Note: the module "R" cannot be unloaded because it was not loaded. WARNING: ignoring environment value of R_HOME R Under development (unstable) (2025-12-13 r89166) -- "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/2025-12-14/deps.csv", task.str = "1472", release = "/scratch/th798/data.table-revdeps/2025-12-14/data.table_release_1.17.8.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-12-14/data.table_master_1.17.99.6329d94b83b72bb1f05dc2a10374e84a61ff950d.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/25892134/R-devel/1472" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/25892134/R-devel/1472/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "tcpl" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/25892134/R-devel/1472/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] "2025-12-14 01:25:30 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/25892134/R-devel/1472/library' (as 'lib' is unspecified) also installing the dependencies 'later', 'triebeard', 'V8', 'htmlwidgets', 'promises', 'scales', 'urltools', 'bigD', 'juicyjuice', 'reactable', 'xfun', 'yaml', 'plyr', 'Rcpp', 'bookdown', 'plotly', 'tcplfit2', 'ggplot2', 'ctxR', 'gt', 'roxygen2', 'knitr', 'prettydoc', 'rmarkdown', 'htmlTable', 'reshape2', 'kableExtra', 'vdiffr', 'httptest', 'rmdformats' trying URL 'http://cloud.r-project.org/src/contrib/later_1.4.4.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/triebeard_0.4.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/V8_8.0.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/htmlwidgets_1.6.4.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/promises_1.5.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/scales_1.4.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/urltools_1.7.3.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/bigD_0.3.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/juicyjuice_0.1.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/reactable_0.4.5.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/xfun_0.54.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/yaml_2.3.12.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/plyr_1.8.9.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/4.6.0/Other/Rcpp_1.1.0.8.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/bookdown_0.46.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/plotly_4.11.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/tcplfit2_0.1.9.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/ggplot2_4.0.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/ctxR_1.1.3.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/gt_1.1.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/roxygen2_7.3.3.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/knitr_1.50.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/prettydoc_0.4.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/rmarkdown_2.30.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/htmlTable_2.4.3.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/reshape2_1.4.5.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/kableExtra_1.4.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/vdiffr_1.0.8.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/httptest_4.2.3.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/rmdformats_1.0.4.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/tcpl_3.3.1.tar.gz' * installing *source* package 'scales' ... ** this is package 'scales' version '1.4.0' ** package 'scales' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scales) * installing *source* package 'bigD' ... ** this is package 'bigD' version '0.3.1' ** package 'bigD' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bigD) * installing *source* package 'xfun' ... ** this is package 'xfun' version '0.54' ** package 'xfun' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c base64.c -o base64.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rand_lcg.c -o rand_lcg.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o xfun.so base64.o init.o rand_lcg.o installing to /tmp/th798/25892134/R-devel/1472/library/00LOCK-xfun/00new/xfun/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (xfun) * installing *source* package 'yaml' ... ** this is package 'yaml' version '2.3.12' ** package 'yaml' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c api.c -o api.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dumper.c -o dumper.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c emitter.c -o emitter.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c implicit.c -o implicit.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c loader.c -o loader.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c parser.c -o parser.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c r_emit.c -o r_emit.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c r_ext.c -o r_ext.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c r_parse.c -o r_parse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c reader.c -o reader.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c scanner.c -o scanner.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I. -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c writer.c -o writer.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o yaml.so api.o dumper.o emitter.o implicit.o loader.o parser.o r_emit.o r_ext.o r_parse.o reader.o scanner.o writer.o installing to /tmp/th798/25892134/R-devel/1472/library/00LOCK-yaml/00new/yaml/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (yaml) * installing *source* package 'Rcpp' ... ** this is package 'Rcpp' version '1.1.0.8.1' ** package 'Rcpp' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c api.cpp -o api.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c attributes.cpp -o attributes.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c barrier.cpp -o barrier.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c date.cpp -o date.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c module.cpp -o module.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/include/ -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rcpp_init.cpp -o rcpp_init.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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 Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o installing to /tmp/th798/25892134/R-devel/1472/library/00LOCK-Rcpp/00new/Rcpp/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 (Rcpp) * installing *source* package 'vdiffr' ... ** this is package 'vdiffr' version '1.0.8' ** package 'vdiffr' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: 'g++ (Spack GCC) 12.2.0' using C++11 /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c compare.cpp -o compare.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cpp11.cpp -o cpp11.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c devSVG.cpp -o devSVG.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c engine_version.cpp -o engine_version.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -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 vdiffr.so compare.o cpp11.o devSVG.o engine_version.o -lpng -lz installing to /tmp/th798/25892134/R-devel/1472/library/00LOCK-vdiffr/00new/vdiffr/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (vdiffr) * installing *source* package 'httptest' ... ** this is package 'httptest' version '4.2.3' ** package 'httptest' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (httptest) * installing *source* package 'later' ... ** this is package 'later' version '1.4.4' ** package 'later' successfully unpacked and MD5 sums checked ** using staged installation Running configure script -latomic linker flag not needed. ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RcppExports.cpp -o RcppExports.o In file included from /tmp/th798/25892134/R-devel/1472/library/Rcpp/include/RcppCommon.h:30, from /tmp/th798/25892134/R-devel/1472/library/Rcpp/include/Rcpp.h:27, from RcppExports.cpp:5: /tmp/th798/25892134/R-devel/1472/library/Rcpp/include/Rcpp/r/check_r_headers.h:35:21: note: '#pragma message: Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410' 35 | #pragma message "Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c callback_registry.cpp -o callback_registry.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c debug.cpp -o debug.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fd.cpp -o fd.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c later.cpp -o later.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c later_posix.cpp -o later_posix.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c later_win32.cpp -o later_win32.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c timer_posix.cpp -o timer_posix.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c timestamp_unix.cpp -o timestamp_unix.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c timestamp_win32.cpp -o timestamp_win32.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c tinycthread.c -o tinycthread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -DRCPP_NO_MODULES -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wref.c -o wref.