_string.o src/utf8_string.cpp /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -O2 -std=c++11 -I ./include -fPIC -c -o src/base64vlq.o src/base64vlq.cpp mkdir lib ar rcvs lib/libsass.a src/cencode.o src/ast.o src/ast_values.o src/ast_supports.o src/ast_sel_cmp.o src/ast_sel_unify.o src/ast_sel_super.o src/ast_sel_weave.o src/ast_selectors.o src/context.o src/constants.o src/fn_utils.o src/fn_miscs.o src/fn_maps.o src/fn_lists.o src/fn_colors.o src/fn_numbers.o src/fn_strings.o src/fn_selectors.o src/color_maps.o src/environment.o src/ast_fwd_decl.o src/bind.o src/file.o src/util.o src/util_string.o src/json.o src/units.o src/values.o src/plugins.o src/source.o src/position.o src/lexer.o src/parser.o src/parser_selectors.o src/prelexer.o src/eval.o src/eval_selectors.o src/expand.o src/listize.o src/cssize.o src/extender.o src/extension.o src/stylesheet.o src/output.o src/inspect.o src/emitter.o src/check_nesting.o src/remove_placeholders.o src/sass.o src/sass_values.o src/sass_context.o src/sass_functions.o src/sass2scss.o src/backtrace.o src/operators.o src/ast2c.o src/c2ast.o src/to_value.o src/source_map.o src/error_handling.o src/memory/allocator.o src/memory/shared_ptr.o src/utf8_string.o src/base64vlq.o a - src/cencode.o a - src/ast.o a - src/ast_values.o a - src/ast_supports.o a - src/ast_sel_cmp.o a - src/ast_sel_unify.o a - src/ast_sel_super.o a - src/ast_sel_weave.o a - src/ast_selectors.o a - src/context.o a - src/constants.o a - src/fn_utils.o a - src/fn_miscs.o a - src/fn_maps.o a - src/fn_lists.o a - src/fn_colors.o a - src/fn_numbers.o a - src/fn_strings.o a - src/fn_selectors.o a - src/color_maps.o a - src/environment.o a - src/ast_fwd_decl.o a - src/bind.o a - src/file.o a - src/util.o a - src/util_string.o a - src/json.o a - src/units.o a - src/values.o a - src/plugins.o a - src/source.o a - src/position.o a - src/lexer.o a - src/parser.o a - src/parser_selectors.o a - src/prelexer.o a - src/eval.o a - src/eval_selectors.o a - src/expand.o a - src/listize.o a - src/cssize.o a - src/extender.o a - src/extension.o a - src/stylesheet.o a - src/output.o a - src/inspect.o a - src/emitter.o a - src/check_nesting.o a - src/remove_placeholders.o a - src/sass.o a - src/sass_values.o a - src/sass_context.o a - src/sass_functions.o a - src/sass2scss.o a - src/backtrace.o a - src/operators.o a - src/ast2c.o a - src/c2ast.o a - src/to_value.o a - src/source_map.o a - src/error_handling.o a - src/memory/allocator.o a - src/memory/shared_ptr.o a - src/utf8_string.o a - src/base64vlq.o make[1]: Leaving directory '/tmp/th798/29939837/RtmpHmAesS/R.INSTALLb37df1a4e4a3e/sass/src/libsass' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o sass.so compile.o init.o ./libsass/lib/libsass.a rm -f libsass/lib/libsass.a installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-sass/00new/sass/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (sass) * installing *source* package 'fontawesome' ... ** this is package 'fontawesome' version '0.5.3' ** package 'fontawesome' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fontawesome) * installing *source* package 'jquerylib' ... ** this is package 'jquerylib' version '0.1.4' ** package 'jquerylib' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (jquerylib) * installing *source* package 'knitr' ... ** this is package 'knitr' version '1.51' ** package 'knitr' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (knitr) * installing *source* package 'restatapi' ... ** this is package 'restatapi' version '0.25.0' ** package 'restatapi' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (restatapi) * installing *source* package 'bslib' ... ** this is package 'bslib' version '0.10.0' ** package 'bslib' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bslib) * installing *source* package 'rmarkdown' ... ** this is package 'rmarkdown' version '2.31' ** package 'rmarkdown' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rmarkdown) > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 261.096 24.463 292.920 > print(Sys.time()) [1] "2026-07-06 11:25:38 MST" > (pkg_Version.tar.gz <- paste0(rev.dep,"_", deps.row[,"Version"], ".tar.gz")) [1] "restatapi_0.25.0.tar.gz" > (pkg.tar.gz <- file.path(local.CRAN, "src", "contrib", pkg_Version.tar.gz)) [1] "/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz" > (rev.dep.release.tar.gz <- normalizePath(pkg.tar.gz, mustWork=TRUE)) [1] "/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz" > pkg.Rcheck <- paste0(rev.dep, ".Rcheck") > > proj.dir <- "~/genomic-ml/data.table-revdeps" > source(file.path(proj.dir, "myStatus.R")) > Rvers <- gsub("[()]", "", gsub(" ", "_", R.version[["version.string"]])) > dir.create(Rvers, showWarnings=FALSE) > Rcheck.list <- list() > for(dt.version.short in c("release", "master")){ + dt.tar.gz <- cargs[[dt.version.short]] + dt.version <- gsub(".tar.gz|/.*?_", "", dt.tar.gz) + print(Sys.time()) + install.packages(dt.tar.gz, repos=NULL) + print(Sys.time()) + check.cmd <- get_check_cmd(rev.dep.release.tar.gz) + system(check.cmd) + print(Sys.time()) + dest.Rcheck <- file.path( + Rvers, + paste0(dt.version, ".Rcheck")) + unlink(dest.Rcheck, recursive=TRUE) + file.rename(pkg.Rcheck, dest.Rcheck) + Rcheck.list[[dt.version]] <- file.path(dest.Rcheck, "00check.log") + } [1] "2026-07-06 11:25:38 MST" Installing package into '/tmp/th798/29939837/R-release/1314/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.18.4' ** package 'data.table' successfully unpacked and MD5 sums checked ** using staged installation zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c assign.c -o assign.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c between.c -o between.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bmerge.c -o bmerge.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c chmatch.c -o chmatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cj.c -o cj.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c coalesce.c -o coalesce.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dogroups.c -o dogroups.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmean.c -o fastmean.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fcast.c -o fcast.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fifelse.c -o fifelse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fmelt.c -o fmelt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c forder.c -o forder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frank.c -o frank.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fread.c -o fread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c freadR.c -o freadR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c froll.c -o froll.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollR.c -o frollR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frolladaptive.c -o frolladaptive.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollapply.c -o frollapply.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fsort.c -o fsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwrite.c -o fwrite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwriteR.c -o fwriteR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c gsumm.c -o gsumm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c hash.c -o hash.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c idatetime.c -o idatetime.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ijoin.c -o ijoin.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c inrange.c -o inrange.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c mergelist.c -o mergelist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nafill.c -o nafill.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c negate.c -o negate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nqrecreateindices.c -o nqrecreateindices.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c openmp-utils.c -o openmp-utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c programming.c -o programming.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c quickselect.c -o quickselect.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rbindlist.c -o rbindlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c reorder.c -o reorder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shellsort.c -o shellsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shift.c -o shift.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c snprintf.c -o snprintf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c subset.c -o subset.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c transpose.c -o transpose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c types.c -o types.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uniqlist.c -o uniqlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.c -o utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vecseq.c -o vecseq.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wrappers.c -o wrappers.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o hash.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fvisibility=hidden -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fvisibility=hidden -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-data.table/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) [1] "2026-07-06 11:26:03 MST" * using log directory '/tmp/th798/29939837/R-release/1314/restatapi.Rcheck' * using R version 4.6.1 (2026-06-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * current time: 2026-07-06 18:26:04 UTC * checking for file 'restatapi/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'restatapi' version '0.25.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'restatapi' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'tinytest.R' ERROR Running the tests in 'tests/tinytest.R' failed. Complete output: > if ( requireNamespace("tinytest", quietly=TRUE) ){ + home <- length(unclass(packageVersion("restatapi"))[[1]]) == 4 + tinytest::test_package("restatapi", at_home = home) + } restatapi: - version 0.25.0 - config file with the API version 2 loaded from GitHub (the 'current' API version number is 2). - 4 from the 28 cores are used for parallel computing, can be changed with 'options(restatapi_cores=...)' - 'auto' method will be used for file download, can be changed with 'options(restatapi_dmethod=...)' - the Table of contents (TOC) was not pre-loaded into the deafult cache ('.restatapi_env'). test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests clean_restatapi_cache - All objects (outside of 'cfg', 'rav', 'cc' and 'dmethod') are removed from '.restatapi_env'. test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/xml get_eurostat_toc - class(xml_leafs): xml_nodeset get_eurostat_toc - number of nodes: 10408 get_eurostat_toc - number of cores: 2 get_eurostat_toc - dim toc: 10408,22 get_eurostat_toc - colnames toc: title.en,title.fr,title.de,code,lastUpdate,lastModified,dataStart,dataEnd,values,source.en,source.fr,source.de,unit.en,unit.fr,unit.de,shortDescription.en,shortDescription.fr,shortDescription.de,metadata.html,metadata.sdmx,downloadLink.tsv,type get_eurostat_toc - cols to keep: title.en,code,type,lastUpdate,lastModified,dataStart,dataEnd,values,unit.en,source.en,shortDescription.en,metadata.html,metadata.sdmx,downloadLink.tsv get_eurostat_toc - The TOC was cached in memory ('toc.xml.en' in '.restatapi_env'). test_restatapi.R.............. 0 tests get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=en trying URL 'https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=en' downloaded 1.9 MB get_eurostat_toc - The TOC was cached in memory ('toc.txt.en' in '.restatapi_env'). test_restatapi.R.............. 0 tests get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. test_restatapi.R.............. 0 tests test_restatapi.R.............. 1 tests OK test_restatapi.R.............. 7 tests OK get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. test_restatapi.R.............. 7 tests OK get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. test_restatapi.R.............. 7 tests OK get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/xml get_eurostat_toc - class(xml_leafs): xml_nodeset get_eurostat_toc - number of nodes: 10408 get_eurostat_toc - number of cores: 2 get_eurostat_toc - dim toc: 10408,22 get_eurostat_toc - colnames toc: title.en,title.fr,title.de,code,lastUpdate,lastModified,dataStart,dataEnd,values,source.en,source.fr,source.de,unit.en,unit.fr,unit.de,shortDescription.en,shortDescription.fr,shortDescription.de,metadata.html,metadata.sdmx,downloadLink.tsv,type get_eurostat_toc - cols to keep: title.de,code,type,lastUpdate,lastModified,dataStart,dataEnd,values,unit.de,source.de,shortDescription.de,metadata.html,metadata.sdmx,downloadLink.tsv get_eurostat_toc - The TOC was cached in memory ('toc.xml.de' in '.restatapi_env'). test_restatapi.R.............. 7 tests OK test_restatapi.R.............. 8 tests OK test_restatapi.R.............. 9 tests OK trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/text?references=children' test_restatapi.R.............. 10 tests OK get_eurostat_dsd - API version:2 get_eurostat_dsd - Trying to download the DSD from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/NAMA_10_GDP?references=children trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/NAMA_10_GDP?references=children' downloaded 3.4 MB get_eurostat_dsd - class(temp): character - is.na(temp): FALSE - file.size(temp): 3585472 - temp: /tmp/th798/29939837/RtmpCEDVOS/fileb5076d390d79 Trying to extract the DSD from: /tmp/th798/29939837/RtmpCEDVOS/fileb5076d390d79 get_eurostat_dsd - concepts:freq,unit,na_item,geo,OBS_FLAG,CONF_STATUS extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="FREQ"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="FREQ"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="UNIT"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="UNIT"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="NA_ITEM"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="NA_ITEM"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="GEO"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="GEO"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="OBS_FLAG"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="OBS_FLAG"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="CONF_STATUS"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="CONF_STATUS"]/s:Code/c:Name[@xml:lang="en"] get_eurostat_dsd - DSD NULL:FALSE get_eurostat_dsd - Trying to download the CC from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/NAMA_10_GDP trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/NAMA_10_GDP' Content type 'application/vnd.sdmx.structure+xml;version=2.1' length 5597 bytes ================================================== downloaded 5597 bytes get_eurostat_dsd - Trying to extract the CC from: /tmp/th798/29939837/RtmpCEDVOS/fileb5076368d6a5c character number of nodes: 5 number of cores: 2 get_eurostat_dsd - The DSD of the NAMA_10_GDP dataset was cached in memory ('NAMA_10_GDP.en.dsd' in '.restatapi_env'). test_restatapi.R.............. 10 tests OK test_restatapi.R.............. 13 tests OK test_restatapi.R.............. 13 tests OK test_restatapi.R.............. 13 tests OK test_restatapi.R.............. 17 tests OK get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: htec_cis3 get_eurostat_data - select_freq: get_eurostat_data - Trying to get from cache: b_htec_cis3-2026.07.06-1-1 get_eurostat_bulk - API version:2 get_eurostat_bulk - class of id, cache, update_cache, cache_dir, compress_file, stringsAsFactors, keep_flags, check_toc, melt, verbose: character - logical -logical - NULL - logical - logical - logical - logical - logical - logical get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/htec_cis3?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: FALSE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: restatapi::get_eurostat_rawidtxtcacheupdate_cachecache_dircompress_filestringsAsFactorskeep_flagscheck_tocTRUEverbose get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_data - The data was downloaded with bulk download. get_eurostat_data - bulk restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags get_eurostat_data - cflags:TRUE get_eurostat_data - restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags get_eurostat_data - processed restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags get_eurostat_data - The data was cached in memory ('b_htec_cis3-2026.07.06-1-1' in '.restatapi_env'). get_eurostat_data - restat NULL?:FALSE id: htec_cis3 filters: date filter: test_restatapi.R.............. 17 tests OK test_restatapi.R.............. 17 tests OK get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: htec_cis3 get_eurostat_data - select_freq: get_eurostat_data - Trying to get from cache: b_htec_cis3-2026.07.06-0-0 get_eurostat_cache - The 'b_htec_cis3-2026.07.06-0-0' was loaded from 'b_htec_cis3-2026.07.06-1-1' in '.restatapi_env'. get_eurostat_data - The data was loaded from cache. get_eurostat_data - cached restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags get_eurostat_data - restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags get_eurostat_data - processed restat - nrow:1006; ncol:6; colnames:indic_in/nace_r1/unit/geo/time/values get_eurostat_data - The data was cached in memory ('b_htec_cis3-2026.07.06-0-0' in '.restatapi_env'). get_eurostat_data - restat NULL?:FALSE id: htec_cis3 filters: date filter: test_restatapi.R.............. 17 tests OK test_restatapi.R.............. 17 tests OK test_restatapi.R.............. 21 tests OK get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/rail_tf_ns20_mk?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid3FALSE get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_rail_tf_ns20_mk-2026.07.06-0' in '.restatapi_env'). get_eurostat_raw - API version:2 get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. get_eurostat_raw - raws of TOC: 7661 get_eurostat_raw - txt bulk url from TOC:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/RAIL_TF_NS20_MK?format=tsv&compressed=true get_eurostat_raw - txt bulk url from cfg:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/rail_tf_ns20_mk?format=TSV&compressed=true get_eurostat_raw - data rowcount in TOC: 12 get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid3TRUEFALSE get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_rail_tf_ns20_mk-2023.02.02-0' in '.restatapi_env'). get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: rail_tf_ns20_mk get_eurostat_data - select_freq: get_eurostat_data - Trying to get from cache: b_rail_tf_ns20_mk-2026.07.06-0-0 get_eurostat_cache - The 'b_rail_tf_ns20_mk-2026.07.06-0-0' was loaded from 'r_rail_tf_ns20_mk-2026.07.06-0' in '.restatapi_env'. get_eurostat_data - The data was loaded from cache. get_eurostat_data - cached restat - nrow:12; ncol:6; colnames:freq/net_seg20/train/unit/time/values get_eurostat_data - restat - nrow:12; ncol:6; colnames:freq/net_seg20/train/unit/time/values get_eurostat_data - processed restat - nrow:12; ncol:5; colnames:net_seg20/train/unit/time/values get_eurostat_data - The data was cached in memory ('b_rail_tf_ns20_mk-2026.07.06-0-0' in '.restatapi_env'). get_eurostat_data - restat NULL?:FALSE id: rail_tf_ns20_mk filters: date filter: test_restatapi.R.............. 26 tests OK get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr?format=sdmx_2.1_structured&compressed=true get_eurostat_raw - file format: gz get_compressed_sdmx - url:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr?format=sdmx_2.1_structured&compressed=true get_compressed_sdmx - format:gz get_compressed_sdmx - xml NULL:FALSE get_eurostat_raw - class(xml_leafs): xml_nodeset get_eurostat_raw - number of nodes: 583 get_eurostat_raw - number of cores: 2 get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid4xmlTRUETRUE get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_agr_r_milkpr-2026.07.06-1' in '.restatapi_env'). test_restatapi.R.............. 26 tests OK get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_data - Trying to get from cache: b_agr_r_milkpr-2026.07.06-1-0 get_eurostat_cache - The 'b_agr_r_milkpr-2026.07.06-1-0' was loaded from 'r_agr_r_milkpr-2026.07.06-1' in '.restatapi_env'. get_eurostat_data - The data was loaded from cache. get_eurostat_data - cached restat - nrow:11870; ncol:7; colnames:geo/milkitem/freq/dairyprod/TIME_PERIOD/OBS_VALUE/OBS_FLAG get_eurostat_data - restat - nrow:11870; ncol:7; colnames:geo/milkitem/freq/dairyprod/TIME_PERIOD/OBS_VALUE/OBS_FLAG get_eurostat_data - processed restat - nrow:11599; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - The data was cached in memory ('b_agr_r_milkpr-2026.07.06-1-0' in '.restatapi_env'). get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: date filter: test_restatapi.R.............. 26 tests OK get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_data - date_filter: 2008 create_filter_table - filters class: numeric; size: 1; filters:2008 create_filter_table - filters: 2008; is numeric: TRUE; call parents: 7 create_filter_table - length df: 1 content df: 2008 create_filter_table - 2008 date filter length: 1, nchar date_filter: 4 get_eurostat_data - date_filter: 2008 nrow dft: 1 -?startPeriod=2008-01-01&endPeriod=2008-12-31 https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2008-01-01&endPeriod=2008-12-31 trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2008-01-01&endPeriod=2008-12-31' downloaded 106 KB get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 410 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:410; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:390; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: date filter: ?startPeriod=2008-01-01&endPeriod=2008-12-31 test_restatapi.R.............. 26 tests OK test_restatapi.R.............. 27 tests OK test_restatapi.R.............. 28 tests OK get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/irt_h_eurcoe_d?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid5TRUE get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_irt_h_eurcoe_d-2026.07.06-0' in '.restatapi_env'). test_restatapi.R.............. 28 tests OK get_eurostat_bulk - API version:2 get_eurostat_bulk - class of id, cache, update_cache, cache_dir, compress_file, stringsAsFactors, keep_flags, check_toc, melt, verbose: character - logical -logical - NULL - logical - logical - logical - logical - logical - logical get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/irt_h_eurcoe_d?