Note: the module "R" cannot be unloaded because it was not loaded. WARNING: ignoring environment value of R_HOME R Under development (unstable) (2025-08-22 r88678) -- "Unsuffered Consequences" Copyright (C) 2025 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) > 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")), + "349", + 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/2025-08-23/deps.csv", task.str = "1213", release = "/scratch/th798/data.table-revdeps/2025-08-23/data.table_release_1.17.8.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-08-23/data.table_master_1.17.99.55bbc3d1646a80ba1d5b2c073c17b9575e7c186a.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/21090361/R-devel/1213" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/21090361/R-devel/1213/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "rgbif" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/21090361/R-devel/1213/library" [2] "/projects/genomic-ml/R/R-devel/library" > options(repos=c(#this should be in ~/.Rprofile too. + CRAN="http://cloud.r-project.org")) > print(Sys.time()) [1] "2025-08-23 01:10:23 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/21090361/R-devel/1213/library' (as 'lib' is unspecified) also installing the dependencies 'curl', 'oai', 'vcr' trying URL 'http://cloud.r-project.org/src/contrib/curl_7.0.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/oai_0.4.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/vcr_2.0.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/rgbif_3.8.2.tar.gz' * installing *source* package 'curl' ... ** this is package 'curl' version '7.0.0' ** package 'curl' 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 -lcurl ** 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 -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 callbacks.c -o callbacks.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 curl.c -o curl.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 download.c -o download.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 dryrun.c -o dryrun.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 escape.c -o escape.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 fetch.c -o fetch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 findport.c -o findport.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 form.c -o form.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 getdate.c -o getdate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 handle.c -o handle.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 ieproxy.c -o ieproxy.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 interrupt.c -o interrupt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 multi.c -o multi.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 nslookup.c -o nslookup.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 options.c -o options.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 reflist.c -o reflist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 split.c -o split.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 ssl.c -o ssl.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 typechecking.c -o typechecking.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 urlparser.c -o urlparser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 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 -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 version.c -o version.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 winidn.c -o winidn.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 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 curl.so callbacks.o curl.o download.o dryrun.o escape.o fetch.o findport.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o urlparser.o utils.o version.o winidn.o writer.o -L/home/th798/.conda/envs/emacs1/lib -lcurl installing to /tmp/th798/21090361/R-devel/1213/library/00LOCK-curl/00new/curl/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 (curl) * installing *source* package 'oai' ... ** this is package 'oai' version '0.4.0' ** package 'oai' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (oai) * installing *source* package 'vcr' ... ** this is package 'vcr' version '2.0.0' ** package 'vcr' 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 (vcr) * installing *source* package 'rgbif' ... ** this is package 'rgbif' version '3.8.2' ** package 'rgbif' 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 (rgbif) The downloaded source packages are in '/tmp/th798/21090361/RtmpVScPJ1/downloaded_packages' > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 36.266 3.291 46.297 > print(Sys.time()) [1] "2025-08-23 01:11:09 MST" > downloaded_packages <- file.path( + tempdir(), + "downloaded_packages") > dl.glob <- file.path( + downloaded_packages, + paste0(rev.dep,"_*.tar.gz")) > rev.dep.dl.row <- cbind(rev.dep, Sys.glob(dl.glob)) > colnames(rev.dep.dl.row) <- c("pkg","path") > rev.dep.release.tar.gz <- normalizePath(rev.dep.dl.row[,"path"], mustWork=TRUE) > 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] "2025-08-23 01:11:09 MST" Installing package into '/tmp/th798/21090361/R-devel/1213/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.17.8' ** 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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.