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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 later.so RcppExports.o callback_registry.o debug.o fd.o init.o later.o later_posix.o later_win32.o timer_posix.o timestamp_unix.o timestamp_win32.o tinycthread.o wref.o -pthread installing to /tmp/th798/25892134/R-devel/1472/library/00LOCK-later/00new/later/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 (later) * installing *source* package 'triebeard' ... ** this is package 'triebeard' version '0.4.1' ** package 'triebeard' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I../inst/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RcppExports.cpp -o RcppExports.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I../inst/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c alter.cpp -o alter.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I../inst/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c create.cpp -o create.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I../inst/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c get.cpp -o get.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I../inst/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c greedy_match.cpp -o greedy_match.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I../inst/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c length.cpp -o length.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I../inst/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c longest_match.cpp -o longest_match.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I../inst/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c prefix_match.cpp -o prefix_match.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -I../inst/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c str.cpp -o str.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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 triebeard.so RcppExports.o alter.o create.o get.o greedy_match.o length.o longest_match.o prefix_match.o str.o installing to /tmp/th798/25892134/R-devel/1472/library/00LOCK-triebeard/00new/triebeard/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 (triebeard) * installing *source* package 'V8' ... ** this is package 'V8' version '8.0.1' ** package 'V8' successfully unpacked and MD5 sums checked ** using staged installation Found C++20 compiler: /packages/gcc/12.2.0-nnbserq/bin/g++ Target architecture: amd64 Getting bundle: v8-rocky-8-amd64.tar.gz Using CXXCPP=/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -E Using PKG_CFLAGS=-I/tmp/th798/25892134/RtmpohPOTu/R.INSTALL24c25b6600c3cd/V8/.deps/include Using PKG_LIBS=-L/tmp/th798/25892134/RtmpohPOTu/R.INSTALL24c25b6600c3cd/V8/.deps/lib -lv8_monolith Running feature test for pointer compression... Enabling pointer compression Running feature test for sandbox... Sandbox not enabled ** libs using C++ compiler: 'g++ (Spack GCC) 12.2.0' using C++20 /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/tmp/th798/25892134/RtmpohPOTu/R.INSTALL24c25b6600c3cd/V8/.deps/include -DV8_COMPRESS_POINTERS -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RcppExports.cpp -o RcppExports.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/tmp/th798/25892134/RtmpohPOTu/R.INSTALL24c25b6600c3cd/V8/.deps/include -DV8_COMPRESS_POINTERS -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bindings.cpp -o bindings.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++20 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o V8.so RcppExports.o bindings.o -L/tmp/th798/25892134/RtmpohPOTu/R.INSTALL24c25b6600c3cd/V8/.deps/lib -lv8_monolith installing to /tmp/th798/25892134/R-devel/1472/library/00LOCK-V8/00new/V8/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 (V8) * installing *source* package 'plyr' ... ** this is package 'plyr' version '1.8.9' ** package 'plyr' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RcppExports.cpp -o RcppExports.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c loop_apply.c -o loop_apply.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c split-numeric.cpp -o split-numeric.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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 plyr.so RcppExports.o loop_apply.o split-numeric.o installing to /tmp/th798/25892134/R-devel/1472/library/00LOCK-plyr/00new/plyr/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (plyr) * installing *source* package 'ggplot2' ... ** this is package 'ggplot2' version '4.0.1' ** package 'ggplot2' 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 (ggplot2) * installing *source* package 'knitr' ... ** this is package 'knitr' version '1.50' ** package 'knitr' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (knitr) * installing *source* package 'promises' ... ** this is package 'promises' version '1.5.0' ** package 'promises' 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 (promises) * installing *source* package 'urltools' ... ** this is package 'urltools' version '1.7.3.1' ** package 'urltools' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RcppExports.cpp -o RcppExports.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c compose.cpp -o compose.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c credentials.cpp -o credentials.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c encoding.cpp -o encoding.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c parameter.cpp -o parameter.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c parsing.cpp -o parsing.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c puny.cpp -o puny.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c punycode.c -o punycode.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c suffix.cpp -o suffix.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utf8.c -o utf8.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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 urltools.so RcppExports.o compose.o credentials.o encoding.o parameter.o parsing.o puny.o punycode.o suffix.o utf8.o installing to /tmp/th798/25892134/R-devel/1472/library/00LOCK-urltools/00new/urltools/libs ** R ** data *** moving datasets to lazyload DB ** 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 (urltools) * installing *source* package 'juicyjuice' ... ** this is package 'juicyjuice' version '0.1.0' ** package 'juicyjuice' 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 (juicyjuice) * installing *source* package 'roxygen2' ... ** this is package 'roxygen2' version '7.3.3' ** package 'roxygen2' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cpp11.cpp -o cpp11.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c escapeExamples.cpp -o escapeExamples.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c isComplete.cpp -o isComplete.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c leadingSpaces.cpp -o leadingSpaces.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c parser2.cpp -o parser2.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wrapUsage.cpp -o wrapUsage.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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 roxygen2.so cpp11.o escapeExamples.o isComplete.o leadingSpaces.o parser2.o wrapUsage.o installing to /tmp/th798/25892134/R-devel/1472/library/00LOCK-roxygen2/00new/roxygen2/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (roxygen2) * installing *source* package 'rmarkdown' ... ** this is package 'rmarkdown' version '2.30' ** package 'rmarkdown' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rmarkdown) * installing *source* package 'reshape2' ... ** this is package 'reshape2' version '1.4.5' ** package 'reshape2' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: 'g++ (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c RcppExports.cpp -o RcppExports.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I'/tmp/th798/25892134/R-devel/1472/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c melt.cpp -o melt.