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: FALSE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: restatapi::get_eurostat_rawidtxtcacheupdate_cachecache_dircompress_filestringsAsFactorskeep_flagscheck_tocTRUEverbose get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_bulk - The bulk data was cached in memory ('b_irt_h_eurcoe_d-2026.07.06-1-0' in '.restatapi_env'). test_restatapi.R.............. 28 tests OK get_eurostat_raw - API version:2 get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. get_eurostat_raw - raws of TOC: 7661 get_eurostat_raw - txt bulk url from TOC:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/IRT_H_EURCOE_D?format=tsv&compressed=true get_eurostat_raw - txt bulk url from cfg:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/irt_h_eurcoe_d?format=sdmx_2.1_structured&compressed=true get_eurostat_raw - data rowcount in TOC: 29862 get_eurostat_raw - file format: gz get_compressed_sdmx - url:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/irt_h_eurcoe_d?format=sdmx_2.1_structured&compressed=true get_compressed_sdmx - format:gz get_compressed_sdmx - xml NULL:FALSE get_eurostat_raw - class(xml_leafs): xml_nodeset get_eurostat_raw - number of nodes: 18 get_eurostat_raw - number of cores: 2 get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid5xmlTRUETRUETRUETRUEFALSE get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_irt_h_eurcoe_d-2009.03.27-1' in '.restatapi_env'). test_restatapi.R.............. 28 tests OK get_eurostat_bulk - API version:2 get_eurostat_cache - The 'b_irt_h_eurcoe_d-2026.07.06-1-0' was loaded from 'b_irt_h_eurcoe_d-2026.07.06-1-0' in '.restatapi_env'. get_eurostat_bulk - The bulk data was cached previously in memory ('b_irt_h_eurcoe_d-2026.07.06-1-0' in '.restatapi_env'). It remained unchanged. test_restatapi.R.............. 28 tests OK test_restatapi.R.............. 29 tests OK test_restatapi.R.............. 31 tests OK trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/agr_r_milkpr?references=children' downloaded 2.9 MB trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/agr_r_milkpr' downloaded 15 KB test_restatapi.R.............. 32 tests OK test_restatapi.R.............. 33 tests OK test_restatapi.R.............. 34 tests OK test_restatapi.R.............. 35 tests OK test_restatapi.R.............. 38 tests OK trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children' downloaded 7.1 MB trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/avia_par_me/?startPeriod=2017-03-01&endPeriod=2017-03-31' downloaded 58 KB trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children' downloaded 7.7 MB test_restatapi.R.............. 39 tests OK test_restatapi.R.............. 40 tests 1 fails test_restatapi.R.............. 40 tests 1 fails test_restatapi.R.............. 41 tests 1 fails get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. test_restatapi.R.............. 41 tests 1 fails get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. create_filter_table - filters class: character; size: 1; filters:AT ...AT- https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT/ trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT/' Content type 'application/vnd.sdmx.genericdata+xml;version=2.1' length 3279 bytes ================================================== downloaded 3279 bytes get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 1 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:29; ncol:6; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue get_eurostat_data - processed restat - nrow:29; ncol:5; colnames:geo/milkitem/dairyprod/time/values get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: ...AT date filter: get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. create_filter_table - filters class: character; size: 1; filters:AT ...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34- https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34/ trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34/' downloaded 31 KB get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 13 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:377; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:377; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: ...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34 date filter: get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_data - date_filter: 2016 create_filter_table - filters class: numeric; size: 1; filters:2016 create_filter_table - filters: 2016; is numeric: TRUE; call parents: 8 create_filter_table - length df: 1 content df: 2016 create_filter_table - 2016 date filter length: 1, nchar date_filter: 4 get_eurostat_data - date_filter: 2016 nrow dft: 1 -?startPeriod=2016-01-01&endPeriod=2016-12-31 https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2016-01-01&endPeriod=2016-12-31 trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2016-01-01&endPeriod=2016-12-31' downloaded 137 KB get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 508 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:508; ncol:6; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue get_eurostat_data - processed restat - nrow:494; ncol:5; colnames:geo/milkitem/dairyprod/time/values get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: date filter: ?startPeriod=2016-01-01&endPeriod=2016-12-31 get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_data - date_filter: 2016 create_filter_table - filters class: character; size: 1; filters:2016 create_filter_table - filters: 2016; is numeric: FALSE; call parents: 8 create_filter_table - length df: 1 content df: 2016 create_filter_table - 2016 date filter length: 1, nchar date_filter: 4 get_eurostat_data - date_filter: 2016 nrow dft: 1 -?startPeriod=2016-01-01&endPeriod=2016-12-31 https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2016-01-01&endPeriod=2016-12-31 trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2016-01-01&endPeriod=2016-12-31' downloaded 137 KB get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 508 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:508; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:494; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: date filter: ?startPeriod=2016-01-01&endPeriod=2016-12-31 get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. create_filter_table - filters class: character; size: 1; filters:AT ...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34+EL11+EL3+EL30+EL51+ES51+ES52+HR+HR02+HR03+HR04+HR06+HR01+ITF5+LV+LV0+LV00+HU22+RO4+SK01+NO01+NO03+NO04+NO05+UKD3+UKK1+TR2+TR5+TR63+TR72+TR8+TR83+TRB1+TRC3- https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34+EL11+EL3+EL30+EL51+ES51+ES52+HR+HR02+HR03+HR04+HR06+HR01+ITF5+LV+LV0+LV00+HU22+RO4+SK01+NO01+NO03+NO04+NO05+UKD3+UKK1+TR2+TR5+TR63+TR72+TR8+TR83+TRB1+TRC3/ trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34+EL11+EL3+EL30+EL51+ES51+ES52+HR+HR02+HR03+HR04+HR06+HR01+ITF5+LV+LV0+LV00+HU22+RO4+SK01+NO01+NO03+NO04+NO05+UKD3+UKK1+TR2+TR5+TR63+TR72+TR8+TR83+TRB1+TRC3/' downloaded 83 KB get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 46 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:1004; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:993; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: ...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34+EL11+EL3+EL30+EL51+ES51+ES52+HR+HR02+HR03+HR04+HR06+HR01+ITF5+LV+LV0+LV00+HU22+RO4+SK01+NO01+NO03+NO04+NO05+UKD3+UKK1+TR2+TR5+TR63+TR72+TR8+TR83+TRB1+TRC3 date filter: test_restatapi.R.............. 45 tests 1 fails get_eurostat_dsd - API version:2 get_eurostat_dsd - Trying to download the DSD from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children' downloaded 8.8 MB get_eurostat_dsd - Warning by the download of the DSD file: URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children': Timeout of 60 seconds was reached utils::download.file(dsd_endpoint, temp, dmethod) get_eurostat_dsd - class(temp): character - is.na(temp): FALSE - file.size(temp): 9196418 - temp: /tmp/th798/29939837/RtmpCEDVOS/fileb507653b3ea94 Trying to extract the DSD from: /tmp/th798/29939837/RtmpCEDVOS/fileb507653b3ea94 get_eurostat_dsd - Error during the extraction of the XML from the downloaded DSD file: AttValue: ' expected [40] read_xml.character(temp) get_eurostat_dsd - The dsd_xml is NULL. Please check in a browser the url below. If it provides valid response you can try again to download the DSD. https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children test_restatapi.R.............. 45 tests 1 fails test_restatapi.R.............. 45 tests 1 fails test_restatapi.R.............. 45 tests 1 fails test_restatapi.R.............. 47 tests 1 fails test_restatapi.R.............. 49 tests 1 fails test_restatapi.R.............. 50 tests 1 fails test_restatapi.R.............. 50 tests 1 fails test_restatapi.R.............. 51 tests 1 fails test_restatapi.R.............. 53 tests 1 fails test_restatapi.R.............. 54 tests 1 fails test_restatapi.R.............. 58 tests 1 fails test_restatapi.R.............. 60 tests 1 fails test_restatapi.R.............. 62 tests 1 fails test_restatapi.R.............. 63 tests 1 fails test_restatapi.R.............. 64 tests 1 fails test_restatapi.R.............. 65 tests 1 fails test_restatapi.R.............. 66 tests 1 fails test_restatapi.R.............. 67 tests 1 fails test_restatapi.R.............. 68 tests 1 fails test_restatapi.R.............. 69 tests 1 fails test_restatapi.R.............. 70 tests 1 fails test_restatapi.R.............. 71 tests 1 fails test_restatapi.R.............. 72 tests 1 fails test_restatapi.R.............. 73 tests 1 fails test_restatapi.R.............. 74 tests 1 fails test_restatapi.R.............. 75 tests 1 fails test_restatapi.R.............. 76 tests 1 fails get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/tus_00age?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid7 get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_tus_00age-2026.07.06-0' in '.restatapi_env'). test_restatapi.R.............. 76 tests 1 fails get_eurostat_dsd - API version:2 get_eurostat_dsd - Trying to download the DSD from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/tus_00age?references=children trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/tus_00age?references=children' downloaded 3.7 MB get_eurostat_dsd - class(temp): character - is.na(temp): FALSE - file.size(temp): 3901770 - temp: /tmp/th798/29939837/RtmpCEDVOS/fileb5076347d32d2 Trying to extract the DSD from: /tmp/th798/29939837/RtmpCEDVOS/fileb5076347d32d2 get_eurostat_dsd - concepts:freq,unit,sex,age,acl00,geo,OBS_FLAG,CONF_STATUS extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="FREQ"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="FREQ"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="UNIT"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="UNIT"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="SEX"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="SEX"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="AGE"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="AGE"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="ACL00"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="ACL00"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="GEO"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="GEO"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="OBS_FLAG"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="OBS_FLAG"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="CONF_STATUS"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="CONF_STATUS"]/s:Code/c:Name[@xml:lang="en"] get_eurostat_dsd - DSD NULL:FALSE get_eurostat_dsd - Trying to download the CC from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/tus_00age trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/tus_00age' Content type 'application/vnd.sdmx.structure+xml;version=2.1' length 3844 bytes ================================================== downloaded 3844 bytes get_eurostat_dsd - Trying to extract the CC from: /tmp/th798/29939837/RtmpCEDVOS/fileb50766da45225 character number of nodes: 7 number of cores: 2 get_eurostat_dsd - The DSD of the tus_00age dataset was cached in memory ('tus_00age.en.dsd' in '.restatapi_env'). test_restatapi.R.............. 76 tests 1 fails create_filter_table - filters class: character; size: 3; filters:TIME_SPHungaryT test_restatapi.R.............. 77 tests 1 fails get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/avia_par_me?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid6 get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_avia_par_me-2026.07.06-0' in '.restatapi_env'). test_restatapi.R.............. 77 tests 1 fails create_filter_table - filters class: character; size: 1; filters:2017:2018 create_filter_table - filters: 2017:2018; is numeric: FALSE; call parents: 6 create_filter_table - length df: 1 content df: 2017:2018 create_filter_table - 2017:2018 date filter length: 1, nchar date_filter: 9 test_restatapi.R.............. 78 tests 1 fails get_eurostat_codelist - API version:2 get_eurostat_codelist - API version:2 get_eurostat_codelist - Trying to download the codelist from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/codelist/ESTAT/SEX trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/codelist/ESTAT/SEX' Content type 'application/vnd.sdmx.structure+xml;version=2.1' length 5483 bytes ================================================== downloaded 5483 bytes Trying to extract the codelist from: /tmp/th798/29939837/RtmpCEDVOS/fileb507658b9ce3d get_eurostat_codelist - codelist NULL:TRUE test_restatapi.R.............. 78 tests 1 fails test_restatapi.R.............. 80 tests 1 fails 4.18.0-553.124.1.el8_10.x86_64 test_restatapi.R.............. 80 tests 1 fails Are we at home:FALSE test_restatapi.R.............. 80 tests 1 fails test_restatapi.R.............. 80 tests 1 fails get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=fr trying URL 'https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=fr' downloaded 2.1 MB get_eurostat_toc - The TOC was cached in memory ('toc.txt.fr' in '.restatapi_env'). test_restatapi.R.............. 80 tests 1 fails get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=de trying URL 'https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=de' downloaded 2.0 MB get_eurostat_toc - The TOC was cached in memory ('toc.txt.de' in '.restatapi_env'). test_restatapi.R.............. 80 tests 1 fails test_restatapi.R.............. 81 tests 1 fails get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_dsd - API version:2 get_eurostat_dsd - Trying to download the DSD from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/agr_r_milkpr?references=children trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/agr_r_milkpr?references=children' downloaded 2.9 MB get_eurostat_dsd - class(temp): character - is.na(temp): FALSE - file.size(temp): 3008178 - temp: /tmp/th798/29939837/RtmpCEDVOS/fileb507639cbadb0 Trying to extract the DSD from: /tmp/th798/29939837/RtmpCEDVOS/fileb507639cbadb0 get_eurostat_dsd - concepts:freq,milkitem,dairyprod,geo,OBS_FLAG,CONF_STATUS extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="FREQ"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="FREQ"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="MILKITEM"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="MILKITEM"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="DAIRYPROD"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="DAIRYPROD"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="GEO"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="GEO"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="OBS_FLAG"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="OBS_FLAG"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="CONF_STATUS"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="CONF_STATUS"]/s:Code/c:Name[@xml:lang="de"] get_eurostat_dsd - DSD NULL:FALSE get_eurostat_dsd - Trying to download the CC from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/agr_r_milkpr trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/agr_r_milkpr' downloaded 15 KB get_eurostat_dsd - Trying to extract the CC from: /tmp/th798/29939837/RtmpCEDVOS/fileb50767462c389 character number of nodes: 5 number of cores: 2 get_eurostat_dsd - The DSD of the agr_r_milkpr dataset was cached in memory ('agr_r_milkpr.de.dsd' in '.restatapi_env'). create_filter_table - filters class: character; size: 2; filters:BE$Ungarn get_eurostat_data - date_filter: 2007-06< create_filter_table - filters class: character; size: 1; filters:2007-06< create_filter_table - filters: 2007-06<; is numeric: FALSE; call parents: 7 create_filter_table - length df: 1 content df: 2007-06< create_filter_table - 2007-06< date filter length: 1, nchar date_filter: 8 get_eurostat_data - date_filter: 2007-06< nrow dft: 1 ...BE+HU-?startPeriod=2007-06-01 https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...BE+HU/?startPeriod=2007-06-01 trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...BE+HU/?startPeriod=2007-06-01' Content type 'application/vnd.sdmx.genericdata+xml;version=2.1' length 3959 bytes ================================================== downloaded 3959 bytes get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 2 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:34; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:34; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: ...BE+HU date filter: ?startPeriod=2007-06-01 test_restatapi.R.............. 81 tests 1 fails get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. create_filter_table - filters class: character; size: 2; filters:BE$Hungary get_eurostat_data - date_filter: 2007-06< create_filter_table - filters class: character; size: 1; filters:2007-06< create_filter_table - filters: 2007-06<; is numeric: FALSE; call parents: 7 create_filter_table - length df: 1 content df: 2007-06< create_filter_table - 2007-06< date filter length: 1, nchar date_filter: 8 get_eurostat_data - date_filter: 2007-06< nrow dft: 1 ...BE+HU-?startPeriod=2007-06-01 https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...BE+HU/?startPeriod=2007-06-01 trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...BE+HU/?startPeriod=2007-06-01' Content type 'application/vnd.sdmx.genericdata+xml;version=2.1' length 3959 bytes ================================================== downloaded 3959 bytes get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 2 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:34; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:34; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: ...BE+HU date filter: ?startPeriod=2007-06-01 test_restatapi.R.............. 81 tests 1 fails test_restatapi.R.............. 82 tests 1 fails clean_restatapi_cache - All objects (outside of 'cfg', 'rav', 'cc' and 'dmethod') are removed from '.restatapi_env'. clean_restatapi_cache - Deleted all .rds files from /tmp/th798/29939837/RtmpCEDVOS test_restatapi.R.............. 82 tests 1 fails There are skipped tests:27-29,54 test_restatapi.R.............. 82 tests 1 fails Skipped tests: 27-29,54 config version: 2 test_restatapi.R.............. 82 tests 1 fails test_restatapi.R.............. 82 tests 1 fails 7.1s ----- FAILED[data]: test_restatapi.R<169--169> call| expect_true(is.null(dt8)) diff| Expected TRUE, got FALSE Error: 1 out of 82 tests failed Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR See '/tmp/th798/29939837/R-release/1314/restatapi.Rcheck/00check.log' for details. [1] "2026-07-06 11:33:49 MST" [1] "2026-07-06 11:33:49 MST" Installing package into '/tmp/th798/29939837/R-release/1314/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.18.99' ** using staged installation zlib 1.2.13 is available ok * checking if OpenMP works with CFLAGS='' LIBS=''... no * checking if OpenMP works with CFLAGS='$(SHLIB_OPENMP_CFLAGS)' LIBS='$(SHLIB_OPENMP_CFLAGS)'... yes ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c assign.c -o assign.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c between.c -o between.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bmerge.c -o bmerge.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c chmatch.c -o chmatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cj.c -o cj.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c coalesce.c -o coalesce.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c deleterows.c -o deleterows.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dogroups.c -o dogroups.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmean.c -o fastmean.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fcast.c -o fcast.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fifelse.c -o fifelse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fmelt.c -o fmelt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c forder.c -o forder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frank.c -o frank.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fread.c -o fread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c freadR.c -o freadR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c froll.c -o froll.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollR.c -o frollR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frolladaptive.c -o frolladaptive.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollapply.c -o frollapply.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fsort.c -o fsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwrite.c -o fwrite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwriteR.c -o fwriteR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c gsumm.c -o gsumm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c hash.c -o hash.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c idatetime.c -o idatetime.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ijoin.c -o ijoin.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c inrange.c -o inrange.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c mergelist.c -o mergelist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nafill.c -o nafill.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c negate.c -o negate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nqrecreateindices.c -o nqrecreateindices.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c openmp-utils.c -o openmp-utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c programming.c -o programming.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c quickselect.c -o quickselect.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rbindlist.c -o rbindlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c reorder.c -o reorder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shellsort.c -o shellsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shift.c -o shift.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c snprintf.c -o snprintf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c subset.c -o subset.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c transpose.c -o transpose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c types.c -o types.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uniqlist.c -o uniqlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.c -o utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vecseq.c -o vecseq.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wrappers.c -o wrappers.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o deleterows.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o hash.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fvisibility=hidden -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fvisibility=hidden -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-data.table/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) [1] "2026-07-06 11:34:16 MST" * using log directory '/tmp/th798/29939837/R-release/1314/restatapi.Rcheck' * using R version 4.6.1 (2026-06-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * current time: 2026-07-06 18:34:17 UTC * checking for file 'restatapi/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'restatapi' version '0.25.