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 installing to /tmp/th798/21090361/R-devel/1213/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] "2025-08-23 01:11:32 MST" * using log directory '/tmp/th798/21090361/R-devel/1213/rgbif.Rcheck' * using R Under development (unstable) (2025-08-22 r88678) * 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 * checking for file 'rgbif/DESCRIPTION' ... OK * this is package 'rgbif' version '3.8.2' * 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 'rgbif' 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 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 'test-all.R' ERROR Running the tests in 'tests/test-all.R' failed. Complete output: > library(testthat) > test_check("rgbif") Loading required package: rgbif [ FAIL 11 | WARN 349 | SKIP 136 | PASS 1166 ] == Skipped tests (136) ========================================================= * On CRAN (136): 'test-country_codes.r:4:3', 'test-dataset_export.R:3:1', 'test-dataset_gridded.R:3:1', 'test-dataset_uuid_funs.R:78:3', 'test-derived_dataset.R:3:3', 'test-derived_dataset.R:51:3', 'test-derived_dataset.R:186:3', 'test-derived_dataset.R:347:3', 'test-downloads.R:3:3', 'test-downloads.R:16:3', 'test-downloads.R:43:3', 'test-downloads.R:80:3', 'test-downloads.R:87:3', 'test-downloads.R:101:3', 'test-downloads.R:116:3', 'test-elevation.R:3:3', 'test-elevation.R:16:3', 'test-elevation.R:32:3', 'test-elevation.R:59:3', 'test-elevation.R:84:3', 'test-enumeration.r:4:3', 'test-enumeration.r:23:3', 'test-gbif_geocode.R:3:5', 'test-gbif_geocode.R:60:3', 'test-gbif_issues_lookup.R:4:3', 'test-gbif_issues_lookup.R:39:3', 'test-gbif_names.R:4:3', 'test-gbif_names.R:28:3', 'test-gbif_photos.R:4:3', 'test-lit_search.R:5:5', 'test-lit_search.R:120:3', 'test-map_fetch.R:3:1', 'test-mvt_fetch.R:4:3', 'test-mvt_fetch.R:15:3', 'test-name_backbone.r:29:3', 'test-name_backbone_checklist.R:4:3', 'test-name_backbone_checklist.R:184:3', 'test-name_backbone_checklist.R:273:3', 'test-name_backbone_checklist.R:368:3', 'test-name_backbone_checklist.R:466:3', 'test-name_backbone_checklist.R:478:3', 'test-name_lookup.r:4:3', 'test-name_lookup.r:61:3', 'test-name_lookup.r:96:3', 'test-name_lookup.r:115:3', 'test-name_lookup.r:130:3', 'test-name_lookup.r:164:3', 'test-name_suggest.r:58:5', 'test-name_usage.r:4:3', 'test-occ_count.r:83:3', 'test-occ_data.R:7:3', 'test-occ_data.R:38:3', 'test-occ_data.R:71:3', 'test-occ_data.R:114:3', 'test-occ_data.R:188:3', 'test-occ_data.R:334:3', 'test-occ_data.R:348:3', 'test-occ_data.R:363:3', 'test-occ_data.R:381:3', 'test-occ_data.R:398:3', 'test-occ_data.R:415:3', 'test-occ_data.R:434:3', 'test-occ_data.R:451:3', 'test-occ_data.R:468:3', 'test-occ_data.R:485:3', 'test-occ_data.R:502:3', 'test-occ_data.R:519:3', 'test-occ_data.R:537:3', 'test-occ_data.R:555:3', 'test-occ_data.R:573:3', 'test-occ_data.R:588:3', 'test-occ_data.R:604:3', 'test-occ_download.R:13:3', 'test-occ_download_cached.R:10:3', 'test-occ_download_cached.R:75:3', 'test-occ_download_cached.R:115:3', 'test-occ_download_cancel.R:2:3', 'test-occ_download_cancel.R:19:3', 'test-occ_download_cancel.R:27:3', 'test-occ_download_dataset_activity.R:4:3', 'test-occ_download_dataset_activity.R:26:3', 'test-occ_download_datasets.R:4:3', 'test-occ_download_datasets.R:27:3', 'test-occ_download_get.R:2:3', 'test-occ_download_import.R:2:3', 'test-occ_download_import.R:17:3', 'test-occ_download_import.R:40:3', 'test-occ_download_import.R:57:3', 'test-occ_download_import.R:83:3', 'test-occ_download_list.R:10:3', 'test-occ_download_list.R:28:3', 'test-occ_download_list.R:51:3', 'test-occ_download_meta.R:2:3', 'test-occ_download_meta.R:37:3', 'test-occ_download_prep.R:2:3', 'test-occ_download_prep.R:37:3', 'test-occ_download_prep.R:54:3', 'test-occ_download_queue.R:14:3', 'test-occ_download_queue.R:36:3', 'test-occ_download_queue.R:77:3', 'test-occ_download_sql.R:3:3', 'test-occ_download_sql.R:17:3', 'test-occ_download_wait.R:2:3', 'test-occ_download_wait.R:21:3', 'test-occ_get.r:43:3', 'test-occ_search.r:7:3', 'test-occ_search.r:35:3', 'test-occ_search.r:67:3', 'test-occ_search.r:101:3', 'test-occ_search.r:114:3', 'test-occ_search.r:128:3', 'test-occ_search.r:143:3', 'test-occ_search.r:161:3', 'test-occ_search.r:178:3', 'test-occ_search.r:195:3', 'test-occ_search.r:214:3', 'test-occ_search.r:231:3', 'test-occ_search.r:248:3', 'test-occ_search.r:266:3', 'test-occ_search.r:283:3', 'test-occ_search.r:300:3', 'test-occ_search.r:318:3', 'test-occ_search.r:336:3', 'test-occ_search.r:354:3', 'test-occ_search.r:369:3', 'test-occ_search.r:386:3', 'test-occ_search.r:436:3', 'test-occ_search.r:510:3', 'test-organizations.r:4:3', 'test-organizations.r:67:3', 'test-print_gbif.R:4:3', 'test-print_gbif.R:23:3', 'test-wkt_large.R:36:3', 'test-wkt_large.R:72:3', 'test-wkt_large.R:91:3', 'test-wkt_parse.R:34:3' == Failed tests ================================================================ -- Error ('test-dataset.R:4:3'): dataset works as expected --------------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/dataset.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 25, column 27 Backtrace: x 1. \-vcr::use_cassette(...) at test-dataset.R:4:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-dataset_doi.R:4:3'): dataset_doi work as expected -------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/dataset_doi.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 34, column 10 Backtrace: x 1. \-vcr::use_cassette(...) at test-dataset_doi.R:4:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-dataset_uuid_funs.R:4:3'): dataset_uuid_funs work as expected -- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/dataset_uuid_funs.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 23, column 88 Backtrace: x 1. \-vcr::use_cassette(...) at test-dataset_uuid_funs.R:4:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-name_usage.r:103:3'): name_usage synonyms route works ---------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/name_usage_data_synonyms.yml) Scanner error: while scanning a quoted scalar at line 53, column 15 found unexpected end of stream at line 55, column 79 Backtrace: x 1. \-vcr::use_cassette(...) at test-name_usage.r:103:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-name_usage.r:170:3'): name_usage speciesProfiles route works --- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/name_usage_data_speciesProfiles.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 60, column 147 Backtrace: x 1. \-vcr::use_cassette(...) at test-name_usage.r:170:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-network.R:5:3'): returns the correct --------------------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/network.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 69, column 42 Backtrace: x 1. \-vcr::use_cassette(...) at test-network.R:5:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-occ_count_.R:4:3'): occ_count_ custom functions work ----------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/occ_count_.