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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 reshape2.so RcppExports.o melt.o installing to /tmp/th798/25892134/R-devel/1472/library/00LOCK-reshape2/00new/reshape2/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (reshape2) * installing *source* package 'htmlwidgets' ... ** this is package 'htmlwidgets' version '1.6.4' ** package 'htmlwidgets' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (htmlwidgets) * installing *source* package 'bookdown' ... ** this is package 'bookdown' version '0.46' ** package 'bookdown' 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 (bookdown) * installing *source* package 'tcplfit2' ... ** this is package 'tcplfit2' version '0.1.9' ** package 'tcplfit2' 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 ** 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 (tcplfit2) * installing *source* package 'ctxR' ... ** this is package 'ctxR' version '1.1.3' ** package 'ctxR' 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 Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/projects/genomic-ml/R/R-devel/library/data.table/libs/data_table.so': /projects/genomic-ml/R/R-devel/library/data.table/libs/data_table.so: undefined symbol: Rf_GetOption Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package 'ctxR' * removing '/tmp/th798/25892134/R-devel/1472/library/ctxR' * installing *source* package 'prettydoc' ... ** this is package 'prettydoc' version '0.4.1' ** package 'prettydoc' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (prettydoc) * installing *source* package 'kableExtra' ... ** this is package 'kableExtra' version '1.4.0' ** package 'kableExtra' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (kableExtra) * installing *source* package 'reactable' ... ** this is package 'reactable' version '0.4.5' ** package 'reactable' 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 (reactable) * installing *source* package 'plotly' ... ** this is package 'plotly' version '4.11.0' ** package 'plotly' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/projects/genomic-ml/R/R-devel/library/data.table/libs/data_table.so': /projects/genomic-ml/R/R-devel/library/data.table/libs/data_table.so: undefined symbol: Rf_GetOption Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package 'plotly' * removing '/tmp/th798/25892134/R-devel/1472/library/plotly' * installing *source* package 'htmlTable' ... ** this is package 'htmlTable' version '2.4.3' ** package 'htmlTable' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (htmlTable) * installing *source* package 'rmdformats' ... ** this is package 'rmdformats' version '1.0.4' ** package 'rmdformats' 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 (rmdformats) * installing *source* package 'gt' ... ** this is package 'gt' version '1.1.0' ** package 'gt' 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 Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/projects/genomic-ml/R/R-devel/library/fansi/libs/fansi.so': /projects/genomic-ml/R/R-devel/library/fansi/libs/fansi.so: undefined symbol: R_nchar Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Execution halted ERROR: lazy loading failed for package 'gt' * removing '/tmp/th798/25892134/R-devel/1472/library/gt' ERROR: dependencies 'plotly', 'ctxR', 'gt' are not available for package 'tcpl' Perhaps try a variation of: install.packages(c('plotly', 'ctxR', 'gt')) * removing '/tmp/th798/25892134/R-devel/1472/library/tcpl' The downloaded source packages are in '/tmp/th798/25892134/RtmpDJEQnu/downloaded_packages' Warning messages: 1: In install.packages(rev.dep, dep = TRUE) : installation of package 'ctxR' had non-zero exit status 2: In install.packages(rev.dep, dep = TRUE) : installation of package 'plotly' had non-zero exit status 3: In install.packages(rev.dep, dep = TRUE) : installation of package 'gt' had non-zero exit status 4: In install.packages(rev.dep, dep = TRUE) : installation of package 'tcpl' had non-zero exit status > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 264.872 19.529 398.632 > print(Sys.time()) [1] "2025-12-14 01:32:09 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] "2025-12-14 01:32:09 MST" Installing package into '/tmp/th798/25892134/R-devel/1472/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/th798/25892134/R-devel/1472/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] "2025-12-14 01:32:40 MST" * using log directory '/tmp/th798/25892134/R-devel/1472/tcpl.Rcheck' * using R Under development (unstable) (2025-12-13 r89166) * 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 'tcpl/DESCRIPTION' ... OK * this is package 'tcpl' version '3.3.1' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR Packages required but not available: 'plotly', 'ctxR', 'gt' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. * DONE Status: 1 ERROR See '/tmp/th798/25892134/R-devel/1472/tcpl.Rcheck/00check.log' for details. [1] "2025-12-14 01:32:47 MST" [1] "2025-12-14 01:32:47 MST" Installing package into '/tmp/th798/25892134/R-devel/1472/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.17.99' ** 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 frollapply.c -o frollapply.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 mergelist.c -o mergelist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 shellsort.c -o shellsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi installing to /tmp/th798/25892134/R-devel/1472/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] "2025-12-14 01:33:23 MST" * using log directory '/tmp/th798/25892134/R-devel/1472/tcpl.Rcheck' * using R Under development (unstable) (2025-12-13 r89166) * 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 'tcpl/DESCRIPTION' ... OK * this is package 'tcpl' version '3.3.1' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... ERROR Packages required but not available: 'plotly', 'ctxR', 'gt' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. * DONE Status: 1 ERROR See '/tmp/th798/25892134/R-devel/1472/tcpl.Rcheck/00check.log' for details. [1] "2025-12-14 01:33:33 MST" > system(paste(c("diff -u", Rcheck.list), collapse=" ")) > library(data.table, lib.loc=R.home("library")) Error: package or namespace load failed for 'data.table' in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/projects/genomic-ml/R/R-devel/library/data.table/libs/data_table.so': /projects/genomic-ml/R/R-devel/library/data.table/libs/data_table.so: undefined symbol: Rf_GetOption Execution halted WARNING: ignoring environment value of R_HOME R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 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/2025-12-14/deps.csv", task.str = "1472", release = "/scratch/th798/data.table-revdeps/2025-12-14/data.table_release_1.17.8.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-12-14/data.table_master_1.17.99.6329d94b83b72bb1f05dc2a10374e84a61ff950d.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/25892134/R-release/1472" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/25892134/R-release/1472/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "tcpl" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/25892134/R-release/1472/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] "2025-12-14 01:33:47 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/25892134/R-release/1472/library' (as 'lib' is unspecified) also installing the dependencies 'gtable', 'S7', 'scales', 'tcplfit2', 'ggplot2', 'ctxR', 'httptest' trying URL 'http://cloud.r-project.org/src/contrib/gtable_0.3.6.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/S7_0.2.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/scales_1.4.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/tcplfit2_0.1.9.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/ggplot2_4.0.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/ctxR_1.1.3.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/httptest_4.2.3.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/tcpl_3.3.1.tar.gz' * installing *source* package 'gtable' ... ** this is package 'gtable' version '0.3.6' ** package 'gtable' 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 (gtable) * installing *source* package 'S7' ... ** this is package 'S7' version '0.2.1' ** package 'S7' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c method-dispatch.c -o method-dispatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c prop.c -o prop.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 S7.so init.o method-dispatch.o prop.o installing to /tmp/th798/25892134/R-release/1472/library/00LOCK-S7/00new/S7/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 (S7) * installing *source* package 'scales' ... ** this is package 'scales' version '1.4.0' ** package 'scales' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scales) * installing *source* package 'ctxR' ... ** this is package 'ctxR' version '1.1.3' ** package 'ctxR' 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 ** 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 (ctxR) * installing *source* package 'httptest' ... ** this is package 'httptest' version '4.2.3' ** package 'httptest' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (httptest) * installing *source* package 'ggplot2' ... ** this is package 'ggplot2' version '4.0.1' ** package 'ggplot2' 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 (ggplot2) * installing *source* package 'tcplfit2' ... ** this is package 'tcplfit2' version '0.1.9' ** package 'tcplfit2' 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 ** 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 (tcplfit2) * installing *source* package 'tcpl' ... ** this is package 'tcpl' version '3.3.1' ** package 'tcpl' 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 ** 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 (tcpl) The downloaded source packages are in '/tmp/th798/25892134/RtmpyvFcwb/downloaded_packages' > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 97.819 4.776 146.352 > print(Sys.time()) [1] "2025-12-14 01:36:14 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] "2025-12-14 01:36:14 MST" Installing package into '/tmp/th798/25892134/R-release/1472/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/th798/25892134/R-release/1472/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] "2025-12-14 