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'restatapi' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'tinytest.R' OK * checking PDF version of manual ... OK * DONE Status: OK [1] "2026-07-06 11:39:16 MST" > system(paste(c("diff -u", Rcheck.list), collapse=" ")) --- R_version_4.6.1_2026-06-24/release_1.18.4.Rcheck/00check.log 2026-07-06 11:33:49.394000413 -0700 +++ R_version_4.6.1_2026-06-24/master_1.18.99.8c4291395093bf68a53853c867ac62cbc138e6fe.Rcheck/00check.log 2026-07-06 11:39:16.568553698 -0700 @@ -6,7 +6,7 @@ GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII -* current time: 2026-07-06 18:26:04 UTC +* current time: 2026-07-06 18:34:17 UTC * checking for file 'restatapi/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'restatapi' version '0.25.0' @@ -51,806 +51,8 @@ * checking for unstated dependencies in examples ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK -* checking tests ... ERROR +* checking tests ... OK Running 'tinytest.R' -Running the tests in 'tests/tinytest.R' failed. -Complete output: - > if ( requireNamespace("tinytest", quietly=TRUE) ){ - + home <- length(unclass(packageVersion("restatapi"))[[1]]) == 4 - + tinytest::test_package("restatapi", at_home = home) - + } - restatapi: - version 0.25.0 - - config file with the API version 2 loaded from GitHub (the 'current' API version number is 2). - - 4 from the 28 cores are used for parallel computing, can be changed with 'options(restatapi_cores=...)' - - 'auto' method will be used for file download, can be changed with 'options(restatapi_dmethod=...)' - - the Table of contents (TOC) was not pre-loaded into the deafult cache ('.restatapi_env'). - - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - clean_restatapi_cache - All objects (outside of 'cfg', 'rav', 'cc' and 'dmethod') are removed from '.restatapi_env'. - - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 0 tests - get_eurostat_toc - API version:2 - number of cores:2 - get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/xml - get_eurostat_toc - class(xml_leafs): xml_nodeset - get_eurostat_toc - number of nodes: 10408 - get_eurostat_toc - number of cores: 2 - get_eurostat_toc - dim toc: 10408,22 - get_eurostat_toc - colnames toc: title.en,title.fr,title.de,code,lastUpdate,lastModified,dataStart,dataEnd,values,source.en,source.fr,source.de,unit.en,unit.fr,unit.de,shortDescription.en,shortDescription.fr,shortDescription.de,metadata.html,metadata.sdmx,downloadLink.tsv,type - get_eurostat_toc - cols to keep: title.en,code,type,lastUpdate,lastModified,dataStart,dataEnd,values,unit.en,source.en,shortDescription.en,metadata.html,metadata.sdmx,downloadLink.tsv - get_eurostat_toc - The TOC was cached in memory ('toc.xml.en' in '.restatapi_env'). - - test_restatapi.R.............. 0 tests - get_eurostat_toc - API version:2 - number of cores:2 - get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=en - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=en' - downloaded 1.9 MB - - get_eurostat_toc - The TOC was cached in memory ('toc.txt.en' in '.restatapi_env'). - - test_restatapi.R.............. 0 tests - get_eurostat_toc - API version:2 - number of cores:2 - - get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. - get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. - - test_restatapi.R.............. 0 tests - test_restatapi.R.............. 1 tests OK - test_restatapi.R.............. 7 tests OK - get_eurostat_toc - API version:2 - number of cores:2 - - get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. - get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. - - test_restatapi.R.............. 7 tests OK - get_eurostat_toc - API version:2 - number of cores:2 - - get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. - get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. - - test_restatapi.R.............. 7 tests OK - get_eurostat_toc - API version:2 - number of cores:2 - get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/xml - get_eurostat_toc - class(xml_leafs): xml_nodeset - get_eurostat_toc - number of nodes: 10408 - get_eurostat_toc - number of cores: 2 - get_eurostat_toc - dim toc: 10408,22 - get_eurostat_toc - colnames toc: title.en,title.fr,title.de,code,lastUpdate,lastModified,dataStart,dataEnd,values,source.en,source.fr,source.de,unit.en,unit.fr,unit.de,shortDescription.en,shortDescription.fr,shortDescription.de,metadata.html,metadata.sdmx,downloadLink.tsv,type - get_eurostat_toc - cols to keep: title.de,code,type,lastUpdate,lastModified,dataStart,dataEnd,values,unit.de,source.de,shortDescription.de,metadata.html,metadata.sdmx,downloadLink.tsv - get_eurostat_toc - The TOC was cached in memory ('toc.xml.de' in '.restatapi_env'). - - test_restatapi.R.............. 7 tests OK - test_restatapi.R.............. 8 tests OK - test_restatapi.R.............. 9 tests OK trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/text?references=children' - - test_restatapi.R.............. 10 tests OK - get_eurostat_dsd - API version:2 - - get_eurostat_dsd - Trying to download the DSD from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/NAMA_10_GDP?references=children - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/NAMA_10_GDP?references=children' - downloaded 3.4 MB - - - get_eurostat_dsd - class(temp): character - is.na(temp): FALSE - file.size(temp): 3585472 - temp: /tmp/th798/29939837/RtmpCEDVOS/fileb5076d390d79 - Trying to extract the DSD from: /tmp/th798/29939837/RtmpCEDVOS/fileb5076d390d79 - get_eurostat_dsd - concepts:freq,unit,na_item,geo,OBS_FLAG,CONF_STATUS - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="FREQ"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="FREQ"]/s:Code/c:Name[@xml:lang="en"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="UNIT"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="UNIT"]/s:Code/c:Name[@xml:lang="en"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="NA_ITEM"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="NA_ITEM"]/s:Code/c:Name[@xml:lang="en"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="GEO"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="GEO"]/s:Code/c:Name[@xml:lang="en"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="OBS_FLAG"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="OBS_FLAG"]/s:Code/c:Name[@xml:lang="en"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="CONF_STATUS"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="CONF_STATUS"]/s:Code/c:Name[@xml:lang="en"] - get_eurostat_dsd - DSD NULL:FALSE - get_eurostat_dsd - Trying to download the CC from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/NAMA_10_GDP - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/NAMA_10_GDP' - Content type 'application/vnd.sdmx.structure+xml;version=2.1' length 5597 bytes - ================================================== - downloaded 5597 bytes - - get_eurostat_dsd - Trying to extract the CC from: /tmp/th798/29939837/RtmpCEDVOS/fileb5076368d6a5c - character - number of nodes: 5 - number of cores: 2 - - get_eurostat_dsd - The DSD of the NAMA_10_GDP dataset was cached in memory ('NAMA_10_GDP.en.dsd' in '.restatapi_env'). - - test_restatapi.R.............. 10 tests OK - test_restatapi.R.............. 13 tests OK - test_restatapi.R.............. 13 tests OK - test_restatapi.R.............. 13 tests OK - test_restatapi.R.............. 17 tests OK get_eurostat_data - footer code option value at start: - get_eurostat_data - footer code option value after reset: - get_eurostat_data - id: htec_cis3 - get_eurostat_data - select_freq: - get_eurostat_data - Trying to get from cache: b_htec_cis3-2026.07.06-1-1 - - get_eurostat_bulk - API version:2 - get_eurostat_bulk - class of id, cache, update_cache, cache_dir, compress_file, stringsAsFactors, keep_flags, check_toc, melt, verbose: - character - logical -logical - NULL - logical - logical - logical - logical - logical - logical - - get_eurostat_raw - API version:2 - get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/htec_cis3?format=TSV&compressed=true - get_eurostat_raw - class(raw): data.tabledata.frame - get_eurostat_raw - caching in raw: FALSE - get_eurostat_raw - local filter: FALSE - get_eurostat_raw - called from: restatapi::get_eurostat_rawidtxtcacheupdate_cachecache_dircompress_filestringsAsFactorskeep_flagscheck_tocTRUEverbose - get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE - get_eurostat_data - The data was downloaded with bulk download. - get_eurostat_data - bulk restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags - get_eurostat_data - cflags:TRUE - get_eurostat_data - restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags - get_eurostat_data - processed restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags - get_eurostat_data - The data was cached in memory ('b_htec_cis3-2026.07.06-1-1' in '.restatapi_env'). - get_eurostat_data - restat NULL?:FALSE - id: htec_cis3 - filters: - date filter: - - test_restatapi.R.............. 17 tests OK - test_restatapi.R.............. 17 tests OK get_eurostat_data - footer code option value at start: - get_eurostat_data - footer code option value after reset: - get_eurostat_data - id: htec_cis3 - get_eurostat_data - select_freq: - get_eurostat_data - Trying to get from cache: b_htec_cis3-2026.07.06-0-0 - - get_eurostat_cache - The 'b_htec_cis3-2026.07.06-0-0' was loaded from 'b_htec_cis3-2026.07.06-1-1' in '.restatapi_env'. - get_eurostat_data - The data was loaded from cache. - get_eurostat_data - cached restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags - get_eurostat_data - restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags - get_eurostat_data - processed restat - nrow:1006; ncol:6; colnames:indic_in/nace_r1/unit/geo/time/values - get_eurostat_data - The data was cached in memory ('b_htec_cis3-2026.07.06-0-0' in '.restatapi_env'). - get_eurostat_data - restat NULL?:FALSE - id: htec_cis3 - filters: - date filter: - - test_restatapi.R.............. 17 tests OK - test_restatapi.R.............. 17 tests OK - test_restatapi.R.............. 21 tests OK - get_eurostat_raw - API version:2 - get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/rail_tf_ns20_mk?format=TSV&compressed=true - get_eurostat_raw - class(raw): data.tabledata.frame - get_eurostat_raw - caching in raw: TRUE - get_eurostat_raw - local filter: FALSE - get_eurostat_raw - called from: get_eurostat_rawtestid3FALSE - get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE - get_eurostat_raw - The raw data was cached in memory ('r_rail_tf_ns20_mk-2026.07.06-0' in '.restatapi_env'). - - get_eurostat_raw - API version:2 - - get_eurostat_toc - API version:2 - number of cores:2 - - get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. - get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. - get_eurostat_raw - raws of TOC: 7661 - get_eurostat_raw - txt bulk url from TOC:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/RAIL_TF_NS20_MK?format=tsv&compressed=true - get_eurostat_raw - txt bulk url from cfg:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/rail_tf_ns20_mk?format=TSV&compressed=true - get_eurostat_raw - data rowcount in TOC: 12 - get_eurostat_raw - class(raw): data.tabledata.frame - get_eurostat_raw - caching in raw: TRUE - get_eurostat_raw - local filter: FALSE - get_eurostat_raw - called from: get_eurostat_rawtestid3TRUEFALSE - get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE - get_eurostat_raw - The raw data was cached in memory ('r_rail_tf_ns20_mk-2023.02.02-0' in '.restatapi_env'). - get_eurostat_data - footer code option value at start: - get_eurostat_data - footer code option value after reset: - get_eurostat_data - id: rail_tf_ns20_mk - get_eurostat_data - select_freq: - get_eurostat_data - Trying to get from cache: b_rail_tf_ns20_mk-2026.07.06-0-0 - - get_eurostat_cache - The 'b_rail_tf_ns20_mk-2026.07.06-0-0' was loaded from 'r_rail_tf_ns20_mk-2026.07.06-0' in '.restatapi_env'. - get_eurostat_data - The data was loaded from cache. - get_eurostat_data - cached restat - nrow:12; ncol:6; colnames:freq/net_seg20/train/unit/time/values - get_eurostat_data - restat - nrow:12; ncol:6; colnames:freq/net_seg20/train/unit/time/values - get_eurostat_data - processed restat - nrow:12; ncol:5; colnames:net_seg20/train/unit/time/values - get_eurostat_data - The data was cached in memory ('b_rail_tf_ns20_mk-2026.07.06-0-0' in '.restatapi_env'). - get_eurostat_data - restat NULL?:FALSE - id: rail_tf_ns20_mk - filters: - date filter: - - test_restatapi.R.............. 26 tests OK - get_eurostat_raw - API version:2 - get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr?format=sdmx_2.1_structured&compressed=true - get_eurostat_raw - file format: gz - - get_compressed_sdmx - url:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr?format=sdmx_2.1_structured&compressed=true - get_compressed_sdmx - format:gz - get_compressed_sdmx - xml NULL:FALSE - get_eurostat_raw - class(xml_leafs): xml_nodeset - get_eurostat_raw - number of nodes: 583 - get_eurostat_raw - number of cores: 2 - get_eurostat_raw - caching in raw: TRUE - get_eurostat_raw - local filter: FALSE - get_eurostat_raw - called from: get_eurostat_rawtestid4xmlTRUETRUE - get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE - get_eurostat_raw - The raw data was cached in memory ('r_agr_r_milkpr-2026.07.06-1' in '.restatapi_env'). - - test_restatapi.R.............. 26 tests OK get_eurostat_data - footer code option value at start: - get_eurostat_data - footer code option value after reset: - get_eurostat_data - id: agr_r_milkpr - get_eurostat_data - select_freq: - get_eurostat_data - Trying to get from cache: b_agr_r_milkpr-2026.07.06-1-0 - - get_eurostat_cache - The 'b_agr_r_milkpr-2026.07.06-1-0' was loaded from 'r_agr_r_milkpr-2026.07.06-1' in '.restatapi_env'. - get_eurostat_data - The data was loaded from cache. - get_eurostat_data - cached restat - nrow:11870; ncol:7; colnames:geo/milkitem/freq/dairyprod/TIME_PERIOD/OBS_VALUE/OBS_FLAG - get_eurostat_data - restat - nrow:11870; ncol:7; colnames:geo/milkitem/freq/dairyprod/TIME_PERIOD/OBS_VALUE/OBS_FLAG - get_eurostat_data - processed restat - nrow:11599; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags - get_eurostat_data - The data was cached in memory ('b_agr_r_milkpr-2026.07.06-1-0' in '.restatapi_env'). - get_eurostat_data - restat NULL?:FALSE - id: agr_r_milkpr - filters: - date filter: - - test_restatapi.R.............. 26 tests OK get_eurostat_data - footer code option value at start: - get_eurostat_data - footer code option value after reset: - get_eurostat_data - id: agr_r_milkpr - get_eurostat_data - select_freq: - get_eurostat_data - date_filter: 2008 - create_filter_table - filters class: numeric; size: 1; filters:2008 - create_filter_table - filters: 2008; is numeric: TRUE; call parents: 7 - create_filter_table - length df: 1 content df: 2008 - create_filter_table - 2008 date filter length: 1, nchar date_filter: 4 - get_eurostat_data - date_filter: 2008 nrow dft: 1 - -?startPeriod=2008-01-01&endPeriod=2008-12-31 - https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2008-01-01&endPeriod=2008-12-31 - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2008-01-01&endPeriod=2008-12-31' - downloaded 106 KB - - get_eurostat_data - class(xml_leafs):xml_nodeset - get_eurostat_data - number of nodes: 410 - get_eurostat_data - number of cores: 2 - get_eurostat_data - footer code option value after retrieval: - get_eurostat_data - restat - nrow:410; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS - get_eurostat_data - processed restat - nrow:390; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags - get_eurostat_data - restat NULL?:FALSE - id: agr_r_milkpr - filters: - date filter: ?startPeriod=2008-01-01&endPeriod=2008-12-31 - - test_restatapi.R.............. 26 tests OK - test_restatapi.R.............. 27 tests OK - test_restatapi.R.............. 28 tests OK - get_eurostat_raw - API version:2 - get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/irt_h_eurcoe_d?format=TSV&compressed=true - get_eurostat_raw - class(raw): data.tabledata.frame - get_eurostat_raw - caching in raw: TRUE - get_eurostat_raw - local filter: FALSE - get_eurostat_raw - called from: get_eurostat_rawtestid5TRUE - get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE - get_eurostat_raw - The raw data was cached in memory ('r_irt_h_eurcoe_d-2026.07.06-0' in '.restatapi_env'). - - test_restatapi.R.............. 28 tests OK - get_eurostat_bulk - API version:2 - get_eurostat_bulk - class of id, cache, update_cache, cache_dir, compress_file, stringsAsFactors, keep_flags, check_toc, melt, verbose: - character - logical -logical - NULL - logical - logical - logical - logical - logical - logical - - get_eurostat_raw - API version:2 - get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/irt_h_eurcoe_d?format=TSV&compressed=true - get_eurostat_raw - class(raw): data.tabledata.frame - get_eurostat_raw - caching in raw: FALSE - get_eurostat_raw - local filter: FALSE - get_eurostat_raw - called from: restatapi::get_eurostat_rawidtxtcacheupdate_cachecache_dircompress_filestringsAsFactorskeep_flagscheck_tocTRUEverbose - get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE - get_eurostat_bulk - The bulk data was cached in memory ('b_irt_h_eurcoe_d-2026.07.06-1-0' in '.restatapi_env'). - - test_restatapi.R.............. 28 tests OK - get_eurostat_raw - API version:2 - - get_eurostat_toc - API version:2 - number of cores:2 - - get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. - get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. - get_eurostat_raw - raws of TOC: 7661 - get_eurostat_raw - txt bulk url from TOC:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/IRT_H_EURCOE_D?format=tsv&compressed=true - get_eurostat_raw - txt bulk url from cfg:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/irt_h_eurcoe_d?format=sdmx_2.1_structured&compressed=true - get_eurostat_raw - data rowcount in TOC: 29862 - get_eurostat_raw - file format: gz - - get_compressed_sdmx - url:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/irt_h_eurcoe_d?format=sdmx_2.1_structured&compressed=true - get_compressed_sdmx - format:gz - get_compressed_sdmx - xml NULL:FALSE - get_eurostat_raw - class(xml_leafs): xml_nodeset - get_eurostat_raw - number of nodes: 18 - get_eurostat_raw - number of cores: 2 - get_eurostat_raw - caching in raw: TRUE - get_eurostat_raw - local filter: FALSE - get_eurostat_raw - called from: get_eurostat_rawtestid5xmlTRUETRUETRUETRUEFALSE - get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE - get_eurostat_raw - The raw data was cached in memory ('r_irt_h_eurcoe_d-2009.03.27-1' in '.restatapi_env'). - - test_restatapi.R.............. 28 tests OK - get_eurostat_bulk - API version:2 - - get_eurostat_cache - The 'b_irt_h_eurcoe_d-2026.07.06-1-0' was loaded from 'b_irt_h_eurcoe_d-2026.07.06-1-0' in '.restatapi_env'. - get_eurostat_bulk - The bulk data was cached previously in memory ('b_irt_h_eurcoe_d-2026.07.06-1-0' in '.restatapi_env'). It remained unchanged. - - test_restatapi.R.............. 28 tests OK - test_restatapi.R.............. 29 tests OK - test_restatapi.R.............. 31 tests OK trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/agr_r_milkpr?references=children' - downloaded 2.9 MB - - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/agr_r_milkpr' - downloaded 15 KB - - - test_restatapi.R.............. 32 tests OK - test_restatapi.R.............. 33 tests OK - test_restatapi.R.............. 34 tests OK - test_restatapi.R.............. 35 tests OK - test_restatapi.R.............. 38 tests OK trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children' - downloaded 7.1 MB - - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/avia_par_me/?startPeriod=2017-03-01&endPeriod=2017-03-31' - downloaded 58 KB - - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children' - downloaded 7.7 MB - - - test_restatapi.R.............. 39 tests OK - test_restatapi.R.............. 40 tests 1 fails - test_restatapi.R.............. 40 tests 1 fails - test_restatapi.R.............. 41 tests 1 fails - get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. - - test_restatapi.R.............. 41 tests 1 fails get_eurostat_data - footer code option value at start: - get_eurostat_data - footer code option value after reset: - get_eurostat_data - id: agr_r_milkpr - get_eurostat_data - select_freq: - - get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. - create_filter_table - filters class: character; size: 1; filters:AT - ...AT- - https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT/ - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT/' - Content type 'application/vnd.sdmx.genericdata+xml;version=2.1' length 3279 bytes - ================================================== - downloaded 3279 bytes - - get_eurostat_data - class(xml_leafs):xml_nodeset - get_eurostat_data - number of nodes: 1 - get_eurostat_data - number of cores: 2 - get_eurostat_data - footer code option value after retrieval: - get_eurostat_data - restat - nrow:29; ncol:6; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue - get_eurostat_data - processed restat - nrow:29; ncol:5; colnames:geo/milkitem/dairyprod/time/values - get_eurostat_data - restat NULL?:FALSE - id: agr_r_milkpr - filters: ...AT - date filter: - get_eurostat_data - footer code option value at start: - get_eurostat_data - footer code option value after reset: - get_eurostat_data - id: agr_r_milkpr - get_eurostat_data - select_freq: - - get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. - create_filter_table - filters class: character; size: 1; filters:AT - ...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34- - https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34/ - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34/' - downloaded 31 KB - - get_eurostat_data - class(xml_leafs):xml_nodeset - get_eurostat_data - number of nodes: 13 - get_eurostat_data - number of cores: 2 - get_eurostat_data - footer code option value after retrieval: - get_eurostat_data - restat - nrow:377; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS - get_eurostat_data - processed restat - nrow:377; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags - get_eurostat_data - restat NULL?:FALSE - id: agr_r_milkpr - filters: ...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34 - date filter: - get_eurostat_data - footer code option value at start: - get_eurostat_data - footer code option value after reset: - get_eurostat_data - id: agr_r_milkpr - get_eurostat_data - select_freq: - get_eurostat_data - date_filter: 2016 - create_filter_table - filters class: numeric; size: 1; filters:2016 - create_filter_table - filters: 2016; is numeric: TRUE; call parents: 8 - create_filter_table - length df: 1 content df: 2016 - create_filter_table - 2016 date filter length: 1, nchar date_filter: 4 - get_eurostat_data - date_filter: 2016 nrow dft: 1 - -?startPeriod=2016-01-01&endPeriod=2016-12-31 - https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2016-01-01&endPeriod=2016-12-31 - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2016-01-01&endPeriod=2016-12-31' - downloaded 137 KB - - get_eurostat_data - class(xml_leafs):xml_nodeset - get_eurostat_data - number of nodes: 508 - get_eurostat_data - number of cores: 2 - get_eurostat_data - footer code option value after retrieval: - get_eurostat_data - restat - nrow:508; ncol:6; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue - get_eurostat_data - processed restat - nrow:494; ncol:5; colnames:geo/milkitem/dairyprod/time/values - get_eurostat_data - restat NULL?:FALSE - id: agr_r_milkpr - filters: - date filter: ?startPeriod=2016-01-01&endPeriod=2016-12-31 - get_eurostat_data - footer code option value at start: - get_eurostat_data - footer code option value after reset: - get_eurostat_data - id: agr_r_milkpr - get_eurostat_data - select_freq: - get_eurostat_data - date_filter: 2016 - create_filter_table - filters class: character; size: 1; filters:2016 - create_filter_table - filters: 2016; is numeric: FALSE; call parents: 8 - create_filter_table - length df: 1 content df: 2016 - create_filter_table - 2016 date filter length: 1, nchar date_filter: 4 - get_eurostat_data - date_filter: 2016 nrow dft: 1 - -?startPeriod=2016-01-01&endPeriod=2016-12-31 - https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2016-01-01&endPeriod=2016-12-31 - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2016-01-01&endPeriod=2016-12-31' - downloaded 137 KB - - get_eurostat_data - class(xml_leafs):xml_nodeset - get_eurostat_data - number of nodes: 508 - get_eurostat_data - number of cores: 2 - get_eurostat_data - footer code option value after retrieval: - get_eurostat_data - restat - nrow:508; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS - get_eurostat_data - processed restat - nrow:494; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags - get_eurostat_data - restat NULL?:FALSE - id: agr_r_milkpr - filters: - date filter: ?startPeriod=2016-01-01&endPeriod=2016-12-31 - get_eurostat_data - footer code option value at start: - get_eurostat_data - footer code option value after reset: - get_eurostat_data - id: agr_r_milkpr - get_eurostat_data - select_freq: - - get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. - create_filter_table - filters class: character; size: 1; filters:AT - ...