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 22, column 2126 Backtrace: x 1. \-vcr::use_cassette(...) at test-occ_count_.R:4:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-occ_data.R:95:3'): returns the correct stuff ------------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/occ_data_depth.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 25, column 12647 Backtrace: x 1. \-vcr::use_cassette(...) at test-occ_data.R:95:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Failure ('test-occ_data.R:179:3'): scientificName basic use works - no synonyms -- hh$data$scientificName[1] not equal to "Pipistrellus hesperus (H.Allen, 1864)". 1/1 mismatches x[1]: "Parastrellus hesperus (H.Allen, 1864)" y[1]: "Pipistrellus hesperus (H.Allen, 1864)" -- Error ('test-occ_search.r:415:3'): returns the correct stuff ---------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/occ_search_depth.yml) Scanner error: while scanning a quoted scalar at line 47, column 15 found unexpected end of stream at line 50, column 12647 Backtrace: x 1. \-vcr::use_cassette(...) at test-occ_search.r:415:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Failure ('test-occ_search.r:501:3'): scientificName basic use works - no synonyms -- hh$data$scientificName[1] not equal to "Pipistrellus hesperus (H.Allen, 1864)". 1/1 mismatches x[1]: "Parastrellus hesperus (H.Allen, 1864)" y[1]: "Pipistrellus hesperus (H.Allen, 1864)" [ FAIL 11 | WARN 349 | SKIP 136 | PASS 1166 ] Error: Test failures Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR See '/tmp/th798/21090361/R-devel/1213/rgbif.Rcheck/00check.log' for details. [1] "2025-08-23 01:14:26 MST" [1] "2025-08-23 01:14:26 MST" Installing package into '/tmp/th798/21090361/R-devel/1213/library' (as 'lib' is unspecified) Warning: invalid package '/scratch/th798/data.table-revdeps/2025-08-23/data.table_master_1.17.99.55bbc3d1646a80ba1d5b2c073c17b9575e7c186a.tar.gz' Error: ERROR: no packages specified [1] "2025-08-23 01:14:26 MST" * using log directory '/tmp/th798/21090361/R-devel/1213/rgbif.Rcheck' * using R Under development (unstable) (2025-08-22 r88678) * 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 * checking for file 'rgbif/DESCRIPTION' ... OK * this is package 'rgbif' version '3.8.2' * 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 'rgbif' 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 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 'test-all.R' ERROR Running the tests in 'tests/test-all.R' failed. Complete output: > library(testthat) > test_check("rgbif") Loading required package: rgbif [ FAIL 11 | WARN 349 | SKIP 136 | PASS 1166 ] == Skipped tests (136) ========================================================= * On CRAN (136): 'test-country_codes.r:4:3', 'test-dataset_export.R:3:1', 'test-dataset_gridded.R:3:1', 'test-dataset_uuid_funs.R:78:3', 'test-derived_dataset.R:3:3', 'test-derived_dataset.R:51:3', 'test-derived_dataset.R:186:3', 'test-derived_dataset.R:347:3', 'test-downloads.R:3:3', 'test-downloads.R:16:3', 'test-downloads.R:43:3', 'test-downloads.R:80:3', 'test-downloads.R:87:3', 'test-downloads.R:101:3', 'test-downloads.R:116:3', 'test-elevation.R:3:3', 'test-elevation.R:16:3', 'test-elevation.R:32:3', 'test-elevation.R:59:3', 'test-elevation.R:84:3', 'test-enumeration.r:4:3', 'test-enumeration.r:23:3', 'test-gbif_geocode.R:3:5', 'test-gbif_geocode.R:60:3', 'test-gbif_issues_lookup.R:4:3', 'test-gbif_issues_lookup.R:39:3', 'test-gbif_names.R:4:3', 'test-gbif_names.R:28:3', 'test-gbif_photos.R:4:3', 'test-lit_search.R:5:5', 'test-lit_search.R:120:3', 'test-map_fetch.R:3:1', 'test-mvt_fetch.R:4:3', 'test-mvt_fetch.R:15:3', 'test-name_backbone.r:29:3', 'test-name_backbone_checklist.R:4:3', 'test-name_backbone_checklist.R:184:3', 'test-name_backbone_checklist.R:273:3', 'test-name_backbone_checklist.R:368:3', 'test-name_backbone_checklist.R:466:3', 'test-name_backbone_checklist.R:478:3', 'test-name_lookup.r:4:3', 'test-name_lookup.r:61:3', 'test-name_lookup.r:96:3', 'test-name_lookup.r:115:3', 'test-name_lookup.r:130:3', 'test-name_lookup.r:164:3', 'test-name_suggest.r:58:5', 'test-name_usage.r:4:3', 'test-occ_count.r:83:3', 'test-occ_data.R:7:3', 'test-occ_data.R:38:3', 'test-occ_data.R:71:3', 'test-occ_data.R:114:3', 'test-occ_data.R:188:3', 'test-occ_data.R:334:3', 'test-occ_data.R:348:3', 'test-occ_data.R:363:3', 'test-occ_data.R:381:3', 'test-occ_data.R:398:3', 'test-occ_data.R:415:3', 'test-occ_data.R:434:3', 'test-occ_data.R:451:3', 'test-occ_data.R:468:3', 'test-occ_data.R:485:3', 'test-occ_data.R:502:3', 'test-occ_data.R:519:3', 'test-occ_data.R:537:3', 'test-occ_data.R:555:3', 'test-occ_data.R:573:3', 'test-occ_data.R:588:3', 'test-occ_data.R:604:3', 'test-occ_download.R:13:3', 'test-occ_download_cached.R:10:3', 'test-occ_download_cached.R:75:3', 'test-occ_download_cached.R:115:3', 'test-occ_download_cancel.R:2:3', 'test-occ_download_cancel.R:19:3', 'test-occ_download_cancel.R:27:3', 'test-occ_download_dataset_activity.R:4:3', 'test-occ_download_dataset_activity.R:26:3', 'test-occ_download_datasets.R:4:3', 'test-occ_download_datasets.R:27:3', 'test-occ_download_get.R:2:3', 'test-occ_download_import.R:2:3', 'test-occ_download_import.R:17:3', 'test-occ_download_import.R:40:3', 'test-occ_download_import.R:57:3', 'test-occ_download_import.R:83:3', 'test-occ_download_list.R:10:3', 'test-occ_download_list.R:28:3', 'test-occ_download_list.R:51:3', 'test-occ_download_meta.R:2:3', 'test-occ_download_meta.R:37:3', 'test-occ_download_prep.R:2:3', 'test-occ_download_prep.R:37:3', 'test-occ_download_prep.R:54:3', 'test-occ_download_queue.R:14:3', 'test-occ_download_queue.R:36:3', 'test-occ_download_queue.R:77:3', 'test-occ_download_sql.R:3:3', 'test-occ_download_sql.R:17:3', 'test-occ_download_wait.R:2:3', 'test-occ_download_wait.R:21:3', 'test-occ_get.r:43:3', 'test-occ_search.r:7:3', 'test-occ_search.r:35:3', 'test-occ_search.r:67:3', 'test-occ_search.r:101:3', 'test-occ_search.r:114:3', 'test-occ_search.r:128:3', 'test-occ_search.r:143:3', 'test-occ_search.r:161:3', 'test-occ_search.r:178:3', 'test-occ_search.r:195:3', 'test-occ_search.r:214:3', 'test-occ_search.r:231:3', 'test-occ_search.r:248:3', 'test-occ_search.r:266:3', 'test-occ_search.r:283:3', 'test-occ_search.r:300:3', 'test-occ_search.r:318:3', 'test-occ_search.r:336:3', 'test-occ_search.r:354:3', 'test-occ_search.r:369:3', 'test-occ_search.r:386:3', 'test-occ_search.r:436:3', 'test-occ_search.r:510:3', 'test-organizations.r:4:3', 'test-organizations.r:67:3', 'test-print_gbif.R:4:3', 'test-print_gbif.R:23:3', 'test-wkt_large.R:36:3', 'test-wkt_large.R:72:3', 'test-wkt_large.R:91:3', 'test-wkt_parse.R:34:3' == Failed tests ================================================================ -- Error ('test-dataset.R:4:3'): dataset works as expected --------------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/dataset.