01:36:35 MST" * using log directory '/tmp/th798/25892134/R-release/1472/tcpl.Rcheck' * using R version 4.5.2 (2025-10-31) * 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 'tcpl/DESCRIPTION' ... OK * this is package 'tcpl' version '3.3.1' * 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 'tcpl' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE get_verbose_tables: no visible global function definition for 'as_gtable' Undefined global functions or variables: as_gtable * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(tcpl) tcpl (v3.3.1) loaded with the following settings: TCPL_DB: NA TCPL_USER: NA TCPL_HOST: https://comptox.epa.gov/ctx-api/bioactivity TCPL_DRVR: API Default settings stored in tcpl config file. See ?tcplConf for more information. > > test_check("tcpl") [ FAIL 44 | WARN 859 | SKIP 5 | PASS 681 ] == Skipped tests (5) =========================================================== * On CRAN (3): 'test-tcplDefine.R:3:3', 'test-tcplDefine.R:9:3', 'test-tcplDefine.R:19:3' * Skipping (2): 'test-tcplPlot.R:16:3', 'test-tcplPlot.R:40:3' == Failed tests ================================================================ -- Failure ('test-tcplPlot.R:209:3'): tcplPlot works for single m4id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:213:3'): tcplPlot works for single m4id compared -- `fn` has length 1, not length 2. -- Failure ('test-tcplPlot.R:227:3'): tcplPlot works for multiple m4id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:233:3'): tcplPlot works for multiple m4id compared -- `fn` has length 1, not length 2. -- Failure ('test-tcplPlot.R:247:3'): tcplPlot works for single aeid compared mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:253:3'): tcplPlot works for single aeid compared mc -- `fn` has length 1, not length 2. -- Failure ('test-tcplPlot.R:267:3'): tcplPlot works for multiple aeid compared mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:273:3'): tcplPlot works for multiple aeid compared mc -- `fn` has length 1, not length 2. -- Failure ('test-tcplPlot.R:287:3'): tcplPlot works for single spid/aeid compared mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:291:3'): tcplPlot works for single spid/aeid compared mc -- `fn` has length 1, not length 2. -- Failure ('test-tcplPlot.R:305:3'): tcplPlot works for multiple spid/aeid compared mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:311:3'): tcplPlot works for multiple spid/aeid compared mc -- `fn` has length 1, not length 2. -- Failure ('test-tcplPlot.R:495:3'): tcplPlot works for single s2id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:499:3'): tcplPlot works for single s2id compared -- `fn` has length 1, not length 2. -- Failure ('test-tcplPlot.R:513:3'): tcplPlot works for multiple s2id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:519:3'): tcplPlot works for multiple s2id compared -- `fn` has length 1, not length 2. -- Failure ('test-tcplPlot.R:533:3'): tcplPlot works for single aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:539:3'): tcplPlot works for single aeid compared sc -- `fn` has length 1, not length 2. -- Failure ('test-tcplPlot.R:553:3'): tcplPlot works for multiple aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:559:3'): tcplPlot works for multiple aeid compared sc -- `fn` has length 1, not length 2. -- Failure ('test-tcplPlot.R:573:3'): tcplPlot works for single spid/aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:577:3'): tcplPlot works for single spid/aeid compared sc -- `fn` has length 1, not length 2. -- Failure ('test-tcplPlot.R:591:3'): tcplPlot works for multiple spid/aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:597:3'): tcplPlot works for multiple spid/aeid compared sc -- `fn` has length 1, not length 2. -- Failure ('test-tcplPlot.R:632:3'): standalone advanced comparison plotting works in mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:634:3'): standalone advanced comparison plotting works in mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:636:3'): standalone advanced comparison plotting works in mc -- `fn` has length 0, not length 2. -- Failure ('test-tcplPlot.R:668:3'): standalone advanced comparison plotting works in sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:670:3'): standalone advanced comparison plotting works in sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:672:3'): standalone advanced comparison plotting works in sc -- `fn` has length 0, not length 2. -- Failure ('test-tcplPlot.R:798:3'): loec plotting works for small comparison plot -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:800:3'): loec plotting works for small comparison plot -- `fn` has length 0, not length 1. -- Failure ('test-tcplPlot.R:820:3'): loec plotting works for large comparison plot -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Failure ('test-tcplPlot.R:826:3'): loec plotting works for large comparison plot -- `fn` has length 2, not length 3. -- Error ('test-tcplggplot2.R:82:3'): tcplggplot2 works for verbose mc small comparison plot -- Error in `as_gtable(anno_tbl)`: could not find function "as_gtable" Backtrace: x 1. +-testthat::expect_false(...) at test-tcplggplot2.R:82:3 2. | \-testthat::quasi_label(enquo(object), label, arg = "object") 3. | \-rlang::eval_bare(expr, quo_get_env(quo)) 4. +-ggplot2::is_ggplot(...) 5. | \-S7::S7_inherits(x, class_ggplot) 6. \-tcpl:::tcplggplot2(dat = dat, compare = "conc_unit", verbose = TRUE) 7. \-tcpl:::get_verbose_tables(dat, type, compare, flags) -- Error ('test-tcplggplot2.R:185:3'): tcplggplot2 works for verbose sc small comparison plot -- Error in `as_gtable(anno_tbl)`: could not find function "as_gtable" Backtrace: x 1. +-testthat::expect_false(...) at test-tcplggplot2.R:185:3 2. | \-testthat::quasi_label(enquo(object), label, arg = "object") 3. | \-rlang::eval_bare(expr, quo_get_env(quo)) 4. +-ggplot2::is_ggplot(...) 5. | \-S7::S7_inherits(x, class_ggplot) 6. \-tcpl:::tcplggplot2(...) 7. \-tcpl:::get_verbose_tables(dat, type, compare, flags) -- Failure ('test-tcplggplot2Utils.R:344:3'): get_verbose_tables returns two tables small compare mc -- Expected `... <- NULL` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Error ('test-tcplggplot2Utils.R:345:3'): get_verbose_tables returns two tables small compare mc -- Error in `eval(code, test_env)`: object 'tbls' not found Backtrace: x 1. \-testthat::expect_length(tbls, 2) at test-tcplggplot2Utils.R:345:3 2. \-testthat::quasi_label(enquo(object), arg = "object") 3. \-rlang::eval_bare(expr, quo_get_env(quo)) -- Failure ('test-tcplggplot2Utils.R:367:3'): get_verbose_tables returns two tables large compare mc -- Expected `... <- NULL` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Error ('test-tcplggplot2Utils.R:368:3'): get_verbose_tables returns two tables large compare mc -- Error in `eval(code, test_env)`: object 'tbls' not found Backtrace: x 1. \-testthat::expect_length(tbls, 2) at test-tcplggplot2Utils.R:368:3 2. \-testthat::quasi_label(enquo(object), arg = "object") 3. \-rlang::eval_bare(expr, quo_get_env(quo)) -- Failure ('test-tcplggplot2Utils.R:390:3'): get_verbose_tables returns two tables small compare sc -- Expected `tbls <- get_verbose_tables(dat = dat, type = "sc", compare = "normalized_data_type")` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Error ('test-tcplggplot2Utils.R:391:3'): get_verbose_tables returns two tables small compare sc -- Error in `eval(code, test_env)`: object 'tbls' not found Backtrace: x 1. \-testthat::expect_length(tbls, 2) at test-tcplggplot2Utils.R:391:3 2. \-testthat::quasi_label(enquo(object), arg = "object") 3. \-rlang::eval_bare(expr, quo_get_env(quo)) -- Failure ('test-tcplggplot2Utils.R:409:3'): get_verbose_tables returns two tables large compare sc -- Expected `tbls <- get_verbose_tables(dat = dat, type = "sc", compare = "normalized_data_type")` to run without any errors. i Actually got a with text: could not find function "as_gtable" -- Error ('test-tcplggplot2Utils.R:410:3'): get_verbose_tables returns two tables large compare sc -- Error in `eval(code, test_env)`: object 'tbls' not found Backtrace: x 1. \-testthat::expect_length(tbls, 2) at test-tcplggplot2Utils.R:410:3 2. \-testthat::quasi_label(enquo(object), arg = "object") 3. \-rlang::eval_bare(expr, quo_get_env(quo)) [ FAIL 44 | WARN 859 | SKIP 5 | PASS 681 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See '/tmp/th798/25892134/R-release/1472/tcpl.Rcheck/00check.log' for details. [1] "2025-12-14 01:41:50 MST" [1] "2025-12-14 01:41:50 MST" Installing package into '/tmp/th798/25892134/R-release/1472/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.17.99' ** 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 frollapply.c -o frollapply.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 mergelist.c -o mergelist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nafill.c -o nafill.