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34+EL11+EL3+EL30+EL51+ES51+ES52+HR+HR02+HR03+HR04+HR06+HR01+ITF5+LV+LV0+LV00+HU22+RO4+SK01+NO01+NO03+NO04+NO05+UKD3+UKK1+TR2+TR5+TR63+TR72+TR8+TR83+TRB1+TRC3- - https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34+EL11+EL3+EL30+EL51+ES51+ES52+HR+HR02+HR03+HR04+HR06+HR01+ITF5+LV+LV0+LV00+HU22+RO4+SK01+NO01+NO03+NO04+NO05+UKD3+UKK1+TR2+TR5+TR63+TR72+TR8+TR83+TRB1+TRC3/ - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34+EL11+EL3+EL30+EL51+ES51+ES52+HR+HR02+HR03+HR04+HR06+HR01+ITF5+LV+LV0+LV00+HU22+RO4+SK01+NO01+NO03+NO04+NO05+UKD3+UKK1+TR2+TR5+TR63+TR72+TR8+TR83+TRB1+TRC3/' - downloaded 83 KB - - get_eurostat_data - class(xml_leafs):xml_nodeset - get_eurostat_data - number of nodes: 46 - get_eurostat_data - number of cores: 2 - get_eurostat_data - footer code option value after retrieval: - get_eurostat_data - restat - nrow:1004; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS - get_eurostat_data - processed restat - nrow:993; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags - get_eurostat_data - restat NULL?:FALSE - id: agr_r_milkpr - filters: ...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34+EL11+EL3+EL30+EL51+ES51+ES52+HR+HR02+HR03+HR04+HR06+HR01+ITF5+LV+LV0+LV00+HU22+RO4+SK01+NO01+NO03+NO04+NO05+UKD3+UKK1+TR2+TR5+TR63+TR72+TR8+TR83+TRB1+TRC3 - date filter: - - test_restatapi.R.............. 45 tests 1 fails - get_eurostat_dsd - API version:2 - - get_eurostat_dsd - Trying to download the DSD from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children' - downloaded 8.8 MB - - get_eurostat_dsd - Warning by the download of the DSD file: - URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children': Timeout of 60 seconds was reached - utils::download.file(dsd_endpoint, temp, dmethod) - - get_eurostat_dsd - class(temp): character - is.na(temp): FALSE - file.size(temp): 9196418 - temp: /tmp/th798/29939837/RtmpCEDVOS/fileb507653b3ea94 - Trying to extract the DSD from: /tmp/th798/29939837/RtmpCEDVOS/fileb507653b3ea94 - get_eurostat_dsd - Error during the extraction of the XML from the downloaded DSD file: - AttValue: ' expected [40] - read_xml.character(temp) - get_eurostat_dsd - The dsd_xml is NULL. Please check in a browser the url below. If it provides valid response you can try again to download the DSD. - https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children - - test_restatapi.R.............. 45 tests 1 fails - test_restatapi.R.............. 45 tests 1 fails - test_restatapi.R.............. 45 tests 1 fails - test_restatapi.R.............. 47 tests 1 fails - test_restatapi.R.............. 49 tests 1 fails - test_restatapi.R.............. 50 tests 1 fails - test_restatapi.R.............. 50 tests 1 fails - test_restatapi.R.............. 51 tests 1 fails - test_restatapi.R.............. 53 tests 1 fails - test_restatapi.R.............. 54 tests 1 fails - test_restatapi.R.............. 58 tests 1 fails - test_restatapi.R.............. 60 tests 1 fails - test_restatapi.R.............. 62 tests 1 fails - test_restatapi.R.............. 63 tests 1 fails - test_restatapi.R.............. 64 tests 1 fails - test_restatapi.R.............. 65 tests 1 fails - test_restatapi.R.............. 66 tests 1 fails - test_restatapi.R.............. 67 tests 1 fails - test_restatapi.R.............. 68 tests 1 fails - test_restatapi.R.............. 69 tests 1 fails - test_restatapi.R.............. 70 tests 1 fails - test_restatapi.R.............. 71 tests 1 fails - test_restatapi.R.............. 72 tests 1 fails - test_restatapi.R.............. 73 tests 1 fails - test_restatapi.R.............. 74 tests 1 fails - test_restatapi.R.............. 75 tests 1 fails - test_restatapi.R.............. 76 tests 1 fails - get_eurostat_raw - API version:2 - get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/tus_00age?format=TSV&compressed=true - get_eurostat_raw - class(raw): data.tabledata.frame - get_eurostat_raw - caching in raw: TRUE - get_eurostat_raw - local filter: FALSE - get_eurostat_raw - called from: get_eurostat_rawtestid7 - get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE - get_eurostat_raw - The raw data was cached in memory ('r_tus_00age-2026.07.06-0' in '.restatapi_env'). - - test_restatapi.R.............. 76 tests 1 fails - get_eurostat_dsd - API version:2 - - get_eurostat_dsd - Trying to download the DSD from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/tus_00age?references=children - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/tus_00age?references=children' - downloaded 3.7 MB - - - get_eurostat_dsd - class(temp): character - is.na(temp): FALSE - file.size(temp): 3901770 - temp: /tmp/th798/29939837/RtmpCEDVOS/fileb5076347d32d2 - Trying to extract the DSD from: /tmp/th798/29939837/RtmpCEDVOS/fileb5076347d32d2 - get_eurostat_dsd - concepts:freq,unit,sex,age,acl00,geo,OBS_FLAG,CONF_STATUS - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="FREQ"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="FREQ"]/s:Code/c:Name[@xml:lang="en"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="UNIT"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="UNIT"]/s:Code/c:Name[@xml:lang="en"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="SEX"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="SEX"]/s:Code/c:Name[@xml:lang="en"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="AGE"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="AGE"]/s:Code/c:Name[@xml:lang="en"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="ACL00"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="ACL00"]/s:Code/c:Name[@xml:lang="en"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="GEO"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="GEO"]/s:Code/c:Name[@xml:lang="en"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="OBS_FLAG"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="OBS_FLAG"]/s:Code/c:Name[@xml:lang="en"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="CONF_STATUS"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="CONF_STATUS"]/s:Code/c:Name[@xml:lang="en"] - get_eurostat_dsd - DSD NULL:FALSE - get_eurostat_dsd - Trying to download the CC from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/tus_00age - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/tus_00age' - Content type 'application/vnd.sdmx.structure+xml;version=2.1' length 3844 bytes - ================================================== - downloaded 3844 bytes - - get_eurostat_dsd - Trying to extract the CC from: /tmp/th798/29939837/RtmpCEDVOS/fileb50766da45225 - character - number of nodes: 7 - number of cores: 2 - - get_eurostat_dsd - The DSD of the tus_00age dataset was cached in memory ('tus_00age.en.dsd' in '.restatapi_env'). - - test_restatapi.R.............. 76 tests 1 fails create_filter_table - filters class: character; size: 3; filters:TIME_SPHungaryT - - test_restatapi.R.............. 77 tests 1 fails - get_eurostat_raw - API version:2 - get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/avia_par_me?format=TSV&compressed=true - get_eurostat_raw - class(raw): data.tabledata.frame - get_eurostat_raw - caching in raw: TRUE - get_eurostat_raw - local filter: FALSE - get_eurostat_raw - called from: get_eurostat_rawtestid6 - get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE - get_eurostat_raw - The raw data was cached in memory ('r_avia_par_me-2026.07.06-0' in '.restatapi_env'). - - test_restatapi.R.............. 77 tests 1 fails create_filter_table - filters class: character; size: 1; filters:2017:2018 - create_filter_table - filters: 2017:2018; is numeric: FALSE; call parents: 6 - create_filter_table - length df: 1 content df: 2017:2018 - create_filter_table - 2017:2018 date filter length: 1, nchar date_filter: 9 - - test_restatapi.R.............. 78 tests 1 fails - get_eurostat_codelist - API version:2 - get_eurostat_codelist - API version:2 - - get_eurostat_codelist - Trying to download the codelist from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/codelist/ESTAT/SEX - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/codelist/ESTAT/SEX' - Content type 'application/vnd.sdmx.structure+xml;version=2.1' length 5483 bytes - ================================================== - downloaded 5483 bytes - - Trying to extract the codelist from: /tmp/th798/29939837/RtmpCEDVOS/fileb507658b9ce3d - get_eurostat_codelist - codelist NULL:TRUE - - test_restatapi.R.............. 78 tests 1 fails - test_restatapi.R.............. 80 tests 1 fails - 4.18.0-553.124.1.el8_10.x86_64 - - test_restatapi.R.............. 80 tests 1 fails - Are we at home:FALSE - - test_restatapi.R.............. 80 tests 1 fails - test_restatapi.R.............. 80 tests 1 fails - get_eurostat_toc - API version:2 - number of cores:2 - get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=fr - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=fr' - downloaded 2.1 MB - - get_eurostat_toc - The TOC was cached in memory ('toc.txt.fr' in '.restatapi_env'). - - test_restatapi.R.............. 80 tests 1 fails - get_eurostat_toc - API version:2 - number of cores:2 - get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=de - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=de' - downloaded 2.0 MB - - get_eurostat_toc - The TOC was cached in memory ('toc.txt.de' in '.restatapi_env'). - - test_restatapi.R.............. 80 tests 1 fails - test_restatapi.R.............. 81 tests 1 fails get_eurostat_data - footer code option value at start: - get_eurostat_data - footer code option value after reset: - get_eurostat_data - id: agr_r_milkpr - get_eurostat_data - select_freq: - - get_eurostat_dsd - API version:2 - - get_eurostat_dsd - Trying to download the DSD from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/agr_r_milkpr?references=children - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/agr_r_milkpr?references=children' - downloaded 2.9 MB - - - get_eurostat_dsd - class(temp): character - is.na(temp): FALSE - file.size(temp): 3008178 - temp: /tmp/th798/29939837/RtmpCEDVOS/fileb507639cbadb0 - Trying to extract the DSD from: /tmp/th798/29939837/RtmpCEDVOS/fileb507639cbadb0 - get_eurostat_dsd - concepts:freq,milkitem,dairyprod,geo,OBS_FLAG,CONF_STATUS - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="FREQ"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="FREQ"]/s:Code/c:Name[@xml:lang="de"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="MILKITEM"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="MILKITEM"]/s:Code/c:Name[@xml:lang="de"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="DAIRYPROD"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="DAIRYPROD"]/s:Code/c:Name[@xml:lang="de"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="GEO"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="GEO"]/s:Code/c:Name[@xml:lang="de"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="OBS_FLAG"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="OBS_FLAG"]/s:Code/c:Name[@xml:lang="de"] - - extract_dsd - API version:2 - extract_dsd - xml_string_clc://s:Codelist[@id="CONF_STATUS"]/s:Code - extract_dsd - xml_string_cln://s:Codelist[@id="CONF_STATUS"]/s:Code/c:Name[@xml:lang="de"] - get_eurostat_dsd - DSD NULL:FALSE - get_eurostat_dsd - Trying to download the CC from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/agr_r_milkpr - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/agr_r_milkpr' - downloaded 15 KB - - get_eurostat_dsd - Trying to extract the CC from: /tmp/th798/29939837/RtmpCEDVOS/fileb50767462c389 - character - number of nodes: 5 - number of cores: 2 - - get_eurostat_dsd - The DSD of the agr_r_milkpr dataset was cached in memory ('agr_r_milkpr.de.dsd' in '.restatapi_env'). - create_filter_table - filters class: character; size: 2; filters:BE$Ungarn - get_eurostat_data - date_filter: 2007-06< - create_filter_table - filters class: character; size: 1; filters:2007-06< - create_filter_table - filters: 2007-06<; is numeric: FALSE; call parents: 7 - create_filter_table - length df: 1 content df: 2007-06< - create_filter_table - 2007-06< date filter length: 1, nchar date_filter: 8 - get_eurostat_data - date_filter: 2007-06< nrow dft: 1 - ...BE+HU-?startPeriod=2007-06-01 - https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...BE+HU/?startPeriod=2007-06-01 - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...BE+HU/?startPeriod=2007-06-01' - Content type 'application/vnd.sdmx.genericdata+xml;version=2.1' length 3959 bytes - ================================================== - downloaded 3959 bytes - - get_eurostat_data - class(xml_leafs):xml_nodeset - get_eurostat_data - number of nodes: 2 - get_eurostat_data - number of cores: 2 - get_eurostat_data - footer code option value after retrieval: - get_eurostat_data - restat - nrow:34; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS - get_eurostat_data - processed restat - nrow:34; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags - get_eurostat_data - restat NULL?:FALSE - id: agr_r_milkpr - filters: ...BE+HU - date filter: ?startPeriod=2007-06-01 - - test_restatapi.R.............. 81 tests 1 fails get_eurostat_data - footer code option value at start: - get_eurostat_data - footer code option value after reset: - get_eurostat_data - id: agr_r_milkpr - get_eurostat_data - select_freq: - - get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. - create_filter_table - filters class: character; size: 2; filters:BE$Hungary - get_eurostat_data - date_filter: 2007-06< - create_filter_table - filters class: character; size: 1; filters:2007-06< - create_filter_table - filters: 2007-06<; is numeric: FALSE; call parents: 7 - create_filter_table - length df: 1 content df: 2007-06< - create_filter_table - 2007-06< date filter length: 1, nchar date_filter: 8 - get_eurostat_data - date_filter: 2007-06< nrow dft: 1 - ...BE+HU-?startPeriod=2007-06-01 - https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...BE+HU/?startPeriod=2007-06-01 - trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...BE+HU/?startPeriod=2007-06-01' - Content type 'application/vnd.sdmx.genericdata+xml;version=2.1' length 3959 bytes - ================================================== - downloaded 3959 bytes - - get_eurostat_data - class(xml_leafs):xml_nodeset - get_eurostat_data - number of nodes: 2 - get_eurostat_data - number of cores: 2 - get_eurostat_data - footer code option value after retrieval: - get_eurostat_data - restat - nrow:34; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS - get_eurostat_data - processed restat - nrow:34; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags - get_eurostat_data - restat NULL?:FALSE - id: agr_r_milkpr - filters: ...BE+HU - date filter: ?startPeriod=2007-06-01 - - test_restatapi.R.............. 81 tests 1 fails - test_restatapi.R.............. 82 tests 1 fails - clean_restatapi_cache - All objects (outside of 'cfg', 'rav', 'cc' and 'dmethod') are removed from '.restatapi_env'. - clean_restatapi_cache - Deleted all .rds files from /tmp/th798/29939837/RtmpCEDVOS - - test_restatapi.R.............. 82 tests 1 fails - - - - - There are skipped tests:27-29,54 - - test_restatapi.R.............. 82 tests 1 fails - - Skipped tests: 27-29,54 - config version: 2 - - test_restatapi.R.............. 82 tests 1 fails - test_restatapi.R.............. 82 tests 1 fails 7.1s - ----- FAILED[data]: test_restatapi.R<169--169> - call| expect_true(is.null(dt8)) - diff| Expected TRUE, got FALSE - Error: 1 out of 82 tests failed - Execution halted * checking PDF version of manual ... OK * DONE -Status: 1 ERROR +Status: OK > library(data.table, lib.loc=R.home("library")) Attaching package: 'data.table' The following object is masked from 'package:base': %notin% > (sig.diff.dt <- myDiff(Rvers)) Key: checking master release 1: tests OK ERROR > > ## If there are significant differences, use git bisect to find when > ## they started. > if(nrow(sig.diff.dt)){ + dt.git <- file.path(task.dir, "data.table.git") + unlink(dt.git, recursive=TRUE, force=TRUE) + system(paste("cd ~/R/data.table && git fetch --tags")) + system(paste("git clone ~/R/data.table", dt.git)) + release.tag <- gsub(".tar.gz|.*_", "", cargs[["release"]]) + rev.parse.cmd <- paste( + "cd", dt.git, "&& git rev-parse master") + master.sha <- system(rev.parse.cmd, intern=TRUE) + merge.base.cmd <- paste( + "cd", dt.git, "&& git merge-base master", release.tag) + merge.base.sha <- system(merge.base.cmd, intern=TRUE) + old.sha <- merge.base.sha + run_R <- file.path(proj.dir, "install_dt_then_check_dep.R") + sig.diff.dt[, first.bad.commit := NA_character_] + sig.diff.dt[, comments := NA_character_] + for(diff.i in 1:nrow(sig.diff.dt)){ + sig.diff.row <- sig.diff.dt[diff.i] + bisect.cmd <- paste( + "cd", dt.git, "&&", + "git bisect start &&", + "git bisect old", old.sha, "&&", + "git bisect new master &&", + "git bisect run", + R.home('bin/Rscript'), + run_R, + shQuote(sig.diff.row$checking), + sig.diff.row$release, + rev.dep.release.tar.gz, + release.tag) + print(bisect.cmd) + bisect.out <- system(bisect.cmd, intern=TRUE) + cat(bisect.out,sep="\n") + if(is.null(attr(bisect.out,"status"))){ + first.bad.sha <- nc::capture_all_str( + bisect.out, + sha="[0-9a-f]+", + " is the first new commit")$sha + parent.cmd <- paste( + "cd ~/R/data.table && git log --pretty=%P -n 1", + first.bad.sha) + parent.sha <- system(parent.cmd, intern=TRUE) + sig.diff.dt[diff.i, first.bad.commit := first.bad.sha] + parent.msg <- paste0("parent=", parent.sha) + this.comment <- if(parent.sha==old.sha){ + paste(parent.msg, "same as git bisect old") + }else if(first.bad.sha==master.sha){ + paste("same as git bisect new=master,", parent.msg) + }else{ + parent.msg + } + sig.diff.dt[diff.i, comments := this.comment] + } + } + ## add CRAN column. + sig.diff.dt[, CRAN := { + flavor <- get_flavor(Rvers) + details <- data.table(flavor=unique(flavor))[, { + base <- "https://www.r-project.org/nosvn/R.check/" + u <- paste0(base, flavor, "/", rev.dep, "-00check.txt") + check.txt <- tempfile() + tryCatch({ + download.file(u, check.txt, quiet=TRUE) + }, error=function(e){ + NULL + }) + check.lines <- if(file.exists(check.txt)){ + readLines(check.txt,encoding="UTF-8") + }else{ + "" + } + repl.lines <- gsub("[\u2018\u2019]", "'", check.lines) + ##gsub("[‘’]", "'", check.lines) does not work with LC_ALL=C. + myStatus(line.vec=repl.lines) + }, by=flavor] + select.dt <- data.table(flavor, checking) + details[select.dt, msg, on=.(flavor, checking)] + }] + dir.create(file.path(job.dir, Rvers)) + diffs.csv <- file.path(job.dir, Rvers, "significant_differences.csv") + data.table::fwrite(sig.diff.dt, diffs.csv) + print(sig.diff.dt) + } Cloning into '/tmp/th798/29939837/R-release/1314/data.table.git'... done. [1] "cd /tmp/th798/29939837/R-release/1314/data.table.git && git bisect start && git bisect old e455714d92b73f716913d3bdb225c90ac67e9d1c && git bisect new master && git bisect run /home/th798/R/R-release/bin/Rscript ~/genomic-ml/data.table-revdeps/install_dt_then_check_dep.R 'tests' ERROR /projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz 1.18.4" Installing package into '/tmp/th798/29939837/R-release/1314/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.18.4' ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-data.table.git/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) Installing package into '/tmp/th798/29939837/R-release/1314/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.18.4' ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' assign.c: In function 'assign': assign.c:552:9: warning: implicit declaration of function 'ATTRIB' [-Wimplicit-function-declaration] 552 | s = ATTRIB(index); | ^~~~~~ assign.c:552:7: warning: assignment to 'SEXP' {aka 'struct SEXPREC *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] 552 | s = ATTRIB(index); | ^ assign.c:561:7: warning: assignment to 'SEXP' {aka 'struct SEXPREC *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] 561 | s = ATTRIB(index); // reset to first element | ^ dogroups.c: In function 'anySpecialStatic': dogroups.c:56:21: warning: implicit declaration of function 'ATTRIB' [-Wimplicit-function-declaration] 56 | for(attribs = ATTRIB(list_el); attribs != R_NilValue; attribs = CDR(attribs)) { | ^~~~~~ dogroups.c:56:19: warning: assignment to 'SEXP' {aka 'struct SEXPREC *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] 56 | for(attribs = ATTRIB(list_el); attribs != R_NilValue; attribs = CDR(attribs)) { | ^ In file included from data.table.h:19, from dogroups.c:1: dogroups.c: In function 'dogroups': /home/th798/R/R-release/include/Rinternals.h:918:33: warning: implicit declaration of function 'Rf_findVar'; did you mean 'Rf_findFun'? [-Wimplicit-function-declaration] 918 | #define findVar Rf_findVar | ^~~~~~~~~~ /home/th798/R/R-release/include/Rinternals.h:357:36: note: in definition of macro 'PROTECT' 357 | #define PROTECT(s) Rf_protect(s) | ^ dogroups.c:86:24: note: in expansion of macro 'findVar' 86 | SEXP SDall = PROTECT(findVar(install(".SDall"), env)); nprotect++; // PROTECT for rchk | ^~~~~~~ /home/th798/R/R-release/include/Rinternals.h:918:33: warning: passing argument 1 of 'Rf_protect' makes pointer from integer without a cast [-Wint-conversion] 918 | #define findVar Rf_findVar /home/th798/R/R-release/include/Rinternals.h:357:36: note: in definition of macro 'PROTECT' 357 | #define PROTECT(s) Rf_protect(s) | ^ dogroups.c:86:24: note: in expansion of macro 'findVar' 86 | SEXP SDall = PROTECT(findVar(install(".SDall"), env)); nprotect++; // PROTECT for rchk | ^~~~~~~ /home/th798/R/R-release/include/Rinternals.h:1117:17: note: expected 'SEXP' {aka 'struct SEXPREC *'} but argument is of type 'int' 1117 | SEXP Rf_protect(SEXP); | ^~~~ /home/th798/R/R-release/include/Rinternals.h:918:33: warning: passing argument 1 of 'Rf_protect' makes pointer from integer without a cast [-Wint-conversion] 918 | #define findVar Rf_findVar /home/th798/R/R-release/include/Rinternals.h:357:36: note: in definition of macro 'PROTECT' 357 | #define PROTECT(s) Rf_protect(s) | ^ dogroups.c:87:21: note: in expansion of macro 'findVar' 87 | SEXP SD = PROTECT(findVar(install(".SD"), env)); nprotect++; | ^~~~~~~ /home/th798/R/R-release/include/Rinternals.h:1117:17: note: expected 'SEXP' {aka 'struct SEXPREC *'} but argument is of type 'int' 1117 | SEXP Rf_protect(SEXP); | ^~~~ /home/th798/R/R-release/include/Rinternals.h:918:33: warning: passing argument 1 of 'Rf_protect' makes pointer from integer without a cast [-Wint-conversion] 918 | #define findVar Rf_findVar /home/th798/R/R-release/include/Rinternals.h:357:36: note: in definition of macro 'PROTECT' 357 | #define PROTECT(s) Rf_protect(s) | ^ dogroups.c:116:17: note: in expansion of macro 'findVar' 116 | N = PROTECT(findVar(install(".N"), env)); nprotect++; // PROTECT for rchk | ^~~~~~~ /home/th798/R/R-release/include/Rinternals.h:1117:17: note: expected 'SEXP' {aka 'struct SEXPREC *'} but argument is of type 'int' 1117 | SEXP Rf_protect(SEXP); | ^~~~ /home/th798/R/R-release/include/Rinternals.h:918:33: warning: passing argument 1 of 'Rf_protect' makes pointer from integer without a cast [-Wint-conversion] 918 | #define findVar Rf_findVar /home/th798/R/R-release/include/Rinternals.h:357:36: note: in definition of macro 'PROTECT' 357 | #define PROTECT(s) Rf_protect(s) | ^ dogroups.c:118:17: note: in expansion of macro 'findVar' 118 | GRP = PROTECT(findVar(install(".GRP"), env)); nprotect++; | ^~~~~~~ /home/th798/R/R-release/include/Rinternals.h:1117:17: note: expected 'SEXP' {aka 'struct SEXPREC *'} but argument is of type 'int' 1117 | SEXP Rf_protect(SEXP); | ^~~~ /home/th798/R/R-release/include/Rinternals.h:918:33: warning: passing argument 1 of 'Rf_protect' makes pointer from integer without a cast [-Wint-conversion] 918 | #define findVar Rf_findVar /home/th798/R/R-release/include/Rinternals.h:357:36: note: in definition of macro 'PROTECT' 357 | #define PROTECT(s) Rf_protect(s) | ^ dogroups.c:120:17: note: in expansion of macro 'findVar' 120 | iSD = PROTECT(findVar(install(".iSD"), env)); nprotect++; // 1-row and possibly no cols (if no i variables are used via JIS) | ^~~~~~~ /home/th798/R/R-release/include/Rinternals.h:1117:17: note: expected 'SEXP' {aka 'struct SEXPREC *'} but argument is of type 'int' 1117 | SEXP Rf_protect(SEXP); | ^~~~ /home/th798/R/R-release/include/Rinternals.h:918:33: warning: passing argument 1 of 'Rf_protect' makes pointer from integer without a cast [-Wint-conversion] 918 | #define findVar Rf_findVar /home/th798/R/R-release/include/Rinternals.h:357:36: note: in definition of macro 'PROTECT' 357 | #define PROTECT(s) Rf_protect(s) | ^ dogroups.c:121:17: note: in expansion of macro 'findVar' 121 | xSD = PROTECT(findVar(install(".xSD"), env)); nprotect++; | ^~~~~~~ /home/th798/R/R-release/include/Rinternals.h:1117:17: note: expected 'SEXP' {aka 'struct SEXPREC *'} but argument is of type 'int' 1117 | SEXP Rf_protect(SEXP); | ^~~~ dogroups.c:134:10: warning: assignment to 'SEXP' {aka 'struct SEXPREC *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] 134 | for (s = ATTRIB(SD); s != R_NilValue && TAG(s)!