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 25, column 27 Backtrace: x 1. \-vcr::use_cassette(...) at test-dataset.R:4:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-dataset_doi.R:4:3'): dataset_doi work as expected -------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/dataset_doi.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 34, column 10 Backtrace: x 1. \-vcr::use_cassette(...) at test-dataset_doi.R:4:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-dataset_uuid_funs.R:4:3'): dataset_uuid_funs work as expected -- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/dataset_uuid_funs.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 23, column 88 Backtrace: x 1. \-vcr::use_cassette(...) at test-dataset_uuid_funs.R:4:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-name_usage.r:103:3'): name_usage synonyms route works ---------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/name_usage_data_synonyms.yml) Scanner error: while scanning a quoted scalar at line 53, column 15 found unexpected end of stream at line 55, column 79 Backtrace: x 1. \-vcr::use_cassette(...) at test-name_usage.r:103:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-name_usage.r:170:3'): name_usage speciesProfiles route works --- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/name_usage_data_speciesProfiles.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 60, column 147 Backtrace: x 1. \-vcr::use_cassette(...) at test-name_usage.r:170:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-network.R:5:3'): returns the correct --------------------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/network.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 69, column 42 Backtrace: x 1. \-vcr::use_cassette(...) at test-network.R:5:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-occ_count_.R:4:3'): occ_count_ custom functions work ----------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/occ_count_.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 22, column 2126 Backtrace: x 1. \-vcr::use_cassette(...) at test-occ_count_.R:4:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-occ_data.R:95:3'): returns the correct stuff ------------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/occ_data_depth.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 25, column 12647 Backtrace: x 1. \-vcr::use_cassette(...) at test-occ_data.R:95:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Failure ('test-occ_data.R:179:3'): scientificName basic use works - no synonyms -- hh$data$scientificName[1] not equal to "Pipistrellus hesperus (H.Allen, 1864)". 1/1 mismatches x[1]: "Parastrellus hesperus (H.Allen, 1864)" y[1]: "Pipistrellus hesperus (H.Allen, 1864)" -- Error ('test-occ_search.r:415:3'): returns the correct stuff ---------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/occ_search_depth.yml) Scanner error: while scanning a quoted scalar at line 47, column 15 found unexpected end of stream at line 50, column 12647 Backtrace: x 1. \-vcr::use_cassette(...) at test-occ_search.r:415:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Failure ('test-occ_search.r:501:3'): scientificName basic use works - no synonyms -- hh$data$scientificName[1] not equal to "Pipistrellus hesperus (H.Allen, 1864)". 1/1 mismatches x[1]: "Parastrellus hesperus (H.Allen, 1864)" y[1]: "Pipistrellus hesperus (H.Allen, 1864)" [ FAIL 11 | WARN 349 | SKIP 136 | PASS 1166 ] Error: Test failures Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR See '/tmp/th798/21090361/R-devel/1213/rgbif.Rcheck/00check.log' for details. [1] "2025-08-23 01:17:18 MST" Warning message: In install.packages(dt.tar.gz, repos = NULL) : installation of package '/scratch/th798/data.table-revdeps/2025-08-23/data.table_master_1.17.99.55bbc3d1646a80ba1d5b2c073c17b9575e7c186a.tar.gz' had non-zero exit status > system(paste(c("diff -u", Rcheck.list), collapse=" ")) > library(data.table, lib.loc=R.home("library")) > (sig.diff.dt <- myDiff(Rvers)) Key: Empty data.table (0 rows and 3 cols): checking,master,release > > ## If there are significant differences, use git bisect to find when > ## they started. > if(nrow(sig.diff.dt)){ + dt.git <- file.path(task.dir, "data.table.git") + system(paste("cd ~/R/data.table && git fetch --tags")) + system(paste("git clone ~/R/data.table", dt.git)) + release.tag <- gsub(".tar.gz|.*_", "", cargs[["release"]]) + rev.parse.cmd <- paste( + "cd", dt.git, "&& git rev-parse master") + master.sha <- system(rev.parse.cmd, intern=TRUE) + merge.base.cmd <- paste( + "cd", dt.git, "&& git merge-base master", release.tag) + merge.base.sha <- system(merge.base.cmd, intern=TRUE) + old.sha <- merge.base.sha + run_R <- file.path(proj.dir, "install_dt_then_check_dep.R") + sig.diff.dt[, first.bad.commit := NA_character_] + sig.diff.dt[, comments := NA_character_] + for(diff.i in 1:nrow(sig.diff.dt)){ + sig.diff.row <- sig.diff.dt[diff.i] + bisect.cmd <- paste( + "cd", dt.git, "&&", + "git bisect start &&", + "git bisect old", old.sha, "&&", + "git bisect new master &&", + "git bisect run", + R.home('bin/Rscript'), + run_R, + shQuote(sig.diff.row$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 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 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) > 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")), + "349", + 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/2025-08-23/deps.csv", task.str = "1213", release = "/scratch/th798/data.table-revdeps/2025-08-23/data.table_release_1.17.8.