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c 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 shellsort.c -o shellsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi installing to /tmp/th798/25892134/R-release/1472/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] "2025-12-14 01:42:12 MST" * using log directory '/tmp/th798/25892134/R-release/1472/tcpl.Rcheck' * using R version 4.5.2 (2025-10-31) * 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 'tcpl/DESCRIPTION' ... OK * this is package 'tcpl' version '3.3.1' * 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 'tcpl' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE get_verbose_tables: no visible global function definition for 'as_gtable' Undefined global functions or variables: as_gtable * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(tcpl) tcpl (v3.3.1) loaded with the following settings: TCPL_DB: NA TCPL_USER: NA TCPL_HOST: https://comptox.epa.gov/ctx-api/bioactivity TCPL_DRVR: API Default settings stored in tcpl config file. See ?tcplConf for more information. > > test_check("tcpl") [ FAIL 157 | WARN 705 | SKIP 5 | PASS 453 ] == Skipped tests (5) =========================================================== * On CRAN (3): 'test-tcplDefine.R:3:3', 'test-tcplDefine.R:9:3', 'test-tcplDefine.R:19:3' * Skipping (2): 'test-tcplPlot.R:16:3', 'test-tcplPlot.R:40:3' == Failed tests ================================================================ -- Error ('test-tcplLoadData.R:213:3'): tcplLoadData loads sc1 data for one s1id -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(type = "sc", lvl = 1, fld = "s1id", val = mocked$s1id) at test-tcplLoadData.R:213:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Error ('test-tcplLoadData.R:231:3'): tcplLoadData loads sc1 data for one acid -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(type = "sc", lvl = 1, fld = "acid", val = mocked$acid) at test-tcplLoadData.R:231:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Error ('test-tcplLoadData.R:287:3'): tcplLoadData loads sc 'agg' data for one aeid -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(type = "sc", lvl = "agg", fld = "aeid", val = mocked$aeid) at test-tcplLoadData.R:287:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Error ('test-tcplLoadData.R:343:3'): tcplLoadData loads mc1 data for one m1id -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(lvl = 1, fld = "m1id", val = mocked$m1id) at test-tcplLoadData.R:343:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Error ('test-tcplLoadData.R:361:3'): tcplLoadData loads mc1 data for one acid -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(lvl = 1, fld = "acid", val = mocked$acid) at test-tcplLoadData.R:361:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Error ('test-tcplLoadData.R:380:3'): tcplLoadData loads mc2 data for one m2id -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(lvl = 2, fld = "m2id", val = mocked$m2id) at test-tcplLoadData.R:380:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Error ('test-tcplLoadData.R:398:3'): tcplLoadData loads mc2 data for one acid -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(lvl = 2, fld = "acid", val = mocked$acid) at test-tcplLoadData.R:398:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Error ('test-tcplLoadData.R:417:3'): tcplLoadData loads mc3 data for one m3id -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(lvl = 3, fld = "m3id", val = mocked$m3id) at test-tcplLoadData.R:417:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Error ('test-tcplLoadData.R:435:3'): tcplLoadData loads mc3 data for one aeid -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(lvl = 3, fld = "aeid", val = mocked$aeid) at test-tcplLoadData.R:435:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Error ('test-tcplLoadData.R:454:3'): tcplLoadData loads mc4 data for one m4id -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(lvl = 4, fld = "m4id", val = mocked$m4id) at test-tcplLoadData.R:454:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Error ('test-tcplLoadData.R:491:3'): tcplLoadData loads mc5 data for one m5id -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(lvl = 5, fld = "m5id", val = mocked$m5id) at test-tcplLoadData.R:491:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Error ('test-tcplLoadData.R:509:3'): tcplLoadData loads mc5 data for one aeid with add.fld = FALSE -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(...) at test-tcplLoadData.R:509:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Error ('test-tcplLoadData.R:528:3'): tcplLoadData loads mc6 data for one m6id -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(lvl = 6, fld = "m6id", val = mocked$m6id) at test-tcplLoadData.R:528:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Error ('test-tcplLoadData.R:546:3'): tcplLoadData loads mc6 data for one aeid -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(lvl = 6, fld = "aeid", val = mocked$aeid) at test-tcplLoadData.R:546:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Error ('test-tcplLoadData.R:565:3'): tcplLoadData loads mc7 data for one m7id -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(lvl = 7, fld = "m7id", val = mocked$m7id) at test-tcplLoadData.R:565:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Error ('test-tcplLoadData.R:583:3'): tcplLoadData loads mc7 data for one aeid -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(lvl = 7, fld = "aeid", val = mocked$aeid) at test-tcplLoadData.R:583:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Error ('test-tcplLoadData.R:602:3'): tcplLoadData loads mc 'agg' data for one aeid -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplLoadData(lvl = "agg", fld = "aeid", val = mocked$aeid) at test-tcplLoadData.R:602:3 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 3. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:91:3'): tcplPlot works for single m4id ------------ Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:92:3'): tcplPlot works for single m4id ------------ Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:93:3'): tcplPlot works for single m4id ------------ Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:95:3'): tcplPlot works for single m4id ------------ `fn` has length 0, not length 2. -- Failure ('test-tcplPlot.R:109:3'): tcplPlot works for multiple m4id --------- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:110:3'): tcplPlot works for multiple m4id --------- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:112:3'): tcplPlot works for multiple m4id ----------- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:112:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:129:3'): tcplPlot works for single aeid mc -------- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:130:3'): tcplPlot works for single aeid mc -------- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:132:3'): tcplPlot works for single aeid mc ---------- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:132:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:149:3'): tcplPlot works for multiple aeid mc ------ Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:150:3'): tcplPlot works for multiple aeid mc ------ Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:151:3'): tcplPlot works for multiple aeid mc ------ Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:152:3'): tcplPlot works for multiple aeid mc ------ Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:154:3'): tcplPlot works for multiple aeid mc -------- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:154:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:171:3'): tcplPlot works for single spid/aeid mc --- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:172:3'): tcplPlot works for single spid/aeid mc --- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:173:3'): tcplPlot works for single spid/aeid mc --- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:175:3'): tcplPlot works for single spid/aeid mc --- `fn` has length 0, not length 2. -- Failure ('test-tcplPlot.R:189:3'): tcplPlot works for multiple spid/aeid mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:190:3'): tcplPlot works for multiple spid/aeid mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:192:3'): tcplPlot works for multiple spid/aeid mc --- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:192:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:209:3'): tcplPlot works for single m4id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:210:3'): tcplPlot works for single m4id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:211:3'): tcplPlot works for single m4id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:213:3'): tcplPlot works for single m4id compared -- `fn` has length 0, not length 2. -- Failure ('test-tcplPlot.R:227:3'): tcplPlot works for multiple m4id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:228:3'): tcplPlot works for multiple m4id compared -- Expected `suppressWarnings(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:230:3'): tcplPlot works for multiple m4id compared -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:230:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:247:3'): tcplPlot works for single aeid compared mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:248:3'): tcplPlot works for single