=R_RowNamesSymbol; s = CDR(s)); // getAttrib0 basically but that's hidden in attrib.c; #loop_counter_not_local_scope_ok | ^ mergelist.c: In function 'mergeIndexAttrib': mergelist.c:25:12: warning: implicit declaration of function 'ATTRIB' [-Wimplicit-function-declaration] 25 | SEXP t = ATTRIB(to), f = ATTRIB(from); | ^~~~~~ mergelist.c:25:12: warning: initialization of 'SEXP' {aka 'struct SEXPREC *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] mergelist.c:25:28: warning: initialization of 'SEXP' {aka 'struct SEXPREC *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] 25 | SEXP t = ATTRIB(to), f = ATTRIB(from); | ^~~~~~ mergelist.c:27:5: warning: implicit declaration of function 'SET_ATTRIB'; did you mean 'ANY_ATTRIB'? [-Wimplicit-function-declaration] 27 | SET_ATTRIB(to, shallow_duplicate(f)); | ^~~~~~~~~~ | ANY_ATTRIB mergelist.c:29:12: warning: assignment to 'SEXP' {aka 'struct SEXPREC *'} from 'int' makes pointer from integer without a cast [-Wint-conversion] 29 | for (t = ATTRIB(to); CDR(t) != R_NilValue; t = CDR(t)); // traverse to end of attributes list of to | ^ mergelist.c: In function 'cbindlist': mergelist.c:87:14: warning: passing argument 1 of 'Rf_isNull' makes pointer from integer without a cast [-Wint-conversion] 87 | if (isNull(ATTRIB(index))) | ^~~~~~~~~~~~~ | | | int In file included from data.table.h:19, from mergelist.c:1: /home/th798/R/R-release/include/Rinternals.h:207:27: note: expected 'SEXP' {aka 'struct SEXPREC *'} but argument is of type 'int' 207 | Rboolean (Rf_isNull)(SEXP s); | ~~~~~^ nafill.c: In function 'nafillR': nafill.c:221:19: warning: implicit declaration of function 'ATTRIB' [-Wimplicit-function-declaration] 221 | if (!isNull(ATTRIB(VECTOR_ELT(x, i)))) | ^~~~~~ nafill.c:221:19: warning: passing argument 1 of 'Rf_isNull' makes pointer from integer without a cast [-Wint-conversion] 221 | if (!isNull(ATTRIB(VECTOR_ELT(x, i)))) | ^~~~~~~~~~~~~~~~~~~~~~~~ | | | int In file included from data.table.h:19, from nafill.c:1: /home/th798/R/R-release/include/Rinternals.h:207:27: note: expected 'SEXP' {aka 'struct SEXPREC *'} but argument is of type 'int' 207 | Rboolean (Rf_isNull)(SEXP s); | ~~~~~^ utils.c: In function 'frev': utils.c:633:5: warning: implicit declaration of function 'SET_ATTRIB'; did you mean 'ANY_ATTRIB'? [-Wimplicit-function-declaration] 633 | SET_ATTRIB(x, R_NilValue); | ^~~~~~~~~~ | ANY_ATTRIB installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-data.table.git/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) Installing package into '/tmp/th798/29939837/R-release/1314/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.18.4' ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' nafill.c: In function 'nafillR': nafill.c:221:19: warning: implicit declaration of function 'ATTRIB' [-Wimplicit-function-declaration] 221 | if (!isNull(ATTRIB(VECTOR_ELT(x, i)))) | ^~~~~~ nafill.c:221:19: warning: passing argument 1 of 'Rf_isNull' makes pointer from integer without a cast [-Wint-conversion] 221 | if (!isNull(ATTRIB(VECTOR_ELT(x, i)))) | ^~~~~~~~~~~~~~~~~~~~~~~~ | | | int In file included from data.table.h:19, from nafill.c:1: /home/th798/R/R-release/include/Rinternals.h:207:27: note: expected 'SEXP' {aka 'struct SEXPREC *'} but argument is of type 'int' 207 | Rboolean (Rf_isNull)(SEXP s); | ~~~~~^ installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-data.table.git/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) Installing package into '/tmp/th798/29939837/R-release/1314/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.18.4' ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-data.table.git/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) See '/tmp/th798/29939837/R-release/1314/data.table.git/restatapi.Rcheck/00check.log' for details. Installing package into '/tmp/th798/29939837/R-release/1314/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.18.4' ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-data.table.git/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) Installing package into '/tmp/th798/29939837/R-release/1314/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.18.4' ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-data.table.git/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) See '/tmp/th798/29939837/R-release/1314/data.table.git/restatapi.Rcheck/00check.log' for details. Installing package into '/tmp/th798/29939837/R-release/1314/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.18.4' ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' installing to /tmp/th798/29939837/R-release/1314/library/00LOCK-data.table.git/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) status: waiting for both good and bad commits status: waiting for bad commit, 1 good commit known Bisecting: 67 revisions left to test after this (roughly 6 steps) [aea17854498508866f3e6c69bec7537fdb1bbf69] `tests/froll.R`: disable `mcparallel` under Valgrind (#7621) running '/home/th798/R/R-release/bin/Rscript' '/home/th798/genomic-ml/data.table-revdeps/install_dt_then_check_dep.R' 'tests' 'ERROR' '/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz' '1.18.4' checking "tests" expected "ERROR" rev_dep_tar_gz "/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz" dt_release_version "1.18.4" zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c assign.c -o assign.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c between.c -o between.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bmerge.c -o bmerge.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c chmatch.c -o chmatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cj.c -o cj.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c coalesce.c -o coalesce.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dogroups.c -o dogroups.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmean.c -o fastmean.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fcast.c -o fcast.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fifelse.c -o fifelse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fmelt.c -o fmelt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c forder.c -o forder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frank.c -o frank.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fread.c -o fread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c freadR.c -o freadR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c froll.c -o froll.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollR.c -o frollR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frolladaptive.c -o frolladaptive.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollapply.c -o frollapply.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fsort.c -o fsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwrite.c -o fwrite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwriteR.c -o fwriteR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c gsumm.c -o gsumm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c hash.c -o hash.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c idatetime.c -o idatetime.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ijoin.c -o ijoin.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c inrange.c -o inrange.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c mergelist.c -o mergelist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nafill.c -o nafill.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c negate.c -o negate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nqrecreateindices.c -o nqrecreateindices.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c openmp-utils.c -o openmp-utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c programming.c -o programming.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c quickselect.c -o quickselect.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rbindlist.c -o rbindlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c reorder.c -o reorder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shellsort.c -o shellsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shift.c -o shift.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c snprintf.c -o snprintf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c subset.c -o subset.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c transpose.c -o transpose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c types.c -o types.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uniqlist.c -o uniqlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.c -o utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vecseq.c -o vecseq.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wrappers.c -o wrappers.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o hash.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fvisibility=hidden -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fvisibility=hidden -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi * using log directory '/tmp/th798/29939837/R-release/1314/data.table.git/restatapi.Rcheck' * using R version 4.6.1 (2026-06-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * current time: 2026-07-06 18:39:50 UTC * checking for file 'restatapi/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'restatapi' version '0.25.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'restatapi' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'tinytest.R' OK * checking PDF version of manual ... OK * DONE Status: OK checking msg 1: for file 'restatapi/DESCRIPTION' OK 2: package namespace information OK 3: package dependencies OK 4: if this is a source package OK 5: if there is a namespace OK 6: for executable files OK 7: for hidden files and directories OK 8: for portable file names OK 9: for sufficient/correct file permissions OK 10: whether package 'restatapi' can be installed OK 11: package directory OK 12: DESCRIPTION meta-information OK 13: top-level files OK 14: for left-over files OK 15: index information OK 16: package subdirectories OK 17: code files for non-ASCII characters OK 18: R files for syntax errors OK 19: whether the package can be loaded OK 20: whether the package can be loaded with stated dependencies OK 21: whether the package can be unloaded cleanly OK 22: whether the namespace can be loaded with stated dependencies OK 23: whether the namespace can be unloaded cleanly OK 24: loading without being on the library search path OK 25: whether startup messages can be suppressed OK 26: dependencies in R code OK 27: S3 generic/method consistency OK 28: replacement functions OK 29: foreign function calls OK 30: R code for possible problems OK 31: Rd files OK 32: Rd metadata OK 33: Rd cross-references OK 34: for missing documentation entries OK 35: for code/documentation mismatches OK 36: Rd \\usage sections OK 37: Rd contents OK 38: for unstated dependencies in examples OK 39: examples OK 40: for unstated dependencies in 'tests' OK 41: tests OK 42: PDF version of manual OK checking msg checking msg 1: tests OK Bisecting: 33 revisions left to test after this (roughly 5 steps) [ce971488a8e08b1d6c6712a7d2d9fc6ee5c3605d] add codetools for vignettes (#7542) running '/home/th798/R/R-release/bin/Rscript' '/home/th798/genomic-ml/data.table-revdeps/install_dt_then_check_dep.R' 'tests' 'ERROR' '/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz' '1.18.4' checking "tests" expected "ERROR" rev_dep_tar_gz "/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz" dt_release_version "1.18.4" zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c assign.c -o assign.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c between.c -o between.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dogroups.c -o dogroups.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmean.c -o fastmean.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fifelse.c -o fifelse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fmelt.c -o fmelt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fread.c -o fread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c froll.c -o froll.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollR.c -o frollR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fsort.c -o fsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c gsumm.c -o gsumm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ijoin.c -o ijoin.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c mergelist.c -o mergelist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nafill.c -o nafill.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c openmp-utils.c -o openmp-utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rbindlist.c -o rbindlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c transpose.c -o transpose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uniqlist.c -o uniqlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.c -o utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wrappers.c -o wrappers.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o hash.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi * using log directory '/tmp/th798/29939837/R-release/1314/data.table.git/restatapi.Rcheck' * using R version 4.6.1 (2026-06-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * current time: 2026-07-06 18:46:38 UTC * checking for file 'restatapi/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'restatapi' version '0.25.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'restatapi' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'tinytest.R' OK * checking PDF version of manual ... OK * DONE Status: OK checking msg 1: for file 'restatapi/DESCRIPTION' OK 2: package namespace information OK 3: package dependencies OK 4: if this is a source package OK 5: if there is a namespace OK 6: for executable files OK 7: for hidden files and directories OK 8: for portable file names OK 9: for sufficient/correct file permissions OK 10: whether package 'restatapi' can be installed OK 11: package directory OK 12: DESCRIPTION meta-information OK 13: top-level files OK 14: for left-over files OK 15: index information OK 16: package subdirectories OK 17: code files for non-ASCII characters OK 18: R files for syntax errors OK 19: whether the package can be loaded OK 20: whether the package can be loaded with stated dependencies OK 21: whether the package can be unloaded cleanly OK 22: whether the namespace can be loaded with stated dependencies OK 23: whether the namespace can be unloaded cleanly OK 24: loading without being on the library search path OK 25: whether startup messages can be suppressed OK 26: dependencies in R code OK 27: S3 generic/method consistency OK 28: replacement functions OK 29: foreign function calls OK 30: R code for possible problems OK 31: Rd files OK 32: Rd metadata OK 33: Rd cross-references OK 34: for missing documentation entries OK 35: for code/documentation mismatches OK 36: Rd \\usage sections OK 37: Rd contents OK 38: for unstated dependencies in examples OK 39: examples OK 40: for unstated dependencies in 'tests' OK 41: tests OK 42: PDF version of manual OK checking msg checking msg 1: tests OK Bisecting: 16 revisions left to test after this (roughly 4 steps) [45f8a12883878e9f31c4d0f980735d9e362ee7f5] fully deprecate hasNA (#7529) running '/home/th798/R/R-release/bin/Rscript' '/home/th798/genomic-ml/data.table-revdeps/install_dt_then_check_dep.R' 'tests' 'ERROR' '/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz' '1.18.4' checking "tests" expected "ERROR" rev_dep_tar_gz "/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz" dt_release_version "1.18.4" zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cj.c -o cj.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nafill.c -o nafill.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o hash.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi * using log directory '/tmp/th798/29939837/R-release/1314/data.table.git/restatapi.Rcheck' * using R version 4.6.1 (2026-06-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * current time: 2026-07-06 18:57:00 UTC * checking for file 'restatapi/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'restatapi' version '0.25.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'restatapi' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'tinytest.R' OK * checking PDF version of manual ... OK * DONE Status: OK checking msg 1: for file 'restatapi/DESCRIPTION' OK 2: package namespace information OK 3: package dependencies OK 4: if this is a source package OK 5: if there is a namespace OK 6: for executable files OK 7: for hidden files and directories OK 8: for portable file names OK 9: for sufficient/correct file permissions OK 10: whether package 'restatapi' can be installed OK 11: package directory OK 12: DESCRIPTION meta-information OK 13: top-level files OK 14: for left-over files OK 15: index information OK 16: package subdirectories OK 17: code files for non-ASCII characters OK 18: R files for syntax errors OK 19: whether the package can be loaded OK 20: whether the package can be loaded with stated dependencies OK 21: whether the package can be unloaded cleanly OK 22: whether the namespace can be loaded with stated dependencies OK 23: whether the namespace can be unloaded cleanly OK 24: loading without being on the library search path OK 25: whether startup messages can be suppressed OK 26: dependencies in R code OK 27: S3 generic/method consistency OK 28: replacement functions OK 29: foreign function calls OK 30: R code for possible problems OK 31: Rd files OK 32: Rd metadata OK 33: Rd cross-references OK 34: for missing documentation entries OK 35: for code/documentation mismatches OK 36: Rd \\usage sections OK 37: Rd contents OK 38: for unstated dependencies in examples OK 39: examples OK 40: for unstated dependencies in 'tests' OK 41: tests OK 42: PDF version of manual OK checking msg checking msg 1: tests OK Bisecting: 8 revisions left to test after this (roughly 3 steps) [6a70af68416e8310f2193b4a644a57e6c8253592] Enable dependabot updates (#7521) running '/home/th798/R/R-release/bin/Rscript' '/home/th798/genomic-ml/data.table-revdeps/install_dt_then_check_dep.R' 'tests' 'ERROR' '/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz' '1.18.4' checking "tests" expected "ERROR" rev_dep_tar_gz "/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz" dt_release_version "1.18.4" zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fcast.c -o fcast.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c subset.c -o subset.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o hash.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi * using log directory '/tmp/th798/29939837/R-release/1314/data.table.git/restatapi.Rcheck' * using R version 4.6.1 (2026-06-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * current time: 2026-07-06 19:02:54 UTC * checking for file 'restatapi/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'restatapi' version '0.25.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'restatapi' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'tinytest.R' ERROR Running the tests in 'tests/tinytest.R' failed. Complete output: > if ( requireNamespace("tinytest", quietly=TRUE) ){ + home <- length(unclass(packageVersion("restatapi"))[[1]]) == 4 + tinytest::test_package("restatapi", at_home = home) + } restatapi: - version 0.25.0 - config file with the API version 2 loaded from GitHub (the 'current' API version number is 2). - 4 from the 28 cores are used for parallel computing, can be changed with 'options(restatapi_cores=...)' - 'auto' method will be used for file download, can be changed with 'options(restatapi_dmethod=...)' - the Table of contents (TOC) was not pre-loaded into the deafult cache ('.restatapi_env'). test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests clean_restatapi_cache - All objects (outside of 'cfg', 'rav', 'cc' and 'dmethod') are removed from '.restatapi_env'. test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/xml get_eurostat_toc - class(xml_leafs): xml_nodeset get_eurostat_toc - number of nodes: 10408 get_eurostat_toc - number of cores: 2 get_eurostat_toc - dim toc: 10408,22 get_eurostat_toc - colnames toc: title.en,title.fr,title.de,code,lastUpdate,lastModified,dataStart,dataEnd,values,source.en,source.fr,source.de,unit.en,unit.fr,unit.de,shortDescription.en,shortDescription.fr,shortDescription.de,metadata.html,metadata.sdmx,downloadLink.tsv,type get_eurostat_toc - cols to keep: title.en,code,type,lastUpdate,lastModified,dataStart,dataEnd,values,unit.en,source.en,shortDescription.en,metadata.html,metadata.sdmx,downloadLink.tsv get_eurostat_toc - The TOC was cached in memory ('toc.xml.en' in '.restatapi_env'). test_restatapi.R.............. 0 tests get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=en trying URL 'https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=en' downloaded 1.9 MB get_eurostat_toc - The TOC was cached in memory ('toc.txt.en' in '.restatapi_env'). test_restatapi.R.............. 0 tests get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. test_restatapi.R.............. 0 tests test_restatapi.R.............. 1 tests OK test_restatapi.R.............. 7 tests OK get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. test_restatapi.R.............. 7 tests OK get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. test_restatapi.R.............. 7 tests OK get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/xml get_eurostat_toc - Warning by the download of the xml version of the TOC file: URL 'https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/xml': Timeout of 60 seconds was reached readBin(3, "raw", 65536) get_eurostat_toc - The TOC is empty. Please check the download link form the line above in a web browser. test_restatapi.R.............. 7 tests OK test_restatapi.R.............. 8 tests OK test_restatapi.R.............. 8 tests OK trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/text?references=children' test_restatapi.R.............. 9 tests OK get_eurostat_dsd - API version:2 get_eurostat_dsd - Trying to download the DSD from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/NAMA_10_GDP?references=children trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/NAMA_10_GDP?references=children' downloaded 3.4 MB get_eurostat_dsd - class(temp): character - is.na(temp): FALSE - file.size(temp): 3585472 - temp: /tmp/th798/29939837/RtmpJbKPrV/filee4af870b7e9bf Trying to extract the DSD from: /tmp/th798/29939837/RtmpJbKPrV/filee4af870b7e9bf get_eurostat_dsd - concepts:freq,unit,na_item,geo,OBS_FLAG,CONF_STATUS extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="FREQ"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="FREQ"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="UNIT"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="UNIT"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="NA_ITEM"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="NA_ITEM"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="GEO"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="GEO"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="OBS_FLAG"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="OBS_FLAG"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="CONF_STATUS"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="CONF_STATUS"]/s:Code/c:Name[@xml:lang="en"] get_eurostat_dsd - DSD NULL:FALSE get_eurostat_dsd - Trying to download the CC from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/NAMA_10_GDP trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/NAMA_10_GDP' Content type 'application/vnd.sdmx.structure+xml;version=2.1' length 5597 bytes ================================================== downloaded 5597 bytes get_eurostat_dsd - Trying to extract the CC from: /tmp/th798/29939837/RtmpJbKPrV/filee4af857c4468 character number of nodes: 5 number of cores: 2 get_eurostat_dsd - The DSD of the NAMA_10_GDP dataset was cached in memory ('NAMA_10_GDP.en.dsd' in '.restatapi_env'). test_restatapi.R.............. 9 tests OK test_restatapi.R.............. 12 tests OK test_restatapi.R.............. 12 tests OK test_restatapi.R.............. 12 tests OK test_restatapi.R.............. 16 tests OK get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: htec_cis3 get_eurostat_data - select_freq: get_eurostat_data - Trying to get from cache: b_htec_cis3-2026.07.06-1-1 get_eurostat_bulk - API version:2 get_eurostat_bulk - class of id, cache, update_cache, cache_dir, compress_file, stringsAsFactors, keep_flags, check_toc, melt, verbose: character - logical -logical - NULL - logical - logical - logical - logical - logical - logical get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/htec_cis3?