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-08-23/data.table_master_1.17.99.55bbc3d1646a80ba1d5b2c073c17b9575e7c186a.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/21090361/R-release/1213" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/21090361/R-release/1213/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "rgbif" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/21090361/R-release/1213/library" [2] "/projects/genomic-ml/R/R-release/library" > options(repos=c(#this should be in ~/.Rprofile too. + CRAN="http://cloud.r-project.org")) > print(Sys.time()) [1] "2025-08-23 01:17:24 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/21090361/R-release/1213/library' (as 'lib' is unspecified) also installing the dependencies 'curl', 'oai', 'vcr' trying URL 'http://cloud.r-project.org/src/contrib/curl_7.0.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/oai_0.4.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/vcr_2.0.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/rgbif_3.8.2.tar.gz' * installing *source* package 'curl' ... ** this is package 'curl' version '7.0.0' ** package 'curl' 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 -lcurl ** 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 -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 callbacks.c -o callbacks.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 curl.c -o curl.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 download.c -o download.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 dryrun.c -o dryrun.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 escape.c -o escape.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 fetch.c -o fetch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 findport.c -o findport.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 form.c -o form.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 getdate.c -o getdate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 handle.c -o handle.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 ieproxy.c -o ieproxy.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 interrupt.c -o interrupt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 multi.c -o multi.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 nslookup.c -o nslookup.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 options.c -o options.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 reflist.c -o reflist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 split.c -o split.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 ssl.c -o ssl.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 typechecking.c -o typechecking.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 urlparser.c -o urlparser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 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 -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 version.c -o version.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 winidn.c -o winidn.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -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 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 curl.so callbacks.o curl.o download.o dryrun.o escape.o fetch.o findport.o form.o getdate.o handle.o ieproxy.o init.o interrupt.o multi.o nslookup.o options.o reflist.o split.o ssl.o typechecking.o urlparser.o utils.o version.o winidn.o writer.o -L/home/th798/.conda/envs/emacs1/lib -lcurl installing to /tmp/th798/21090361/R-release/1213/library/00LOCK-curl/00new/curl/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 (curl) * installing *source* package 'oai' ... ** this is package 'oai' version '0.4.0' ** package 'oai' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (oai) * installing *source* package 'vcr' ... ** this is package 'vcr' version '2.0.0' ** package 'vcr' 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 (vcr) * installing *source* package 'rgbif' ... ** this is package 'rgbif' version '3.8.2' ** package 'rgbif' 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 (rgbif) The downloaded source packages are in '/tmp/th798/21090361/RtmpeS2hGF/downloaded_packages' > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 37.126 3.138 44.884 > print(Sys.time()) [1] "2025-08-23 01:18:09 MST" > downloaded_packages <- file.path( + tempdir(), + "downloaded_packages") > dl.glob <- file.path( + downloaded_packages, + paste0(rev.dep,"_*.tar.gz")) > rev.dep.dl.row <- cbind(rev.dep, Sys.glob(dl.glob)) > colnames(rev.dep.dl.row) <- c("pkg","path") > rev.dep.release.tar.gz <- normalizePath(rev.dep.dl.row[,"path"], mustWork=TRUE) > 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] "2025-08-23 01:18:09 MST" Installing package into '/tmp/th798/21090361/R-release/1213/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.17.8' ** 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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 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 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 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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 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 -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.