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: FALSE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: restatapi::get_eurostat_rawidtxtcacheupdate_cachecache_dircompress_filestringsAsFactorskeep_flagscheck_tocTRUEverbose get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_data - The data was downloaded with bulk download. get_eurostat_data - bulk restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags get_eurostat_data - cflags:TRUE get_eurostat_data - restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags get_eurostat_data - processed restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags get_eurostat_data - The data was cached in memory ('b_htec_cis3-2026.07.06-1-1' in '.restatapi_env'). get_eurostat_data - restat NULL?:FALSE id: htec_cis3 filters: date filter: test_restatapi.R.............. 16 tests OK test_restatapi.R.............. 16 tests OK get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: htec_cis3 get_eurostat_data - select_freq: get_eurostat_data - Trying to get from cache: b_htec_cis3-2026.07.06-0-0 get_eurostat_cache - The 'b_htec_cis3-2026.07.06-0-0' was loaded from 'b_htec_cis3-2026.07.06-1-1' in '.restatapi_env'. get_eurostat_data - The data was loaded from cache. get_eurostat_data - cached restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags get_eurostat_data - restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags get_eurostat_data - processed restat - nrow:1006; ncol:6; colnames:indic_in/nace_r1/unit/geo/time/values get_eurostat_data - The data was cached in memory ('b_htec_cis3-2026.07.06-0-0' in '.restatapi_env'). get_eurostat_data - restat NULL?:FALSE id: htec_cis3 filters: date filter: test_restatapi.R.............. 16 tests OK test_restatapi.R.............. 16 tests OK test_restatapi.R.............. 20 tests OK get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/rail_tf_ns20_mk?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid3FALSE get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_rail_tf_ns20_mk-2026.07.06-0' in '.restatapi_env'). get_eurostat_raw - API version:2 get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. get_eurostat_raw - raws of TOC: 7661 get_eurostat_raw - txt bulk url from TOC:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/RAIL_TF_NS20_MK?format=tsv&compressed=true get_eurostat_raw - txt bulk url from cfg:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/rail_tf_ns20_mk?format=TSV&compressed=true get_eurostat_raw - data rowcount in TOC: 12 get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid3TRUEFALSE get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_rail_tf_ns20_mk-2023.02.02-0' in '.restatapi_env'). get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: rail_tf_ns20_mk get_eurostat_data - select_freq: get_eurostat_data - Trying to get from cache: b_rail_tf_ns20_mk-2026.07.06-0-0 get_eurostat_cache - The 'b_rail_tf_ns20_mk-2026.07.06-0-0' was loaded from 'r_rail_tf_ns20_mk-2026.07.06-0' in '.restatapi_env'. get_eurostat_data - The data was loaded from cache. get_eurostat_data - cached restat - nrow:12; ncol:6; colnames:freq/net_seg20/train/unit/time/values get_eurostat_data - restat - nrow:12; ncol:6; colnames:freq/net_seg20/train/unit/time/values get_eurostat_data - processed restat - nrow:12; ncol:5; colnames:net_seg20/train/unit/time/values get_eurostat_data - The data was cached in memory ('b_rail_tf_ns20_mk-2026.07.06-0-0' in '.restatapi_env'). get_eurostat_data - restat NULL?:FALSE id: rail_tf_ns20_mk filters: date filter: test_restatapi.R.............. 25 tests OK get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr?format=sdmx_2.1_structured&compressed=true get_eurostat_raw - file format: gz get_compressed_sdmx - url:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr?format=sdmx_2.1_structured&compressed=true get_compressed_sdmx - format:gz get_compressed_sdmx - xml NULL:FALSE get_eurostat_raw - class(xml_leafs): xml_nodeset get_eurostat_raw - number of nodes: 583 get_eurostat_raw - number of cores: 2 get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid4xmlTRUETRUE get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_agr_r_milkpr-2026.07.06-1' in '.restatapi_env'). test_restatapi.R.............. 25 tests OK get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_data - Trying to get from cache: b_agr_r_milkpr-2026.07.06-1-0 get_eurostat_cache - The 'b_agr_r_milkpr-2026.07.06-1-0' was loaded from 'r_agr_r_milkpr-2026.07.06-1' in '.restatapi_env'. get_eurostat_data - The data was loaded from cache. get_eurostat_data - cached restat - nrow:11870; ncol:7; colnames:geo/milkitem/freq/dairyprod/TIME_PERIOD/OBS_VALUE/OBS_FLAG get_eurostat_data - restat - nrow:11870; ncol:7; colnames:geo/milkitem/freq/dairyprod/TIME_PERIOD/OBS_VALUE/OBS_FLAG get_eurostat_data - processed restat - nrow:11599; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - The data was cached in memory ('b_agr_r_milkpr-2026.07.06-1-0' in '.restatapi_env'). get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: date filter: test_restatapi.R.............. 25 tests OK get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_data - date_filter: 2008 create_filter_table - filters class: numeric; size: 1; filters:2008 create_filter_table - filters: 2008; is numeric: TRUE; call parents: 7 create_filter_table - length df: 1 content df: 2008 create_filter_table - 2008 date filter length: 1, nchar date_filter: 4 get_eurostat_data - date_filter: 2008 nrow dft: 1 -?startPeriod=2008-01-01&endPeriod=2008-12-31 https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2008-01-01&endPeriod=2008-12-31 trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2008-01-01&endPeriod=2008-12-31' downloaded 106 KB get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 410 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:410; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:390; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: date filter: ?startPeriod=2008-01-01&endPeriod=2008-12-31 test_restatapi.R.............. 25 tests OK test_restatapi.R.............. 26 tests OK test_restatapi.R.............. 27 tests OK get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/irt_h_eurcoe_d?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid5TRUE get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_irt_h_eurcoe_d-2026.07.06-0' in '.restatapi_env'). test_restatapi.R.............. 27 tests OK get_eurostat_bulk - API version:2 get_eurostat_bulk - class of id, cache, update_cache, cache_dir, compress_file, stringsAsFactors, keep_flags, check_toc, melt, verbose: character - logical -logical - NULL - logical - logical - logical - logical - logical - logical get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/irt_h_eurcoe_d?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: FALSE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: restatapi::get_eurostat_rawidtxtcacheupdate_cachecache_dircompress_filestringsAsFactorskeep_flagscheck_tocTRUEverbose get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_bulk - The bulk data was cached in memory ('b_irt_h_eurcoe_d-2026.07.06-1-0' in '.restatapi_env'). test_restatapi.R.............. 27 tests OK get_eurostat_raw - API version:2 get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. get_eurostat_raw - raws of TOC: 7661 get_eurostat_raw - txt bulk url from TOC:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/IRT_H_EURCOE_D?format=tsv&compressed=true get_eurostat_raw - txt bulk url from cfg:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/irt_h_eurcoe_d?format=sdmx_2.1_structured&compressed=true get_eurostat_raw - data rowcount in TOC: 29862 get_eurostat_raw - file format: gz get_compressed_sdmx - url:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/irt_h_eurcoe_d?format=sdmx_2.1_structured&compressed=true get_compressed_sdmx - format:gz get_compressed_sdmx - xml NULL:FALSE get_eurostat_raw - class(xml_leafs): xml_nodeset get_eurostat_raw - number of nodes: 18 get_eurostat_raw - number of cores: 2 get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid5xmlTRUETRUETRUETRUEFALSE get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_irt_h_eurcoe_d-2009.03.27-1' in '.restatapi_env'). test_restatapi.R.............. 27 tests OK get_eurostat_bulk - API version:2 get_eurostat_cache - The 'b_irt_h_eurcoe_d-2026.07.06-1-0' was loaded from 'b_irt_h_eurcoe_d-2026.07.06-1-0' in '.restatapi_env'. get_eurostat_bulk - The bulk data was cached previously in memory ('b_irt_h_eurcoe_d-2026.07.06-1-0' in '.restatapi_env'). It remained unchanged. test_restatapi.R.............. 27 tests OK test_restatapi.R.............. 28 tests OK test_restatapi.R.............. 30 tests OK trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/agr_r_milkpr?references=children' downloaded 2.9 MB trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/agr_r_milkpr' downloaded 15 KB test_restatapi.R.............. 31 tests OK test_restatapi.R.............. 32 tests OK test_restatapi.R.............. 33 tests OK test_restatapi.R.............. 34 tests OK test_restatapi.R.............. 37 tests OK trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children' downloaded 4.7 MB trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/avia_par_me/?startPeriod=2017-03-01&endPeriod=2017-03-31' downloaded 58 KB trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children' downloaded 6.4 MB test_restatapi.R.............. 38 tests OK test_restatapi.R.............. 39 tests 1 fails test_restatapi.R.............. 39 tests 1 fails test_restatapi.R.............. 40 tests 1 fails get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. test_restatapi.R.............. 40 tests 1 fails get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. create_filter_table - filters class: character; size: 1; filters:AT ...AT- https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT/ trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT/' Content type 'application/vnd.sdmx.genericdata+xml;version=2.1' length 3279 bytes ================================================== downloaded 3279 bytes get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 1 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:29; ncol:6; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue get_eurostat_data - processed restat - nrow:29; ncol:5; colnames:geo/milkitem/dairyprod/time/values get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: ...AT date filter: get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. create_filter_table - filters class: character; size: 1; filters:AT ...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34- https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34/ trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34/' downloaded 31 KB get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 13 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:377; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:377; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: ...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34 date filter: get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_data - date_filter: 2016 create_filter_table - filters class: numeric; size: 1; filters:2016 create_filter_table - filters: 2016; is numeric: TRUE; call parents: 8 create_filter_table - length df: 1 content df: 2016 create_filter_table - 2016 date filter length: 1, nchar date_filter: 4 get_eurostat_data - date_filter: 2016 nrow dft: 1 -?startPeriod=2016-01-01&endPeriod=2016-12-31 https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2016-01-01&endPeriod=2016-12-31 trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2016-01-01&endPeriod=2016-12-31' downloaded 137 KB get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 508 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:508; ncol:6; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue get_eurostat_data - processed restat - nrow:494; ncol:5; colnames:geo/milkitem/dairyprod/time/values get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: date filter: ?startPeriod=2016-01-01&endPeriod=2016-12-31 get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_data - date_filter: 2016 create_filter_table - filters class: character; size: 1; filters:2016 create_filter_table - filters: 2016; is numeric: FALSE; call parents: 8 create_filter_table - length df: 1 content df: 2016 create_filter_table - 2016 date filter length: 1, nchar date_filter: 4 get_eurostat_data - date_filter: 2016 nrow dft: 1 -?startPeriod=2016-01-01&endPeriod=2016-12-31 https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2016-01-01&endPeriod=2016-12-31 trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2016-01-01&endPeriod=2016-12-31' downloaded 137 KB get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 508 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:508; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:494; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: date filter: ?startPeriod=2016-01-01&endPeriod=2016-12-31 get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. create_filter_table - filters class: character; size: 1; filters:AT ...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34+EL11+EL3+EL30+EL51+ES51+ES52+HR+HR02+HR03+HR04+HR06+HR01+ITF5+LV+LV0+LV00+HU22+RO4+SK01+NO01+NO03+NO04+NO05+UKD3+UKK1+TR2+TR5+TR63+TR72+TR8+TR83+TRB1+TRC3- https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34+EL11+EL3+EL30+EL51+ES51+ES52+HR+HR02+HR03+HR04+HR06+HR01+ITF5+LV+LV0+LV00+HU22+RO4+SK01+NO01+NO03+NO04+NO05+UKD3+UKK1+TR2+TR5+TR63+TR72+TR8+TR83+TRB1+TRC3/ trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34+EL11+EL3+EL30+EL51+ES51+ES52+HR+HR02+HR03+HR04+HR06+HR01+ITF5+LV+LV0+LV00+HU22+RO4+SK01+NO01+NO03+NO04+NO05+UKD3+UKK1+TR2+TR5+TR63+TR72+TR8+TR83+TRB1+TRC3/' downloaded 83 KB get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 46 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:1004; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:993; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: ...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34+EL11+EL3+EL30+EL51+ES51+ES52+HR+HR02+HR03+HR04+HR06+HR01+ITF5+LV+LV0+LV00+HU22+RO4+SK01+NO01+NO03+NO04+NO05+UKD3+UKK1+TR2+TR5+TR63+TR72+TR8+TR83+TRB1+TRC3 date filter: test_restatapi.R.............. 44 tests 1 fails get_eurostat_dsd - API version:2 get_eurostat_dsd - Trying to download the DSD from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children' downloaded 18.2 MB get_eurostat_dsd - class(temp): character - is.na(temp): FALSE - file.size(temp): 19069969 - temp: /tmp/th798/29939837/RtmpJbKPrV/filee4af83c46ac8b Trying to extract the DSD from: /tmp/th798/29939837/RtmpJbKPrV/filee4af83c46ac8b get_eurostat_dsd - concepts:freq,unit,tra_meas,airp_pr,OBS_FLAG,CONF_STATUS extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="FREQ"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="FREQ"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="UNIT"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="UNIT"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="TRA_MEAS"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="TRA_MEAS"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="AIRP_PR"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="AIRP_PR"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="OBS_FLAG"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="OBS_FLAG"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="CONF_STATUS"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="CONF_STATUS"]/s:Code/c:Name[@xml:lang="de"] get_eurostat_dsd - DSD NULL:FALSE get_eurostat_dsd - Trying to download the CC from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/avia_par_me trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/avia_par_me' Content type 'application/vnd.sdmx.structure+xml;version=2.1' length 7996 bytes ================================================== downloaded 7996 bytes get_eurostat_dsd - Trying to extract the CC from: /tmp/th798/29939837/RtmpJbKPrV/filee4af818f23ab3 character number of nodes: 5 number of cores: 2 get_eurostat_dsd - The DSD of the avia_par_me dataset was cached in memory ('avia_par_me.de.dsd' in '.restatapi_env'). test_restatapi.R.............. 44 tests 1 fails test_restatapi.R.............. 44 tests 1 fails test_restatapi.R.............. 44 tests 1 fails test_restatapi.R.............. 46 tests 1 fails test_restatapi.R.............. 48 tests 1 fails test_restatapi.R.............. 49 tests 1 fails test_restatapi.R.............. 50 tests 1 fails test_restatapi.R.............. 51 tests 1 fails test_restatapi.R.............. 53 tests 1 fails test_restatapi.R.............. 54 tests 1 fails test_restatapi.R.............. 58 tests 1 fails test_restatapi.R.............. 60 tests 1 fails test_restatapi.R.............. 62 tests 1 fails test_restatapi.R.............. 63 tests 1 fails test_restatapi.R.............. 64 tests 1 fails test_restatapi.R.............. 65 tests 1 fails test_restatapi.R.............. 66 tests 1 fails test_restatapi.R.............. 67 tests 1 fails test_restatapi.R.............. 68 tests 1 fails test_restatapi.R.............. 69 tests 1 fails test_restatapi.R.............. 70 tests 1 fails test_restatapi.R.............. 71 tests 1 fails test_restatapi.R.............. 72 tests 1 fails test_restatapi.R.............. 73 tests 1 fails test_restatapi.R.............. 74 tests 1 fails test_restatapi.R.............. 75 tests 1 fails test_restatapi.R.............. 76 tests 1 fails get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/tus_00age?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid7 get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_tus_00age-2026.07.06-0' in '.restatapi_env'). test_restatapi.R.............. 76 tests 1 fails get_eurostat_dsd - API version:2 get_eurostat_dsd - Trying to download the DSD from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/tus_00age?references=children trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/tus_00age?references=children' downloaded 3.7 MB get_eurostat_dsd - class(temp): character - is.na(temp): FALSE - file.size(temp): 3901770 - temp: /tmp/th798/29939837/RtmpJbKPrV/filee4af812d4fd5 Trying to extract the DSD from: /tmp/th798/29939837/RtmpJbKPrV/filee4af812d4fd5 get_eurostat_dsd - concepts:freq,unit,sex,age,acl00,geo,OBS_FLAG,CONF_STATUS extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="FREQ"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="FREQ"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="UNIT"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="UNIT"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="SEX"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="SEX"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="AGE"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="AGE"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="ACL00"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="ACL00"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="GEO"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="GEO"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="OBS_FLAG"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="OBS_FLAG"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="CONF_STATUS"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="CONF_STATUS"]/s:Code/c:Name[@xml:lang="en"] get_eurostat_dsd - DSD NULL:FALSE get_eurostat_dsd - Trying to download the CC from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/tus_00age trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/tus_00age' Content type 'application/vnd.sdmx.structure+xml;version=2.1' length 3844 bytes ================================================== downloaded 3844 bytes get_eurostat_dsd - Trying to extract the CC from: /tmp/th798/29939837/RtmpJbKPrV/filee4af87629503 character number of nodes: 7 number of cores: 2 get_eurostat_dsd - The DSD of the tus_00age dataset was cached in memory ('tus_00age.en.dsd' in '.restatapi_env'). test_restatapi.R.............. 76 tests 1 fails create_filter_table - filters class: character; size: 3; filters:TIME_SPHungaryT test_restatapi.R.............. 77 tests 1 fails get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/avia_par_me?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid6 get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_avia_par_me-2026.07.06-0' in '.restatapi_env'). test_restatapi.R.............. 77 tests 1 fails create_filter_table - filters class: character; size: 1; filters:2017:2018 create_filter_table - filters: 2017:2018; is numeric: FALSE; call parents: 6 create_filter_table - length df: 1 content df: 2017:2018 create_filter_table - 2017:2018 date filter length: 1, nchar date_filter: 9 test_restatapi.R.............. 78 tests 1 fails get_eurostat_codelist - API version:2 get_eurostat_codelist - API version:2 get_eurostat_codelist - Trying to download the codelist from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/codelist/ESTAT/SEX trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/codelist/ESTAT/SEX' Content type 'application/vnd.sdmx.structure+xml;version=2.1' length 5483 bytes ================================================== downloaded 5483 bytes Trying to extract the codelist from: /tmp/th798/29939837/RtmpJbKPrV/filee4af82e0806fc get_eurostat_codelist - codelist NULL:TRUE test_restatapi.R.............. 78 tests 1 fails test_restatapi.R.............. 80 tests 1 fails 4.18.0-553.124.1.el8_10.x86_64 test_restatapi.R.............. 80 tests 1 fails Are we at home:FALSE test_restatapi.R.............. 80 tests 1 fails test_restatapi.R.............. 80 tests 1 fails get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=fr trying URL 'https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=fr' downloaded 2.1 MB get_eurostat_toc - The TOC was cached in memory ('toc.txt.fr' in '.restatapi_env'). test_restatapi.R.............. 80 tests 1 fails get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=de trying URL 'https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=de' downloaded 2.0 MB get_eurostat_toc - The TOC was cached in memory ('toc.txt.de' in '.restatapi_env'). test_restatapi.R.............. 80 tests 1 fails test_restatapi.R.............. 81 tests 1 fails get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_dsd - API version:2 get_eurostat_dsd - Trying to download the DSD from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/agr_r_milkpr?references=children trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/agr_r_milkpr?references=children' downloaded 2.9 MB get_eurostat_dsd - class(temp): character - is.na(temp): FALSE - file.size(temp): 3008178 - temp: /tmp/th798/29939837/RtmpJbKPrV/filee4af85f1874e8 Trying to extract the DSD from: /tmp/th798/29939837/RtmpJbKPrV/filee4af85f1874e8 get_eurostat_dsd - concepts:freq,milkitem,dairyprod,geo,OBS_FLAG,CONF_STATUS extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="FREQ"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="FREQ"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="MILKITEM"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="MILKITEM"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="DAIRYPROD"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="DAIRYPROD"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="GEO"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="GEO"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="OBS_FLAG"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="OBS_FLAG"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="CONF_STATUS"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="CONF_STATUS"]/s:Code/c:Name[@xml:lang="de"] get_eurostat_dsd - DSD NULL:FALSE get_eurostat_dsd - Trying to download the CC from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/agr_r_milkpr trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/agr_r_milkpr' downloaded 15 KB get_eurostat_dsd - Trying to extract the CC from: /tmp/th798/29939837/RtmpJbKPrV/filee4af817fdd5cb character number of nodes: 5 number of cores: 2 get_eurostat_dsd - The DSD of the agr_r_milkpr dataset was cached in memory ('agr_r_milkpr.de.dsd' in '.restatapi_env'). create_filter_table - filters class: character; size: 2; filters:BE$Ungarn get_eurostat_data - date_filter: 2007-06< create_filter_table - filters class: character; size: 1; filters:2007-06< create_filter_table - filters: 2007-06<; is numeric: FALSE; call parents: 7 create_filter_table - length df: 1 content df: 2007-06< create_filter_table - 2007-06< date filter length: 1, nchar date_filter: 8 get_eurostat_data - date_filter: 2007-06< nrow dft: 1 ...BE+HU-?startPeriod=2007-06-01 https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...BE+HU/?startPeriod=2007-06-01 trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...BE+HU/?startPeriod=2007-06-01' Content type 'application/vnd.sdmx.genericdata+xml;version=2.1' length 3959 bytes ================================================== downloaded 3959 bytes get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 2 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:34; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:34; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: ...BE+HU date filter: ?startPeriod=2007-06-01 test_restatapi.R.............. 81 tests 1 fails get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. create_filter_table - filters class: character; size: 2; filters:BE$Hungary get_eurostat_data - date_filter: 2007-06< create_filter_table - filters class: character; size: 1; filters:2007-06< create_filter_table - filters: 2007-06<; is numeric: FALSE; call parents: 7 create_filter_table - length df: 1 content df: 2007-06< create_filter_table - 2007-06< date filter length: 1, nchar date_filter: 8 get_eurostat_data - date_filter: 2007-06< nrow dft: 1 ...BE+HU-?startPeriod=2007-06-01 https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...BE+HU/?startPeriod=2007-06-01 trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...BE+HU/?startPeriod=2007-06-01' Content type 'application/vnd.sdmx.genericdata+xml;version=2.1' length 3959 bytes ================================================== downloaded 3959 bytes get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 2 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:34; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:34; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: ...BE+HU date filter: ?startPeriod=2007-06-01 test_restatapi.R.............. 81 tests 1 fails test_restatapi.R.............. 82 tests 1 fails clean_restatapi_cache - All objects (outside of 'cfg', 'rav', 'cc' and 'dmethod') are removed from '.restatapi_env'. clean_restatapi_cache - Deleted all .rds files from /tmp/th798/29939837/RtmpJbKPrV test_restatapi.R.............. 82 tests 1 fails There are skipped tests:9,27-29 test_restatapi.R.............. 82 tests 1 fails Skipped tests: 9,27-29 config version: 2 test_restatapi.R.............. 82 tests 1 fails test_restatapi.R.............. 82 tests 1 fails 6.7s ----- FAILED[data]: test_restatapi.R<169--169> call| expect_true(is.null(dt8)) diff| Expected TRUE, got FALSE Error: 1 out of 82 tests failed Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR checking msg 1: for file 'restatapi/DESCRIPTION' OK 2: package namespace information OK 3: package dependencies OK 4: if this is a source package OK 5: if there is a namespace OK 6: for executable files OK 7: for hidden files and directories OK 8: for portable file names OK 9: for sufficient/correct file permissions OK 10: whether package 'restatapi' can be installed OK 11: package directory OK 12: DESCRIPTION meta-information OK 13: top-level files OK 14: for left-over files OK 15: index information OK 16: package subdirectories OK 17: code files for non-ASCII characters OK 18: R files for syntax errors OK 19: whether the package can be loaded OK 20: whether the package can be loaded with stated dependencies OK 21: whether the package can be unloaded cleanly OK 22: whether the namespace can be loaded with stated dependencies OK 23: whether the namespace can be unloaded cleanly OK 24: loading without being on the library search path OK 25: whether startup messages can be suppressed OK 26: dependencies in R code OK 27: S3 generic/method consistency OK 28: replacement functions OK 29: foreign function calls OK 30: R code for possible problems OK 31: Rd files OK 32: Rd metadata OK 33: Rd cross-references OK 34: for missing documentation entries OK 35: for code/documentation mismatches OK 36: Rd \\usage sections OK 37: Rd contents OK 38: for unstated dependencies in examples OK 39: examples OK 40: for unstated dependencies in 'tests' OK 41: tests ERROR 42: PDF version of manual OK checking msg checking msg 1: tests ERROR Bisecting: 4 revisions left to test after this (roughly 2 steps) [3acb570527ce94d5dd2fffc5d2bdc295f4e4041a] Bump actions/checkout from 4 to 6 (#7526) running '/home/th798/R/R-release/bin/Rscript' '/home/th798/genomic-ml/data.table-revdeps/install_dt_then_check_dep.R' 'tests' 'ERROR' '/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz' '1.18.4' checking "tests" expected "ERROR" rev_dep_tar_gz "/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz" dt_release_version "1.18.4" zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o hash.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi * using log directory '/tmp/th798/29939837/R-release/1314/data.table.git/restatapi.Rcheck' * using R version 4.6.1 (2026-06-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * current time: 2026-07-06 19:11:23 UTC * checking for file 'restatapi/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'restatapi' version '0.25.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'restatapi' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'tinytest.R' OK * checking PDF version of manual ... OK * DONE Status: OK checking msg 1: for file 'restatapi/DESCRIPTION' OK 2: package namespace information OK 3: package dependencies OK 4: if this is a source package OK 5: if there is a namespace OK 6: for executable files OK 7: for hidden files and directories OK 8: for portable file names OK 9: for sufficient/correct file permissions OK 10: whether package 'restatapi' can be installed OK 11: package directory OK 12: DESCRIPTION meta-information OK 13: top-level files OK 14: for left-over files OK 15: index information OK 16: package subdirectories OK 17: code files for non-ASCII characters OK 18: R files for syntax errors OK 19: whether the package can be loaded OK 20: whether the package can be loaded with stated dependencies OK 21: whether the package can be unloaded cleanly OK 22: whether the namespace can be loaded with stated dependencies OK 23: whether the namespace can be unloaded cleanly OK 24: loading without being on the library search path OK 25: whether startup messages can be suppressed OK 26: dependencies in R code OK 27: S3 generic/method consistency OK 28: replacement functions OK 29: foreign function calls OK 30: R code for possible problems OK 31: Rd files OK 32: Rd metadata OK 33: Rd cross-references OK 34: for missing documentation entries OK 35: for code/documentation mismatches OK 36: Rd \\usage sections OK 37: Rd contents OK 38: for unstated dependencies in examples OK 39: examples OK 40: for unstated dependencies in 'tests' OK 41: tests OK 42: PDF version of manual OK checking msg checking msg 1: tests OK Bisecting: 1 revision left to test after this (roughly 1 step) [b904202818a336071f1f976a0ca52bcdd0c4a030] Bump actions/upload-artifact from 4 to 6 (#7523) running '/home/th798/R/R-release/bin/Rscript' '/home/th798/genomic-ml/data.table-revdeps/install_dt_then_check_dep.R' 'tests' 'ERROR' '/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz' '1.18.4' checking "tests" expected "ERROR" rev_dep_tar_gz "/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz" dt_release_version "1.18.4" zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o hash.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi * using log directory '/tmp/th798/29939837/R-release/1314/data.table.git/restatapi.Rcheck' * using R version 4.6.1 (2026-06-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * current time: 2026-07-06 19:17:04 UTC * checking for file 'restatapi/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'restatapi' version '0.25.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'restatapi' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'tinytest.R' ERROR Running the tests in 'tests/tinytest.R' failed. Complete output: > if ( requireNamespace("tinytest", quietly=TRUE) ){ + home <- length(unclass(packageVersion("restatapi"))[[1]]) == 4 + tinytest::test_package("restatapi", at_home = home) + } restatapi: - version 0.25.0 - config file with the API version 2 loaded from GitHub (the 'current' API version number is 2). - 4 from the 28 cores are used for parallel computing, can be changed with 'options(restatapi_cores=...)' - 'auto' method will be used for file download, can be changed with 'options(restatapi_dmethod=...)' - the Table of contents (TOC) was not pre-loaded into the deafult cache ('.restatapi_env'). test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests clean_restatapi_cache - All objects (outside of 'cfg', 'rav', 'cc' and 'dmethod') are removed from '.restatapi_env'. test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests test_restatapi.R.............. 0 tests get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/xml get_eurostat_toc - class(xml_leafs): xml_nodeset get_eurostat_toc - number of nodes: 10408 get_eurostat_toc - number of cores: 2 get_eurostat_toc - dim toc: 10408,22 get_eurostat_toc - colnames toc: title.en,title.fr,title.de,code,lastUpdate,lastModified,dataStart,dataEnd,values,source.en,source.fr,source.de,unit.en,unit.fr,unit.de,shortDescription.en,shortDescription.fr,shortDescription.de,metadata.html,metadata.sdmx,downloadLink.tsv,type get_eurostat_toc - cols to keep: title.en,code,type,lastUpdate,lastModified,dataStart,dataEnd,values,unit.en,source.en,shortDescription.en,metadata.html,metadata.sdmx,downloadLink.tsv get_eurostat_toc - The TOC was cached in memory ('toc.xml.en' in '.restatapi_env'). test_restatapi.R.............. 0 tests get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=en trying URL 'https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=en' downloaded 1.9 MB get_eurostat_toc - The TOC was cached in memory ('toc.txt.en' in '.restatapi_env'). test_restatapi.R.............. 0 tests get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. test_restatapi.R.............. 0 tests test_restatapi.R.............. 1 tests OK test_restatapi.R.............. 7 tests OK get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. test_restatapi.R.............. 7 tests OK get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. test_restatapi.R.............. 7 tests OK get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/xml get_eurostat_toc - class(xml_leafs): xml_nodeset get_eurostat_toc - number of nodes: 10408 get_eurostat_toc - number of cores: 2 get_eurostat_toc - dim toc: 10408,22 get_eurostat_toc - colnames toc: title.en,title.fr,title.de,code,lastUpdate,lastModified,dataStart,dataEnd,values,source.en,source.fr,source.de,unit.en,unit.fr,unit.de,shortDescription.en,shortDescription.fr,shortDescription.de,metadata.html,metadata.sdmx,downloadLink.tsv,type get_eurostat_toc - cols to keep: title.de,code,type,lastUpdate,lastModified,dataStart,dataEnd,values,unit.de,source.de,shortDescription.de,metadata.html,metadata.sdmx,downloadLink.tsv get_eurostat_toc - The TOC was cached in memory ('toc.xml.de' in '.restatapi_env'). test_restatapi.R.............. 7 tests OK test_restatapi.R.............. 8 tests OK test_restatapi.R.............. 9 tests OK trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/text?references=children' test_restatapi.R.............. 10 tests OK get_eurostat_dsd - API version:2 get_eurostat_dsd - Trying to download the DSD from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/NAMA_10_GDP?references=children trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/NAMA_10_GDP?references=children' downloaded 3.4 MB get_eurostat_dsd - class(temp): character - is.na(temp): FALSE - file.size(temp): 3585472 - temp: /tmp/th798/29939837/RtmpaGyx58/filef62f23e776338 Trying to extract the DSD from: /tmp/th798/29939837/RtmpaGyx58/filef62f23e776338 get_eurostat_dsd - concepts:freq,unit,na_item,geo,OBS_FLAG,CONF_STATUS extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="FREQ"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="FREQ"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="UNIT"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="UNIT"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="NA_ITEM"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="NA_ITEM"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="GEO"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="GEO"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="OBS_FLAG"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="OBS_FLAG"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="CONF_STATUS"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="CONF_STATUS"]/s:Code/c:Name[@xml:lang="en"] get_eurostat_dsd - DSD NULL:FALSE get_eurostat_dsd - Trying to download the CC from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/NAMA_10_GDP trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/NAMA_10_GDP' Content type 'application/vnd.sdmx.structure+xml;version=2.1' length 5597 bytes ================================================== downloaded 5597 bytes get_eurostat_dsd - Trying to extract the CC from: /tmp/th798/29939837/RtmpaGyx58/filef62f23a06dd9a character number of nodes: 5 number of cores: 2 get_eurostat_dsd - The DSD of the NAMA_10_GDP dataset was cached in memory ('NAMA_10_GDP.en.dsd' in '.restatapi_env'). test_restatapi.R.............. 10 tests OK test_restatapi.R.............. 13 tests OK test_restatapi.R.............. 13 tests OK test_restatapi.R.............. 13 tests OK test_restatapi.R.............. 17 tests OK get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: htec_cis3 get_eurostat_data - select_freq: get_eurostat_data - Trying to get from cache: b_htec_cis3-2026.07.06-1-1 get_eurostat_bulk - API version:2 get_eurostat_bulk - class of id, cache, update_cache, cache_dir, compress_file, stringsAsFactors, keep_flags, check_toc, melt, verbose: character - logical -logical - NULL - logical - logical - logical - logical - logical - logical get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/htec_cis3?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: FALSE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: restatapi::get_eurostat_rawidtxtcacheupdate_cachecache_dircompress_filestringsAsFactorskeep_flagscheck_tocTRUEverbose get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_data - The data was downloaded with bulk download. get_eurostat_data - bulk restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags get_eurostat_data - cflags:TRUE get_eurostat_data - restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags get_eurostat_data - processed restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags get_eurostat_data - The data was cached in memory ('b_htec_cis3-2026.07.06-1-1' in '.restatapi_env'). get_eurostat_data - restat NULL?:FALSE id: htec_cis3 filters: date filter: test_restatapi.R.............. 17 tests OK test_restatapi.R.............. 17 tests OK get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: htec_cis3 get_eurostat_data - select_freq: get_eurostat_data - Trying to get from cache: b_htec_cis3-2026.07.06-0-0 get_eurostat_cache - The 'b_htec_cis3-2026.07.06-0-0' was loaded from 'b_htec_cis3-2026.07.06-1-1' in '.restatapi_env'. get_eurostat_data - The data was loaded from cache. get_eurostat_data - cached restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags get_eurostat_data - restat - nrow:1006; ncol:7; colnames:indic_in/nace_r1/unit/geo/time/values/flags get_eurostat_data - processed restat - nrow:1006; ncol:6; colnames:indic_in/nace_r1/unit/geo/time/values get_eurostat_data - The data was cached in memory ('b_htec_cis3-2026.07.06-0-0' in '.restatapi_env'). get_eurostat_data - restat NULL?:FALSE id: htec_cis3 filters: date filter: test_restatapi.R.............. 17 tests OK test_restatapi.R.............. 17 tests OK test_restatapi.R.............. 21 tests OK get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/rail_tf_ns20_mk?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid3FALSE get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_rail_tf_ns20_mk-2026.07.06-0' in '.restatapi_env'). get_eurostat_raw - API version:2 get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. get_eurostat_raw - raws of TOC: 7661 get_eurostat_raw - txt bulk url from TOC:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/RAIL_TF_NS20_MK?format=tsv&compressed=true get_eurostat_raw - txt bulk url from cfg:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/rail_tf_ns20_mk?format=TSV&compressed=true get_eurostat_raw - data rowcount in TOC: 12 get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid3TRUEFALSE get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_rail_tf_ns20_mk-2023.02.02-0' in '.restatapi_env'). get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: rail_tf_ns20_mk get_eurostat_data - select_freq: get_eurostat_data - Trying to get from cache: b_rail_tf_ns20_mk-2026.07.06-0-0 get_eurostat_cache - The 'b_rail_tf_ns20_mk-2026.07.06-0-0' was loaded from 'r_rail_tf_ns20_mk-2026.07.06-0' in '.restatapi_env'. get_eurostat_data - The data was loaded from cache. get_eurostat_data - cached restat - nrow:12; ncol:6; colnames:freq/net_seg20/train/unit/time/values get_eurostat_data - restat - nrow:12; ncol:6; colnames:freq/net_seg20/train/unit/time/values get_eurostat_data - processed restat - nrow:12; ncol:5; colnames:net_seg20/train/unit/time/values get_eurostat_data - The data was cached in memory ('b_rail_tf_ns20_mk-2026.07.06-0-0' in '.restatapi_env'). get_eurostat_data - restat NULL?:FALSE id: rail_tf_ns20_mk filters: date filter: test_restatapi.R.............. 26 tests OK get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr?format=sdmx_2.1_structured&compressed=true get_eurostat_raw - file format: gz get_compressed_sdmx - url:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr?format=sdmx_2.1_structured&compressed=true get_compressed_sdmx - format:gz get_compressed_sdmx - xml NULL:FALSE get_eurostat_raw - class(xml_leafs): xml_nodeset get_eurostat_raw - number of nodes: 583 get_eurostat_raw - number of cores: 2 get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid4xmlTRUETRUE get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_agr_r_milkpr-2026.07.06-1' in '.restatapi_env'). test_restatapi.R.............. 26 tests OK get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_data - Trying to get from cache: b_agr_r_milkpr-2026.07.06-1-0 get_eurostat_cache - The 'b_agr_r_milkpr-2026.07.06-1-0' was loaded from 'r_agr_r_milkpr-2026.07.06-1' in '.restatapi_env'. get_eurostat_data - The data was loaded from cache. get_eurostat_data - cached restat - nrow:11870; ncol:7; colnames:geo/milkitem/freq/dairyprod/TIME_PERIOD/OBS_VALUE/OBS_FLAG get_eurostat_data - restat - nrow:11870; ncol:7; colnames:geo/milkitem/freq/dairyprod/TIME_PERIOD/OBS_VALUE/OBS_FLAG get_eurostat_data - processed restat - nrow:11599; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - The data was cached in memory ('b_agr_r_milkpr-2026.07.06-1-0' in '.restatapi_env'). get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: date filter: test_restatapi.R.............. 26 tests OK get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_data - date_filter: 2008 create_filter_table - filters class: numeric; size: 1; filters:2008 create_filter_table - filters: 2008; is numeric: TRUE; call parents: 7 create_filter_table - length df: 1 content df: 2008 create_filter_table - 2008 date filter length: 1, nchar date_filter: 4 get_eurostat_data - date_filter: 2008 nrow dft: 1 -?startPeriod=2008-01-01&endPeriod=2008-12-31 https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2008-01-01&endPeriod=2008-12-31 trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2008-01-01&endPeriod=2008-12-31' downloaded 106 KB get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 410 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:410; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:390; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: date filter: ?startPeriod=2008-01-01&endPeriod=2008-12-31 test_restatapi.R.............. 26 tests OK test_restatapi.R.............. 27 tests OK test_restatapi.R.............. 28 tests OK get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/irt_h_eurcoe_d?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid5TRUE get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_irt_h_eurcoe_d-2026.07.06-0' in '.restatapi_env'). test_restatapi.R.............. 28 tests OK get_eurostat_bulk - API version:2 get_eurostat_bulk - class of id, cache, update_cache, cache_dir, compress_file, stringsAsFactors, keep_flags, check_toc, melt, verbose: character - logical -logical - NULL - logical - logical - logical - logical - logical - logical get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/irt_h_eurcoe_d?