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 installing to /tmp/th798/21090361/R-release/1213/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] "2025-08-23 01:18:33 MST" * using log directory '/tmp/th798/21090361/R-release/1213/rgbif.Rcheck' * using R version 4.5.1 (2025-06-13) * 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 * checking for file 'rgbif/DESCRIPTION' ... OK * this is package 'rgbif' version '3.8.2' * 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 'rgbif' 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 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 'test-all.R' ERROR Running the tests in 'tests/test-all.R' failed. Complete output: > library(testthat) > test_check("rgbif") Loading required package: rgbif [ FAIL 11 | WARN 349 | SKIP 136 | PASS 1166 ] == Skipped tests (136) ========================================================= * On CRAN (136): 'test-country_codes.r:4:3', 'test-dataset_export.R:3:1', 'test-dataset_gridded.R:3:1', 'test-dataset_uuid_funs.R:78:3', 'test-derived_dataset.R:3:3', 'test-derived_dataset.R:51:3', 'test-derived_dataset.R:186:3', 'test-derived_dataset.R:347:3', 'test-downloads.R:3:3', 'test-downloads.R:16:3', 'test-downloads.R:43:3', 'test-downloads.R:80:3', 'test-downloads.R:87:3', 'test-downloads.R:101:3', 'test-downloads.R:116:3', 'test-elevation.R:3:3', 'test-elevation.R:16:3', 'test-elevation.R:32:3', 'test-elevation.R:59:3', 'test-elevation.R:84:3', 'test-enumeration.r:4:3', 'test-enumeration.r:23:3', 'test-gbif_geocode.R:3:5', 'test-gbif_geocode.R:60:3', 'test-gbif_issues_lookup.R:4:3', 'test-gbif_issues_lookup.R:39:3', 'test-gbif_names.R:4:3', 'test-gbif_names.R:28:3', 'test-gbif_photos.R:4:3', 'test-lit_search.R:5:5', 'test-lit_search.R:120:3', 'test-map_fetch.R:3:1', 'test-mvt_fetch.R:4:3', 'test-mvt_fetch.R:15:3', 'test-name_backbone.r:29:3', 'test-name_backbone_checklist.R:4:3', 'test-name_backbone_checklist.R:184:3', 'test-name_backbone_checklist.R:273:3', 'test-name_backbone_checklist.R:368:3', 'test-name_backbone_checklist.R:466:3', 'test-name_backbone_checklist.R:478:3', 'test-name_lookup.r:4:3', 'test-name_lookup.r:61:3', 'test-name_lookup.r:96:3', 'test-name_lookup.r:115:3', 'test-name_lookup.r:130:3', 'test-name_lookup.r:164:3', 'test-name_suggest.r:58:5', 'test-name_usage.r:4:3', 'test-occ_count.r:83:3', 'test-occ_data.R:7:3', 'test-occ_data.R:38:3', 'test-occ_data.R:71:3', 'test-occ_data.R:114:3', 'test-occ_data.R:188:3', 'test-occ_data.R:334:3', 'test-occ_data.R:348:3', 'test-occ_data.R:363:3', 'test-occ_data.R:381:3', 'test-occ_data.R:398:3', 'test-occ_data.R:415:3', 'test-occ_data.R:434:3', 'test-occ_data.R:451:3', 'test-occ_data.R:468:3', 'test-occ_data.R:485:3', 'test-occ_data.R:502:3', 'test-occ_data.R:519:3', 'test-occ_data.R:537:3', 'test-occ_data.R:555:3', 'test-occ_data.R:573:3', 'test-occ_data.R:588:3', 'test-occ_data.R:604:3', 'test-occ_download.R:13:3', 'test-occ_download_cached.R:10:3', 'test-occ_download_cached.R:75:3', 'test-occ_download_cached.R:115:3', 'test-occ_download_cancel.R:2:3', 'test-occ_download_cancel.R:19:3', 'test-occ_download_cancel.R:27:3', 'test-occ_download_dataset_activity.R:4:3', 'test-occ_download_dataset_activity.R:26:3', 'test-occ_download_datasets.R:4:3', 'test-occ_download_datasets.R:27:3', 'test-occ_download_get.R:2:3', 'test-occ_download_import.R:2:3', 'test-occ_download_import.R:17:3', 'test-occ_download_import.R:40:3', 'test-occ_download_import.R:57:3', 'test-occ_download_import.R:83:3', 'test-occ_download_list.R:10:3', 'test-occ_download_list.R:28:3', 'test-occ_download_list.R:51:3', 'test-occ_download_meta.R:2:3', 'test-occ_download_meta.R:37:3', 'test-occ_download_prep.R:2:3', 'test-occ_download_prep.R:37:3', 'test-occ_download_prep.R:54:3', 'test-occ_download_queue.R:14:3', 'test-occ_download_queue.R:36:3', 'test-occ_download_queue.R:77:3', 'test-occ_download_sql.R:3:3', 'test-occ_download_sql.R:17:3', 'test-occ_download_wait.R:2:3', 'test-occ_download_wait.R:21:3', 'test-occ_get.r:43:3', 'test-occ_search.r:7:3', 'test-occ_search.r:35:3', 'test-occ_search.r:67:3', 'test-occ_search.r:101:3', 'test-occ_search.r:114:3', 'test-occ_search.r:128:3', 'test-occ_search.r:143:3', 'test-occ_search.r:161:3', 'test-occ_search.r:178:3', 'test-occ_search.r:195:3', 'test-occ_search.r:214:3', 'test-occ_search.r:231:3', 'test-occ_search.r:248:3', 'test-occ_search.r:266:3', 'test-occ_search.r:283:3', 'test-occ_search.r:300:3', 'test-occ_search.r:318:3', 'test-occ_search.r:336:3', 'test-occ_search.r:354:3', 'test-occ_search.r:369:3', 'test-occ_search.r:386:3', 'test-occ_search.r:436:3', 'test-occ_search.r:510:3', 'test-organizations.r:4:3', 'test-organizations.r:67:3', 'test-print_gbif.R:4:3', 'test-print_gbif.R:23:3', 'test-wkt_large.R:36:3', 'test-wkt_large.R:72:3', 'test-wkt_large.R:91:3', 'test-wkt_parse.R:34:3' == Failed tests ================================================================ -- Error ('test-dataset.R:4:3'): dataset works as expected --------------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/dataset.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 25, column 27 Backtrace: x 1. \-vcr::use_cassette(...) at test-dataset.R:4:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-dataset_doi.R:4:3'): dataset_doi work as expected -------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/dataset_doi.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 34, column 10 Backtrace: x 1. \-vcr::use_cassette(...) at test-dataset_doi.R:4:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-dataset_uuid_funs.R:4:3'): dataset_uuid_funs work as expected -- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/dataset_uuid_funs.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 23, column 88 Backtrace: x 1. \-vcr::use_cassette(...) at test-dataset_uuid_funs.R:4:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-name_usage.r:103:3'): name_usage synonyms route works ---------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/name_usage_data_synonyms.yml) Scanner error: while scanning a quoted scalar at line 53, column 15 found unexpected end of stream at line 55, column 79 Backtrace: x 1. \-vcr::use_cassette(...) at test-name_usage.r:103:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-name_usage.r:170:3'): name_usage speciesProfiles route works --- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/name_usage_data_speciesProfiles.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 60, column 147 Backtrace: x 1. \-vcr::use_cassette(...) at test-name_usage.r:170:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-network.R:5:3'): returns the correct --------------------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/network.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 69, column 42 Backtrace: x 1. \-vcr::use_cassette(...) at test-network.R:5:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-occ_count_.R:4:3'): occ_count_ custom functions work ----------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/occ_count_.