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: FALSE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: restatapi::get_eurostat_rawidtxtcacheupdate_cachecache_dircompress_filestringsAsFactorskeep_flagscheck_tocTRUEverbose get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_bulk - The bulk data was cached in memory ('b_irt_h_eurcoe_d-2026.07.06-1-0' in '.restatapi_env'). test_restatapi.R.............. 28 tests OK get_eurostat_raw - API version:2 get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_cache - The 'toc.xml.en' was loaded from 'toc.xml.en' in '.restatapi_env'. get_eurostat_toc - The TOC was cached previously in memory ('toc.xml.en' in '.restatapi_env'). It remained unchanged. get_eurostat_raw - raws of TOC: 7661 get_eurostat_raw - txt bulk url from TOC:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/IRT_H_EURCOE_D?format=tsv&compressed=true get_eurostat_raw - txt bulk url from cfg:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/irt_h_eurcoe_d?format=sdmx_2.1_structured&compressed=true get_eurostat_raw - data rowcount in TOC: 29862 get_eurostat_raw - file format: gz get_compressed_sdmx - url:https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/irt_h_eurcoe_d?format=sdmx_2.1_structured&compressed=true get_compressed_sdmx - format:gz get_compressed_sdmx - xml NULL:FALSE get_eurostat_raw - class(xml_leafs): xml_nodeset get_eurostat_raw - number of nodes: 18 get_eurostat_raw - number of cores: 2 get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid5xmlTRUETRUETRUETRUEFALSE get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_irt_h_eurcoe_d-2009.03.27-1' in '.restatapi_env'). test_restatapi.R.............. 28 tests OK get_eurostat_bulk - API version:2 get_eurostat_cache - The 'b_irt_h_eurcoe_d-2026.07.06-1-0' was loaded from 'b_irt_h_eurcoe_d-2026.07.06-1-0' in '.restatapi_env'. get_eurostat_bulk - The bulk data was cached previously in memory ('b_irt_h_eurcoe_d-2026.07.06-1-0' in '.restatapi_env'). It remained unchanged. test_restatapi.R.............. 28 tests OK test_restatapi.R.............. 29 tests OK test_restatapi.R.............. 31 tests OK trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/agr_r_milkpr?references=children' downloaded 2.9 MB trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/agr_r_milkpr' downloaded 15 KB test_restatapi.R.............. 32 tests OK test_restatapi.R.............. 33 tests OK test_restatapi.R.............. 34 tests OK test_restatapi.R.............. 35 tests OK test_restatapi.R.............. 38 tests OK trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children' downloaded 8.9 MB trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/avia_par_me/?startPeriod=2017-03-01&endPeriod=2017-03-31' downloaded 58 KB trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children' downloaded 8.0 MB test_restatapi.R.............. 39 tests OK test_restatapi.R.............. 40 tests 1 fails test_restatapi.R.............. 40 tests 1 fails test_restatapi.R.............. 41 tests 1 fails get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. test_restatapi.R.............. 41 tests 1 fails get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. create_filter_table - filters class: character; size: 1; filters:AT ...AT- https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT/ trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT/' Content type 'application/vnd.sdmx.genericdata+xml;version=2.1' length 3279 bytes ================================================== downloaded 3279 bytes get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 1 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:29; ncol:6; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue get_eurostat_data - processed restat - nrow:29; ncol:5; colnames:geo/milkitem/dairyprod/time/values get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: ...AT date filter: get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. create_filter_table - filters class: character; size: 1; filters:AT ...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34- https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34/ trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34/' downloaded 31 KB get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 13 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:377; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:377; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: ...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34 date filter: get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_data - date_filter: 2016 create_filter_table - filters class: numeric; size: 1; filters:2016 create_filter_table - filters: 2016; is numeric: TRUE; call parents: 8 create_filter_table - length df: 1 content df: 2016 create_filter_table - 2016 date filter length: 1, nchar date_filter: 4 get_eurostat_data - date_filter: 2016 nrow dft: 1 -?startPeriod=2016-01-01&endPeriod=2016-12-31 https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2016-01-01&endPeriod=2016-12-31 trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2016-01-01&endPeriod=2016-12-31' downloaded 137 KB get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 508 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:508; ncol:6; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue get_eurostat_data - processed restat - nrow:494; ncol:5; colnames:geo/milkitem/dairyprod/time/values get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: date filter: ?startPeriod=2016-01-01&endPeriod=2016-12-31 get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_data - date_filter: 2016 create_filter_table - filters class: character; size: 1; filters:2016 create_filter_table - filters: 2016; is numeric: FALSE; call parents: 8 create_filter_table - length df: 1 content df: 2016 create_filter_table - 2016 date filter length: 1, nchar date_filter: 4 get_eurostat_data - date_filter: 2016 nrow dft: 1 -?startPeriod=2016-01-01&endPeriod=2016-12-31 https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2016-01-01&endPeriod=2016-12-31 trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/?startPeriod=2016-01-01&endPeriod=2016-12-31' downloaded 137 KB get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 508 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:508; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:494; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: date filter: ?startPeriod=2016-01-01&endPeriod=2016-12-31 get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. create_filter_table - filters class: character; size: 1; filters:AT ...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34+EL11+EL3+EL30+EL51+ES51+ES52+HR+HR02+HR03+HR04+HR06+HR01+ITF5+LV+LV0+LV00+HU22+RO4+SK01+NO01+NO03+NO04+NO05+UKD3+UKK1+TR2+TR5+TR63+TR72+TR8+TR83+TRB1+TRC3- https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34+EL11+EL3+EL30+EL51+ES51+ES52+HR+HR02+HR03+HR04+HR06+HR01+ITF5+LV+LV0+LV00+HU22+RO4+SK01+NO01+NO03+NO04+NO05+UKD3+UKK1+TR2+TR5+TR63+TR72+TR8+TR83+TRB1+TRC3/ trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34+EL11+EL3+EL30+EL51+ES51+ES52+HR+HR02+HR03+HR04+HR06+HR01+ITF5+LV+LV0+LV00+HU22+RO4+SK01+NO01+NO03+NO04+NO05+UKD3+UKK1+TR2+TR5+TR63+TR72+TR8+TR83+TRB1+TRC3/' downloaded 83 KB get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 46 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:1004; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:993; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: ...AT+AT1+AT11+AT12+AT13+AT2+AT21+AT22+AT3+AT31+AT32+AT33+AT34+EL11+EL3+EL30+EL51+ES51+ES52+HR+HR02+HR03+HR04+HR06+HR01+ITF5+LV+LV0+LV00+HU22+RO4+SK01+NO01+NO03+NO04+NO05+UKD3+UKK1+TR2+TR5+TR63+TR72+TR8+TR83+TRB1+TRC3 date filter: test_restatapi.R.............. 45 tests 1 fails get_eurostat_dsd - API version:2 get_eurostat_dsd - Trying to download the DSD from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children' downloaded 7.1 MB get_eurostat_dsd - Warning by the download of the DSD file: URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children': Timeout of 60 seconds was reached utils::download.file(dsd_endpoint, temp, dmethod) get_eurostat_dsd - class(temp): character - is.na(temp): FALSE - file.size(temp): 7463240 - temp: /tmp/th798/29939837/RtmpaGyx58/filef62f2494ba6fd Trying to extract the DSD from: /tmp/th798/29939837/RtmpaGyx58/filef62f2494ba6fd get_eurostat_dsd - Error during the extraction of the XML from the downloaded DSD file: expected '>' [73] read_xml.character(temp) get_eurostat_dsd - The dsd_xml is NULL. Please check in a browser the url below. If it provides valid response you can try again to download the DSD. https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/avia_par_me?references=children test_restatapi.R.............. 45 tests 1 fails test_restatapi.R.............. 45 tests 1 fails test_restatapi.R.............. 45 tests 1 fails test_restatapi.R.............. 47 tests 1 fails test_restatapi.R.............. 49 tests 1 fails test_restatapi.R.............. 50 tests 1 fails test_restatapi.R.............. 50 tests 1 fails test_restatapi.R.............. 51 tests 1 fails test_restatapi.R.............. 53 tests 1 fails test_restatapi.R.............. 54 tests 1 fails test_restatapi.R.............. 58 tests 1 fails test_restatapi.R.............. 60 tests 1 fails test_restatapi.R.............. 62 tests 1 fails test_restatapi.R.............. 63 tests 1 fails test_restatapi.R.............. 64 tests 1 fails test_restatapi.R.............. 65 tests 1 fails test_restatapi.R.............. 66 tests 1 fails test_restatapi.R.............. 67 tests 1 fails test_restatapi.R.............. 68 tests 1 fails test_restatapi.R.............. 69 tests 1 fails test_restatapi.R.............. 70 tests 1 fails test_restatapi.R.............. 71 tests 1 fails test_restatapi.R.............. 72 tests 1 fails test_restatapi.R.............. 73 tests 1 fails test_restatapi.R.............. 74 tests 1 fails test_restatapi.R.............. 75 tests 1 fails test_restatapi.R.............. 76 tests 1 fails get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/tus_00age?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid7 get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_tus_00age-2026.07.06-0' in '.restatapi_env'). test_restatapi.R.............. 76 tests 1 fails get_eurostat_dsd - API version:2 get_eurostat_dsd - Trying to download the DSD from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/tus_00age?references=children trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/tus_00age?references=children' downloaded 3.7 MB get_eurostat_dsd - class(temp): character - is.na(temp): FALSE - file.size(temp): 3901770 - temp: /tmp/th798/29939837/RtmpaGyx58/filef62f22be80d2e Trying to extract the DSD from: /tmp/th798/29939837/RtmpaGyx58/filef62f22be80d2e get_eurostat_dsd - concepts:freq,unit,sex,age,acl00,geo,OBS_FLAG,CONF_STATUS extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="FREQ"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="FREQ"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="UNIT"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="UNIT"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="SEX"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="SEX"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="AGE"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="AGE"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="ACL00"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="ACL00"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="GEO"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="GEO"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="OBS_FLAG"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="OBS_FLAG"]/s:Code/c:Name[@xml:lang="en"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="CONF_STATUS"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="CONF_STATUS"]/s:Code/c:Name[@xml:lang="en"] get_eurostat_dsd - DSD NULL:FALSE get_eurostat_dsd - Trying to download the CC from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/tus_00age trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/tus_00age' Content type 'application/vnd.sdmx.structure+xml;version=2.1' length 3844 bytes ================================================== downloaded 3844 bytes get_eurostat_dsd - Trying to extract the CC from: /tmp/th798/29939837/RtmpaGyx58/filef62f22481c2f3 character number of nodes: 7 number of cores: 2 get_eurostat_dsd - The DSD of the tus_00age dataset was cached in memory ('tus_00age.en.dsd' in '.restatapi_env'). test_restatapi.R.............. 76 tests 1 fails create_filter_table - filters class: character; size: 3; filters:TIME_SPHungaryT test_restatapi.R.............. 77 tests 1 fails get_eurostat_raw - API version:2 get_eurostat_raw - bulk url: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/avia_par_me?format=TSV&compressed=true get_eurostat_raw - class(raw): data.tabledata.frame get_eurostat_raw - caching in raw: TRUE get_eurostat_raw - local filter: FALSE get_eurostat_raw - called from: get_eurostat_rawtestid6 get_eurostat_raw - get_eurostat_raw in sys.call(): FALSE get_eurostat_raw - The raw data was cached in memory ('r_avia_par_me-2026.07.06-0' in '.restatapi_env'). test_restatapi.R.............. 77 tests 1 fails create_filter_table - filters class: character; size: 1; filters:2017:2018 create_filter_table - filters: 2017:2018; is numeric: FALSE; call parents: 6 create_filter_table - length df: 1 content df: 2017:2018 create_filter_table - 2017:2018 date filter length: 1, nchar date_filter: 9 test_restatapi.R.............. 78 tests 1 fails get_eurostat_codelist - API version:2 get_eurostat_codelist - API version:2 get_eurostat_codelist - Trying to download the codelist from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/codelist/ESTAT/SEX trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/codelist/ESTAT/SEX' Content type 'application/vnd.sdmx.structure+xml;version=2.1' length 5483 bytes ================================================== downloaded 5483 bytes Trying to extract the codelist from: /tmp/th798/29939837/RtmpaGyx58/filef62f23d77813c get_eurostat_codelist - codelist NULL:TRUE test_restatapi.R.............. 78 tests 1 fails test_restatapi.R.............. 80 tests 1 fails 4.18.0-553.124.1.el8_10.x86_64 test_restatapi.R.............. 80 tests 1 fails Are we at home:FALSE test_restatapi.R.............. 80 tests 1 fails test_restatapi.R.............. 80 tests 1 fails get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=fr trying URL 'https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=fr' downloaded 2.1 MB get_eurostat_toc - The TOC was cached in memory ('toc.txt.fr' in '.restatapi_env'). test_restatapi.R.............. 80 tests 1 fails get_eurostat_toc - API version:2 - number of cores:2 get_eurostat_toc - Downloading https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=de trying URL 'https://ec.europa.eu/eurostat/api/dissemination/catalogue/toc/txt?lang=de' downloaded 2.0 MB get_eurostat_toc - The TOC was cached in memory ('toc.txt.de' in '.restatapi_env'). test_restatapi.R.............. 80 tests 1 fails test_restatapi.R.............. 81 tests 1 fails get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_dsd - API version:2 get_eurostat_dsd - Trying to download the DSD from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/agr_r_milkpr?references=children trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/datastructure/ESTAT/agr_r_milkpr?references=children' downloaded 2.9 MB get_eurostat_dsd - class(temp): character - is.na(temp): FALSE - file.size(temp): 3008178 - temp: /tmp/th798/29939837/RtmpaGyx58/filef62f23bfee045 Trying to extract the DSD from: /tmp/th798/29939837/RtmpaGyx58/filef62f23bfee045 get_eurostat_dsd - concepts:freq,milkitem,dairyprod,geo,OBS_FLAG,CONF_STATUS extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="FREQ"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="FREQ"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="MILKITEM"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="MILKITEM"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="GEO"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="GEO"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="DAIRYPROD"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="DAIRYPROD"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="OBS_FLAG"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="OBS_FLAG"]/s:Code/c:Name[@xml:lang="de"] extract_dsd - API version:2 extract_dsd - xml_string_clc://s:Codelist[@id="CONF_STATUS"]/s:Code extract_dsd - xml_string_cln://s:Codelist[@id="CONF_STATUS"]/s:Code/c:Name[@xml:lang="de"] get_eurostat_dsd - DSD NULL:FALSE get_eurostat_dsd - Trying to download the CC from: https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/agr_r_milkpr trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/contentconstraint/ESTAT/agr_r_milkpr' downloaded 15 KB get_eurostat_dsd - Trying to extract the CC from: /tmp/th798/29939837/RtmpaGyx58/filef62f2655f4ca7 character number of nodes: 5 number of cores: 2 get_eurostat_dsd - The DSD of the agr_r_milkpr dataset was cached in memory ('agr_r_milkpr.de.dsd' in '.restatapi_env'). create_filter_table - filters class: character; size: 2; filters:BE$Ungarn get_eurostat_data - date_filter: 2007-06< create_filter_table - filters class: character; size: 1; filters:2007-06< create_filter_table - filters: 2007-06<; is numeric: FALSE; call parents: 7 create_filter_table - length df: 1 content df: 2007-06< create_filter_table - 2007-06< date filter length: 1, nchar date_filter: 8 get_eurostat_data - date_filter: 2007-06< nrow dft: 1 ...BE+HU-?startPeriod=2007-06-01 https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...BE+HU/?startPeriod=2007-06-01 trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...BE+HU/?startPeriod=2007-06-01' Content type 'application/vnd.sdmx.genericdata+xml;version=2.1' length 3959 bytes ================================================== downloaded 3959 bytes get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 2 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:34; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:34; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: ...BE+HU date filter: ?startPeriod=2007-06-01 test_restatapi.R.............. 81 tests 1 fails get_eurostat_data - footer code option value at start: get_eurostat_data - footer code option value after reset: get_eurostat_data - id: agr_r_milkpr get_eurostat_data - select_freq: get_eurostat_cache - The 'agr_r_milkpr.en.dsd' was loaded from 'agr_r_milkpr.en.dsd' in '.restatapi_env'. create_filter_table - filters class: character; size: 2; filters:BE$Hungary get_eurostat_data - date_filter: 2007-06< create_filter_table - filters class: character; size: 1; filters:2007-06< create_filter_table - filters: 2007-06<; is numeric: FALSE; call parents: 7 create_filter_table - length df: 1 content df: 2007-06< create_filter_table - 2007-06< date filter length: 1, nchar date_filter: 8 get_eurostat_data - date_filter: 2007-06< nrow dft: 1 ...BE+HU-?startPeriod=2007-06-01 https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...BE+HU/?startPeriod=2007-06-01 trying URL 'https://ec.europa.eu/eurostat/api/dissemination/sdmx/2.1/data/agr_r_milkpr/...BE+HU/?startPeriod=2007-06-01' Content type 'application/vnd.sdmx.genericdata+xml;version=2.1' length 3959 bytes ================================================== downloaded 3959 bytes get_eurostat_data - class(xml_leafs):xml_nodeset get_eurostat_data - number of nodes: 2 get_eurostat_data - number of cores: 2 get_eurostat_data - footer code option value after retrieval: get_eurostat_data - restat - nrow:34; ncol:7; colnames:geo/milkitem/freq/dairyprod/obsTime/obsValue/OBS_STATUS get_eurostat_data - processed restat - nrow:34; ncol:6; colnames:geo/milkitem/dairyprod/time/values/flags get_eurostat_data - restat NULL?:FALSE id: agr_r_milkpr filters: ...BE+HU date filter: ?startPeriod=2007-06-01 test_restatapi.R.............. 81 tests 1 fails test_restatapi.R.............. 82 tests 1 fails clean_restatapi_cache - All objects (outside of 'cfg', 'rav', 'cc' and 'dmethod') are removed from '.restatapi_env'. clean_restatapi_cache - Deleted all .rds files from /tmp/th798/29939837/RtmpaGyx58 test_restatapi.R.............. 82 tests 1 fails There are skipped tests:27-29,54 test_restatapi.R.............. 82 tests 1 fails Skipped tests: 27-29,54 config version: 2 test_restatapi.R.............. 82 tests 1 fails test_restatapi.R.............. 82 tests 1 fails 7.2s ----- FAILED[data]: test_restatapi.R<169--169> call| expect_true(is.null(dt8)) diff| Expected TRUE, got FALSE Error: 1 out of 82 tests failed Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR checking msg 1: for file 'restatapi/DESCRIPTION' OK 2: package namespace information OK 3: package dependencies OK 4: if this is a source package OK 5: if there is a namespace OK 6: for executable files OK 7: for hidden files and directories OK 8: for portable file names OK 9: for sufficient/correct file permissions OK 10: whether package 'restatapi' can be installed OK 11: package directory OK 12: DESCRIPTION meta-information OK 13: top-level files OK 14: for left-over files OK 15: index information OK 16: package subdirectories OK 17: code files for non-ASCII characters OK 18: R files for syntax errors OK 19: whether the package can be loaded OK 20: whether the package can be loaded with stated dependencies OK 21: whether the package can be unloaded cleanly OK 22: whether the namespace can be loaded with stated dependencies OK 23: whether the namespace can be unloaded cleanly OK 24: loading without being on the library search path OK 25: whether startup messages can be suppressed OK 26: dependencies in R code OK 27: S3 generic/method consistency OK 28: replacement functions OK 29: foreign function calls OK 30: R code for possible problems OK 31: Rd files OK 32: Rd metadata OK 33: Rd cross-references OK 34: for missing documentation entries OK 35: for code/documentation mismatches OK 36: Rd \\usage sections OK 37: Rd contents OK 38: for unstated dependencies in examples OK 39: examples OK 40: for unstated dependencies in 'tests' OK 41: tests ERROR 42: PDF version of manual OK checking msg checking msg 1: tests ERROR Bisecting: 0 revisions left to test after this (roughly 0 steps) [ea9f0da52258305f1d893394895f55fdbbce5af1] Bump actions/cache from 4 to 5 (#7524) running '/home/th798/R/R-release/bin/Rscript' '/home/th798/genomic-ml/data.table-revdeps/install_dt_then_check_dep.R' 'tests' 'ERROR' '/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz' '1.18.4' checking "tests" expected "ERROR" rev_dep_tar_gz "/projects/genomic-ml/CRAN/src/contrib/restatapi_0.25.0.tar.gz" dt_release_version "1.18.4" zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o hash.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi * using log directory '/tmp/th798/29939837/R-release/1314/data.table.git/restatapi.Rcheck' * using R version 4.6.1 (2026-06-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * current time: 2026-07-06 19:26:08 UTC * checking for file 'restatapi/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'restatapi' version '0.25.0' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package 'restatapi' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'tinytest.R' OK * checking PDF version of manual ... OK * DONE Status: OK checking msg 1: for file 'restatapi/DESCRIPTION' OK 2: package namespace information OK 3: package dependencies OK 4: if this is a source package OK 5: if there is a namespace OK 6: for executable files OK 7: for hidden files and directories OK 8: for portable file names OK 9: for sufficient/correct file permissions OK 10: whether package 'restatapi' can be installed OK 11: package directory OK 12: DESCRIPTION meta-information OK 13: top-level files OK 14: for left-over files OK 15: index information OK 16: package subdirectories OK 17: code files for non-ASCII characters OK 18: R files for syntax errors OK 19: whether the package can be loaded OK 20: whether the package can be loaded with stated dependencies OK 21: whether the package can be unloaded cleanly OK 22: whether the namespace can be loaded with stated dependencies OK 23: whether the namespace can be unloaded cleanly OK 24: loading without being on the library search path OK 25: whether startup messages can be suppressed OK 26: dependencies in R code OK 27: S3 generic/method consistency OK 28: replacement functions OK 29: foreign function calls OK 30: R code for possible problems OK 31: Rd files OK 32: Rd metadata OK 33: Rd cross-references OK 34: for missing documentation entries OK 35: for code/documentation mismatches OK 36: Rd \\usage sections OK 37: Rd contents OK 38: for unstated dependencies in examples OK 39: examples OK 40: for unstated dependencies in 'tests' OK 41: tests OK 42: PDF version of manual OK checking msg checking msg 1: tests OK ea9f0da52258305f1d893394895f55fdbbce5af1 is the first new commit commit ea9f0da52258305f1d893394895f55fdbbce5af1 Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri Dec 26 10:11:45 2025 -0800 Bump actions/cache from 4 to 5 (#7524) Bumps [actions/cache](https://github.com/actions/cache) from 4 to 5. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/v4...v5) --- updated-dependencies: - dependency-name: actions/cache dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> .github/workflows/R-CMD-check.yaml | 2 +- .github/workflows/pkgup.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) bisect found first bad commit Key: checking master release first.bad.commit 1: tests OK ERROR ea9f0da52258305f1d893394895f55fdbbce5af1 comments CRAN 1: parent=b904202818a336071f1f976a0ca52bcdd0c4a030 OK >