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 22, column 2126 Backtrace: x 1. \-vcr::use_cassette(...) at test-occ_count_.R:4:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-occ_data.R:95:3'): returns the correct stuff ------------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/occ_data_depth.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 25, column 12647 Backtrace: x 1. \-vcr::use_cassette(...) at test-occ_data.R:95:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Failure ('test-occ_data.R:179:3'): scientificName basic use works - no synonyms -- hh$data$scientificName[1] not equal to "Pipistrellus hesperus (H.Allen, 1864)". 1/1 mismatches x[1]: "Parastrellus hesperus (H.Allen, 1864)" y[1]: "Pipistrellus hesperus (H.Allen, 1864)" -- Error ('test-occ_search.r:415:3'): returns the correct stuff ---------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/occ_search_depth.yml) Scanner error: while scanning a quoted scalar at line 47, column 15 found unexpected end of stream at line 50, column 12647 Backtrace: x 1. \-vcr::use_cassette(...) at test-occ_search.r:415:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Failure ('test-occ_search.r:501:3'): scientificName basic use works - no synonyms -- hh$data$scientificName[1] not equal to "Pipistrellus hesperus (H.Allen, 1864)". 1/1 mismatches x[1]: "Parastrellus hesperus (H.Allen, 1864)" y[1]: "Pipistrellus hesperus (H.Allen, 1864)" [ FAIL 11 | WARN 349 | SKIP 136 | PASS 1166 ] Error: Test failures Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR See '/tmp/th798/21090361/R-release/1213/rgbif.Rcheck/00check.log' for details. [1] "2025-08-23 01:21:36 MST" [1] "2025-08-23 01:21:36 MST" Installing package into '/tmp/th798/21090361/R-release/1213/library' (as 'lib' is unspecified) Warning: invalid package '/scratch/th798/data.table-revdeps/2025-08-23/data.table_master_1.17.99.55bbc3d1646a80ba1d5b2c073c17b9575e7c186a.tar.gz' Error: ERROR: no packages specified [1] "2025-08-23 01:21:36 MST" * using log directory '/tmp/th798/21090361/R-release/1213/rgbif.Rcheck' * using R version 4.5.1 (2025-06-13) * 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 * checking for file 'rgbif/DESCRIPTION' ... OK * this is package 'rgbif' version '3.8.2' * 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 'rgbif' 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 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 'test-all.R' ERROR Running the tests in 'tests/test-all.R' failed. Complete output: > library(testthat) > test_check("rgbif") Loading required package: rgbif [ FAIL 11 | WARN 349 | SKIP 136 | PASS 1166 ] == Skipped tests (136) ========================================================= * On CRAN (136): 'test-country_codes.r:4:3', 'test-dataset_export.R:3:1', 'test-dataset_gridded.R:3:1', 'test-dataset_uuid_funs.R:78:3', 'test-derived_dataset.R:3:3', 'test-derived_dataset.R:51:3', 'test-derived_dataset.R:186:3', 'test-derived_dataset.R:347:3', 'test-downloads.R:3:3', 'test-downloads.R:16:3', 'test-downloads.R:43:3', 'test-downloads.R:80:3', 'test-downloads.R:87:3', 'test-downloads.R:101:3', 'test-downloads.R:116:3', 'test-elevation.R:3:3', 'test-elevation.R:16:3', 'test-elevation.R:32:3', 'test-elevation.R:59:3', 'test-elevation.R:84:3', 'test-enumeration.r:4:3', 'test-enumeration.r:23:3', 'test-gbif_geocode.R:3:5', 'test-gbif_geocode.R:60:3', 'test-gbif_issues_lookup.R:4:3', 'test-gbif_issues_lookup.R:39:3', 'test-gbif_names.R:4:3', 'test-gbif_names.R:28:3', 'test-gbif_photos.R:4:3', 'test-lit_search.R:5:5', 'test-lit_search.R:120:3', 'test-map_fetch.R:3:1', 'test-mvt_fetch.R:4:3', 'test-mvt_fetch.R:15:3', 'test-name_backbone.r:29:3', 'test-name_backbone_checklist.R:4:3', 'test-name_backbone_checklist.R:184:3', 'test-name_backbone_checklist.R:273:3', 'test-name_backbone_checklist.R:368:3', 'test-name_backbone_checklist.R:466:3', 'test-name_backbone_checklist.R:478:3', 'test-name_lookup.r:4:3', 'test-name_lookup.r:61:3', 'test-name_lookup.r:96:3', 'test-name_lookup.r:115:3', 'test-name_lookup.r:130:3', 'test-name_lookup.r:164:3', 'test-name_suggest.r:58:5', 'test-name_usage.r:4:3', 'test-occ_count.r:83:3', 'test-occ_data.R:7:3', 'test-occ_data.R:38:3', 'test-occ_data.R:71:3', 'test-occ_data.R:114:3', 'test-occ_data.R:188:3', 'test-occ_data.R:334:3', 'test-occ_data.R:348:3', 'test-occ_data.R:363:3', 'test-occ_data.R:381:3', 'test-occ_data.R:398:3', 'test-occ_data.R:415:3', 'test-occ_data.R:434:3', 'test-occ_data.R:451:3', 'test-occ_data.R:468:3', 'test-occ_data.R:485:3', 'test-occ_data.R:502:3', 'test-occ_data.R:519:3', 'test-occ_data.R:537:3', 'test-occ_data.R:555:3', 'test-occ_data.R:573:3', 'test-occ_data.R:588:3', 'test-occ_data.R:604:3', 'test-occ_download.R:13:3', 'test-occ_download_cached.R:10:3', 'test-occ_download_cached.R:75:3', 'test-occ_download_cached.R:115:3', 'test-occ_download_cancel.R:2:3', 'test-occ_download_cancel.R:19:3', 'test-occ_download_cancel.R:27:3', 'test-occ_download_dataset_activity.R:4:3', 'test-occ_download_dataset_activity.R:26:3', 'test-occ_download_datasets.R:4:3', 'test-occ_download_datasets.R:27:3', 'test-occ_download_get.R:2:3', 'test-occ_download_import.R:2:3', 'test-occ_download_import.R:17:3', 'test-occ_download_import.R:40:3', 'test-occ_download_import.R:57:3', 'test-occ_download_import.R:83:3', 'test-occ_download_list.R:10:3', 'test-occ_download_list.R:28:3', 'test-occ_download_list.R:51:3', 'test-occ_download_meta.R:2:3', 'test-occ_download_meta.R:37:3', 'test-occ_download_prep.R:2:3', 'test-occ_download_prep.R:37:3', 'test-occ_download_prep.R:54:3', 'test-occ_download_queue.R:14:3', 'test-occ_download_queue.R:36:3', 'test-occ_download_queue.R:77:3', 'test-occ_download_sql.R:3:3', 'test-occ_download_sql.R:17:3', 'test-occ_download_wait.R:2:3', 'test-occ_download_wait.R:21:3', 'test-occ_get.r:43:3', 'test-occ_search.r:7:3', 'test-occ_search.r:35:3', 'test-occ_search.r:67:3', 'test-occ_search.r:101:3', 'test-occ_search.r:114:3', 'test-occ_search.r:128:3', 'test-occ_search.r:143:3', 'test-occ_search.r:161:3', 'test-occ_search.r:178:3', 'test-occ_search.r:195:3', 'test-occ_search.r:214:3', 'test-occ_search.r:231:3', 'test-occ_search.r:248:3', 'test-occ_search.r:266:3', 'test-occ_search.r:283:3', 'test-occ_search.r:300:3', 'test-occ_search.r:318:3', 'test-occ_search.r:336:3', 'test-occ_search.r:354:3', 'test-occ_search.r:369:3', 'test-occ_search.r:386:3', 'test-occ_search.r:436:3', 'test-occ_search.r:510:3', 'test-organizations.r:4:3', 'test-organizations.r:67:3', 'test-print_gbif.R:4:3', 'test-print_gbif.R:23:3', 'test-wkt_large.R:36:3', 'test-wkt_large.R:72:3', 'test-wkt_large.R:91:3', 'test-wkt_parse.R:34:3' == Failed tests ================================================================ -- Error ('test-dataset.R:4:3'): dataset works as expected --------------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/dataset.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 25, column 27 Backtrace: x 1. \-vcr::use_cassette(...) at test-dataset.R:4:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-dataset_doi.R:4:3'): dataset_doi work as expected -------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/dataset_doi.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 34, column 10 Backtrace: x 1. \-vcr::use_cassette(...) at test-dataset_doi.R:4:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-dataset_uuid_funs.R:4:3'): dataset_uuid_funs work as expected -- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/dataset_uuid_funs.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 23, column 88 Backtrace: x 1. \-vcr::use_cassette(...) at test-dataset_uuid_funs.R:4:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-name_usage.r:103:3'): name_usage synonyms route works ---------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/name_usage_data_synonyms.yml) Scanner error: while scanning a quoted scalar at line 53, column 15 found unexpected end of stream at line 55, column 79 Backtrace: x 1. \-vcr::use_cassette(...) at test-name_usage.r:103:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-name_usage.r:170:3'): name_usage speciesProfiles route works --- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/name_usage_data_speciesProfiles.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 60, column 147 Backtrace: x 1. \-vcr::use_cassette(...) at test-name_usage.r:170:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-network.R:5:3'): returns the correct --------------------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/network.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 69, column 42 Backtrace: x 1. \-vcr::use_cassette(...) at test-network.R:5:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-occ_count_.R:4:3'): occ_count_ custom functions work ----------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/occ_count_.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 22, column 2126 Backtrace: x 1. \-vcr::use_cassette(...) at test-occ_count_.R:4:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Error ('test-occ_data.R:95:3'): returns the correct stuff ------------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/occ_data_depth.yml) Scanner error: while scanning a quoted scalar at line 22, column 15 found unexpected end of stream at line 25, column 12647 Backtrace: x 1. \-vcr::use_cassette(...) at test-occ_data.R:95:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Failure ('test-occ_data.R:179:3'): scientificName basic use works - no synonyms -- hh$data$scientificName[1] not equal to "Pipistrellus hesperus (H.Allen, 1864)". 1/1 mismatches x[1]: "Parastrellus hesperus (H.Allen, 1864)" y[1]: "Pipistrellus hesperus (H.Allen, 1864)" -- Error ('test-occ_search.r:415:3'): returns the correct stuff ---------------- Error in `yaml.load(string, error.label = error.label, ...)`: (../fixtures/occ_search_depth.yml) Scanner error: while scanning a quoted scalar at line 47, column 15 found unexpected end of stream at line 50, column 12647 Backtrace: x 1. \-vcr::use_cassette(...) at test-occ_search.r:415:3 2. \-vcr::local_cassette(...) 3. \-vcr::insert_cassette(...) 4. +-base::withCallingHandlers(cassette$insert(), error = function(e) cassette_pop()) 5. \-cassette$insert() 6. \-self$serializer$deserialize() 7. \-yaml::read_yaml(self$path) 8. \-yaml::yaml.load(string, error.label = error.label, ...) -- Failure ('test-occ_search.r:501:3'): scientificName basic use works - no synonyms -- hh$data$scientificName[1] not equal to "Pipistrellus hesperus (H.Allen, 1864)". 1/1 mismatches x[1]: "Parastrellus hesperus (H.Allen, 1864)" y[1]: "Pipistrellus hesperus (H.Allen, 1864)" [ FAIL 11 | WARN 349 | SKIP 136 | PASS 1166 ] Error: Test failures Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR See '/tmp/th798/21090361/R-release/1213/rgbif.Rcheck/00check.log' for details. [1] "2025-08-23 01:24:08 MST" Warning message: In install.packages(dt.tar.gz, repos = NULL) : installation of package '/scratch/th798/data.table-revdeps/2025-08-23/data.table_master_1.17.99.55bbc3d1646a80ba1d5b2c073c17b9575e7c186a.tar.gz' had non-zero exit status > system(paste(c("diff -u", Rcheck.list), collapse=" ")) > library(data.table, lib.loc=R.home("library")) > (sig.diff.dt <- myDiff(Rvers)) Key: Empty data.table (0 rows and 3 cols): checking,master,release > > ## If there are significant differences, use git bisect to find when > ## they started. > if(nrow(sig.diff.dt)){ + dt.git <- file.path(task.dir, "data.table.git") + system(paste("cd ~/R/data.table && git fetch --tags")) + system(paste("git clone ~/R/data.table", dt.git)) + release.tag <- gsub(".tar.gz|.*_", "", cargs[["release"]]) + rev.parse.cmd <- paste( + "cd", dt.git, "&& git rev-parse master") + master.sha <- system(rev.parse.cmd, intern=TRUE) + merge.base.cmd <- paste( + "cd", dt.git, "&& git merge-base master", release.tag) + merge.base.sha <- system(merge.base.cmd, intern=TRUE) + old.sha <- merge.base.sha + run_R <- file.path(proj.dir, "install_dt_then_check_dep.R") + sig.diff.dt[, first.bad.commit := NA_character_] + sig.diff.dt[, comments := NA_character_] + for(diff.i in 1:nrow(sig.diff.dt)){ + sig.diff.row <- sig.diff.dt[diff.i] + bisect.cmd <- paste( + "cd", dt.git, "&&", + "git bisect start &&", + "git bisect old", old.sha, "&&", + "git bisect new master &&", + "git bisect run", + R.home('bin/Rscript'), + run_R, + shQuote(sig.diff.row$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) + } >