aeid compared mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:250:3'): tcplPlot works for single aeid compared mc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:250:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:267:3'): tcplPlot works for multiple aeid compared mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:268:3'): tcplPlot works for multiple aeid compared mc -- Expected `suppressWarnings(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:270:3'): tcplPlot works for multiple aeid compared mc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:270:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:287:3'): tcplPlot works for single spid/aeid compared mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:288:3'): tcplPlot works for single spid/aeid compared mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:289:3'): tcplPlot works for single spid/aeid compared mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:291:3'): tcplPlot works for single spid/aeid compared mc -- `fn` has length 0, not length 2. -- Failure ('test-tcplPlot.R:305:3'): tcplPlot works for multiple spid/aeid compared mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:306:3'): tcplPlot works for multiple spid/aeid compared mc -- Expected `suppressWarnings(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:308:3'): tcplPlot works for multiple spid/aeid compared mc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:308:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:325:3'): tcplPlot works for large comparisons greater than group.threshold mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:326:3'): tcplPlot works for large comparisons greater than group.threshold mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:328:3'): tcplPlot works for large comparisons greater than group.threshold mc -- `fn` has length 0, not length 2. -- Failure ('test-tcplPlot.R:342:3'): tcplPlot works for large comparisons greater than group.threshold sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:343:3'): tcplPlot works for large comparisons greater than group.threshold sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:345:3'): tcplPlot works for large comparisons greater than group.threshold sc -- `fn` has length 0, not length 2. -- Error ('test-tcplPlot.R:359:3'): tcplPlot errors if 'compare' or 'by' are not fields in 'dat' -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:359:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:378:3'): tcplPlot works for single s2id ----------- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:379:3'): tcplPlot works for single s2id ----------- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:380:3'): tcplPlot works for single s2id ----------- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:382:3'): tcplPlot works for single s2id ----------- `fn` has length 0, not length 2. -- Failure ('test-tcplPlot.R:396:3'): tcplPlot works for multiple s2id --------- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:397:3'): tcplPlot works for multiple s2id --------- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:399:3'): tcplPlot works for multiple s2id ----------- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:399:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(...) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:416:3'): tcplPlot works for single aeid sc -------- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:417:3'): tcplPlot works for single aeid sc -------- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:419:3'): tcplPlot works for single aeid sc ---------- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:419:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(...) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:436:3'): tcplPlot works for multiple aeid sc ------ Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:437:3'): tcplPlot works for multiple aeid sc ------ Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:438:3'): tcplPlot works for multiple aeid sc ------ Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:440:3'): tcplPlot works for multiple aeid sc -------- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:440:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(...) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:457:3'): tcplPlot works for single spid/aeid sc --- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:458:3'): tcplPlot works for single spid/aeid sc --- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:459:3'): tcplPlot works for single spid/aeid sc --- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:461:3'): tcplPlot works for single spid/aeid sc --- `fn` has length 0, not length 2. -- Failure ('test-tcplPlot.R:475:3'): tcplPlot works for multiple spid/aeid sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:476:3'): tcplPlot works for multiple spid/aeid sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:478:3'): tcplPlot works for multiple spid/aeid sc --- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:478:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(...) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:495:3'): tcplPlot works for single s2id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:496:3'): tcplPlot works for single s2id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:497:3'): tcplPlot works for single s2id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:499:3'): tcplPlot works for single s2id compared -- `fn` has length 0, not length 2. -- Failure ('test-tcplPlot.R:513:3'): tcplPlot works for multiple s2id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:514:3'): tcplPlot works for multiple s2id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:516:3'): tcplPlot works for multiple s2id compared -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:516:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(...) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:533:3'): tcplPlot works for single aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:534:3'): tcplPlot works for single aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:536:3'): tcplPlot works for single aeid compared sc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:536:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(...) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:553:3'): tcplPlot works for multiple aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:554:3'): tcplPlot works for multiple aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:556:3'): tcplPlot works for multiple aeid compared sc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:556:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(...) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:573:3'): tcplPlot works for single spid/aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:574:3'): tcplPlot works for single spid/aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:575:3'): tcplPlot works for single spid/aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:577:3'): tcplPlot works for single spid/aeid compared sc -- `fn` has length 0, not length 2. -- Failure ('test-tcplPlot.R:591:3'): tcplPlot works for multiple spid/aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:592:3'): tcplPlot works for multiple spid/aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:594:3'): tcplPlot works for multiple spid/aeid compared sc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:594:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(...) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Error ('test-tcplPlot.R:614:3'): standalone plotting works in mc ------------ Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplPlot.R:614:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplPlot.R:631:3'): standalone advanced comparison plotting works in mc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplPlot.R:631:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplPlot.R:650:3'): standalone plotting works in sc ------------ Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "s2id", val = mocked$s2id) at test-tcplPlot.R:650:3 2. \-tcpl::tcplLoadData(...) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplPlot.R:667:3'): standalone advanced comparison plotting works in sc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "s2id", val = mocked$s2id) at test-tcplPlot.R:667:3 2. \-tcpl::tcplLoadData(...) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:689:3'): ggplot output works in mc ---------------- Expected `... <- NULL` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:690:3'): ggplot output works in mc ------------------ Error in `eval(code, test_env)`: object 'otpt' not found Backtrace: x 1. +-testthat::expect_true(ggplot2::is_ggplot(otpt)) at test-tcplPlot.R:690:3 2. | \-testthat::quasi_label(enquo(object), label, arg = "object") 3. | \-rlang::eval_bare(expr, quo_get_env(quo)) 4. \-ggplot2::is_ggplot(otpt) 5. \-S7::S7_inherits(x, class_ggplot) -- Failure ('test-tcplPlot.R:705:3'): ggplot output comparison plotting works in mc -- Expected `... <- NULL` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:706:3'): ggplot output comparison plotting works in mc -- Error in `eval(code, test_env)`: object 'otpt' not found Backtrace: x 1. +-testthat::expect_true(ggplot2::is_ggplot(otpt)) at test-tcplPlot.R:706:3 2. | \-testthat::quasi_label(enquo(object), label, arg = "object") 3. | \-rlang::eval_bare(expr, quo_get_env(quo)) 4. \-ggplot2::is_ggplot(otpt) 5. \-S7::S7_inherits(x, class_ggplot) -- Failure ('test-tcplPlot.R:721:3'): ggplot output works in sc ---------------- Expected `... <- NULL` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:722:3'): ggplot output works in sc ------------------ Error in `eval(code, test_env)`: object 'otpt' not found Backtrace: x 1. +-testthat::expect_true(ggplot2::is_ggplot(otpt)) at test-tcplPlot.R:722:3 2. | \-testthat::quasi_label(enquo(object), label, arg = "object") 3. | \-rlang::eval_bare(expr, quo_get_env(quo)) 4. \-ggplot2::is_ggplot(otpt) 5. \-S7::S7_inherits(x, class_ggplot) -- Failure ('test-tcplPlot.R:737:3'): ggplot output comparison plotting works in sc -- Expected `... <- NULL` to run without any errors. i Actually got a with text: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Error ('test-tcplPlot.R:738:3'): ggplot output comparison plotting works in sc -- Error in `eval(code, test_env)`: object 'otpt' not found Backtrace: x 1. +-testthat::expect_true(ggplot2::is_ggplot(otpt)) at test-tcplPlot.R:738:3 2. | \-testthat::quasi_label(enquo(object), label, arg = "object") 3. | \-rlang::eval_bare(expr, quo_get_env(quo)) 4. \-ggplot2::is_ggplot(otpt) 5. \-S7::S7_inherits(x, class_ggplot) -- Error ('test-tcplPlot.R:753:3'): ggplot output returns specific warnings and errors -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. +-testthat::expect_error(...) at test-tcplPlot.R:753:3 2. | \-testthat:::expect_condition_matching(...) 3. | \-testthat:::quasi_capture(...) 4. | +-testthat (local) .capture(...) 5. | | \-base::withCallingHandlers(...) 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 7. \-tcpl::tcplPlot(...) 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 11. \-data.table:::`[.data.table`(...) -- Error ('test-tcplPlot.R:776:3'): loec plotting works for single plot -------- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplPlot.R:776:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplPlot.R:795:3'): loec plotting works for small comparison plot -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplPlot.R:795:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplPlot.R:814:3'): loec plotting works for large comparison plot -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplPlot.R:814:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplPlotLoadData.R:30:3'): tcplPlotLoadData loads all necessary mc data -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplPlotLoadData.R:30:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplPlotLoadData.R:57:3'): tcplPlotLoadData loads all necessary sc data -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplPlotLoadData.R:57:3 2. \-tcpl::tcplLoadData(...) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplPlotUtils.R:57:3'): tcplPlotValidate properly validates 'by' -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplPlotUtils.R:57:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplPlotUtils.R:75:3'): tcplPlotValidate properly validates 'dat' as a list or a data.table -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplPlotUtils.R:75:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplPlotUtils.R:135:3'): tcplPlotSetYRange correctly sets yrange for mc data -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplPlotUtils.R:135:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplPlotUtils.R:170:3'): tcplPlotSetYRange correctly sets yrange for sc data -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplPlotUtils.R:170:3 2. \-tcpl::tcplLoadData(...) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplPlotUtils.R:194:3'): tcplPlotLoadWllt replaces NA dtxsid and chnm with well type description -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplPlotUtils.R:194:3 2. \-tcpl::tcplLoadData(lvl = "agg", fld = "m4id", val = dat$m4id) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2.R:32:3'): tcplggplot2 works for mc single plot ----- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplggplot2.R:32:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2.R:48:3'): tcplggplot2 works for verbose mc single plot -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplggplot2.R:48:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2.R:64:3'): tcplggplot2 works for mc small comparison plot -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2.R:64:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2.R:81:3'): tcplggplot2 works for verbose mc small comparison plot -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2.R:81:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2.R:97:3'): tcplggplot2 works for mc large comparison plot -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2.R:97:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2.R:114:3'): tcplggplot2 works for verbose (flags table) mc large comparison plot -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2.R:114:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2.R:136:3'): tcplggplot2 works for sc single plot ---- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "s2id", val = mocked$s2id) at test-tcplggplot2.R:136:3 2. \-tcpl::tcplLoadData(...) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2.R:152:3'): tcplggplot2 works for verbose sc single plot -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "s2id", val = mocked$s2id) at test-tcplggplot2.R:152:3 2. \-tcpl::tcplLoadData(...) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2.R:168:3'): tcplggplot2 works for sc small comparison plot -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplggplot2.R:168:3 2. \-tcpl::tcplLoadData(...) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2.R:184:3'): tcplggplot2 works for verbose sc small comparison plot -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplggplot2.R:184:3 2. \-tcpl::tcplLoadData(...) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2.R:200:3'): tcplggplot2 works for sc large comparison plot -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplggplot2.R:200:3 2. \-tcpl::tcplLoadData(...) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2.R:217:3'): tcplggplot2 correctly performs checks and validates parameters -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2.R:217:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2Utils.R:46:3'): tcplfit2_fun works ------------------ Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplggplot2Utils.R:46:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2Utils.R:86:3'): get_plot_title creates full title for single plot mc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplggplot2Utils.R:86:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2Utils.R:108:3'): get_plot_title creates full title for aeid compare plot mc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplggplot2Utils.R:108:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2Utils.R:126:3'): get_plot_title creates full title for chem compare plot mc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2Utils.R:126:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2Utils.R:149:3'): get_plot_title creates full title for other compare plot mc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2Utils.R:149:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2Utils.R:172:3'): get_plot_title creates full title for single plot sc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "s2id", val = mocked$s2id) at test-tcplggplot2Utils.R:172:3 2. \-tcpl::tcplLoadData(...) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2Utils.R:194:3'): get_plot_title creates full title for aeid compare plot sc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "s2id", val = mocked$s2id) at test-tcplggplot2Utils.R:194:3 2. \-tcpl::tcplLoadData(...) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2Utils.R:212:3'): get_plot_title creates full title for chem compare plot sc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplggplot2Utils.R:212:3 2. \-tcpl::tcplLoadData(...) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2Utils.R:235:3'): get_plot_title creates full title for other compare plot sc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplggplot2Utils.R:235:3 2. \-tcpl::tcplLoadData(...) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2Utils.R:262:3'): get_plot_caption returns list of flags for a single plot -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplggplot2Utils.R:262:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2Utils.R:278:3'): get_plot_caption returns list of flags for a compare plot -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2Utils.R:278:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2Utils.R:341:3'): get_verbose_tables returns two tables small compare mc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2Utils.R:341:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2Utils.R:364:3'): get_verbose_tables returns two tables large compare mc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2Utils.R:364:3 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2Utils.R:387:3'): get_verbose_tables returns two tables small compare sc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplggplot2Utils.R:387:3 2. \-tcpl::tcplLoadData(...) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) -- Error ('test-tcplggplot2Utils.R:406:3'): get_verbose_tables returns two tables large compare sc -- Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplggplot2Utils.R:406:3 2. \-tcpl::tcplLoadData(...) 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] 4. \-data.table:::`[.data.table`(...) [ FAIL 157 | WARN 705 | SKIP 5 | PASS 453 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See '/tmp/th798/25892134/R-release/1472/tcpl.Rcheck/00check.log' for details. [1] "2025-12-14 01:45:12 MST" > system(paste(c("diff -u", Rcheck.list), collapse=" ")) --- R_version_4.5.2_2025-10-31/release_1.17.8.Rcheck/00check.log 2025-12-14 01:41:50.027224198 -0700 +++ R_version_4.5.2_2025-10-31/master_1.17.99.6329d94b83b72bb1f05dc2a10374e84a61ff950d.Rcheck/00check.log 2025-12-14 01:45:12.081876488 -0700 @@ -82,7 +82,7 @@ Default settings stored in tcpl config file. See ?tcplConf for more information. > > test_check("tcpl") - [ FAIL 44 | WARN 859 | SKIP 5 | PASS 681 ] + [ FAIL 157 | WARN 705 | SKIP 5 | PASS 453 ] == Skipped tests (5) =========================================================== * On CRAN (3): 'test-tcplDefine.R:3:3', 'test-tcplDefine.R:9:3', @@ -90,178 +90,1049 @@ * Skipping (2): 'test-tcplPlot.R:16:3', 'test-tcplPlot.R:40:3' == Failed tests ================================================================ + -- Error ('test-tcplLoadData.R:213:3'): tcplLoadData loads sc1 data for one s1id -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(type = "sc", lvl = 1, fld = "s1id", val = mocked$s1id) at test-tcplLoadData.R:213:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplLoadData.R:231:3'): tcplLoadData loads sc1 data for one acid -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(type = "sc", lvl = 1, fld = "acid", val = mocked$acid) at test-tcplLoadData.R:231:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplLoadData.R:287:3'): tcplLoadData loads sc 'agg' data for one aeid -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(type = "sc", lvl = "agg", fld = "aeid", val = mocked$aeid) at test-tcplLoadData.R:287:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplLoadData.R:343:3'): tcplLoadData loads mc1 data for one m1id -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(lvl = 1, fld = "m1id", val = mocked$m1id) at test-tcplLoadData.R:343:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplLoadData.R:361:3'): tcplLoadData loads mc1 data for one acid -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(lvl = 1, fld = "acid", val = mocked$acid) at test-tcplLoadData.R:361:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplLoadData.R:380:3'): tcplLoadData loads mc2 data for one m2id -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(lvl = 2, fld = "m2id", val = mocked$m2id) at test-tcplLoadData.R:380:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplLoadData.R:398:3'): tcplLoadData loads mc2 data for one acid -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(lvl = 2, fld = "acid", val = mocked$acid) at test-tcplLoadData.R:398:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplLoadData.R:417:3'): tcplLoadData loads mc3 data for one m3id -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(lvl = 3, fld = "m3id", val = mocked$m3id) at test-tcplLoadData.R:417:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplLoadData.R:435:3'): tcplLoadData loads mc3 data for one aeid -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(lvl = 3, fld = "aeid", val = mocked$aeid) at test-tcplLoadData.R:435:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplLoadData.R:454:3'): tcplLoadData loads mc4 data for one m4id -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(lvl = 4, fld = "m4id", val = mocked$m4id) at test-tcplLoadData.R:454:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplLoadData.R:491:3'): tcplLoadData loads mc5 data for one m5id -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(lvl = 5, fld = "m5id", val = mocked$m5id) at test-tcplLoadData.R:491:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplLoadData.R:509:3'): tcplLoadData loads mc5 data for one aeid with add.fld = FALSE -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(...) at test-tcplLoadData.R:509:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplLoadData.R:528:3'): tcplLoadData loads mc6 data for one m6id -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(lvl = 6, fld = "m6id", val = mocked$m6id) at test-tcplLoadData.R:528:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplLoadData.R:546:3'): tcplLoadData loads mc6 data for one aeid -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(lvl = 6, fld = "aeid", val = mocked$aeid) at test-tcplLoadData.R:546:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplLoadData.R:565:3'): tcplLoadData loads mc7 data for one m7id -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(lvl = 7, fld = "m7id", val = mocked$m7id) at test-tcplLoadData.R:565:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplLoadData.R:583:3'): tcplLoadData loads mc7 data for one aeid -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(lvl = 7, fld = "aeid", val = mocked$aeid) at test-tcplLoadData.R:583:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplLoadData.R:602:3'): tcplLoadData loads mc 'agg' data for one aeid -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplLoadData(lvl = "agg", fld = "aeid", val = mocked$aeid) at test-tcplLoadData.R:602:3 + 2. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 3. \-data.table:::`[.data.table`(...) + -- Failure ('test-tcplPlot.R:91:3'): tcplPlot works for single m4id ------------ + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:92:3'): tcplPlot works for single m4id ------------ + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:93:3'): tcplPlot works for single m4id ------------ + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:95:3'): tcplPlot works for single m4id ------------ + `fn` has length 0, not length 2. + -- Failure ('test-tcplPlot.R:109:3'): tcplPlot works for multiple m4id --------- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:110:3'): tcplPlot works for multiple m4id --------- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:112:3'): tcplPlot works for multiple m4id ----------- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:112:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) + -- Failure ('test-tcplPlot.R:129:3'): tcplPlot works for single aeid mc -------- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:130:3'): tcplPlot works for single aeid mc -------- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:132:3'): tcplPlot works for single aeid mc ---------- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:132:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) + -- Failure ('test-tcplPlot.R:149:3'): tcplPlot works for multiple aeid mc ------ + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:150:3'): tcplPlot works for multiple aeid mc ------ + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:151:3'): tcplPlot works for multiple aeid mc ------ + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:152:3'): tcplPlot works for multiple aeid mc ------ + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:154:3'): tcplPlot works for multiple aeid mc -------- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:154:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) + -- Failure ('test-tcplPlot.R:171:3'): tcplPlot works for single spid/aeid mc --- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:172:3'): tcplPlot works for single spid/aeid mc --- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:173:3'): tcplPlot works for single spid/aeid mc --- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:175:3'): tcplPlot works for single spid/aeid mc --- + `fn` has length 0, not length 2. + -- Failure ('test-tcplPlot.R:189:3'): tcplPlot works for multiple spid/aeid mc -- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:190:3'): tcplPlot works for multiple spid/aeid mc -- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:192:3'): tcplPlot works for multiple spid/aeid mc --- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:192:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:209:3'): tcplPlot works for single m4id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:210:3'): tcplPlot works for single m4id compared -- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:211:3'): tcplPlot works for single m4id compared -- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:213:3'): tcplPlot works for single m4id compared -- - `fn` has length 1, not length 2. + `fn` has length 0, not length 2. -- Failure ('test-tcplPlot.R:227:3'): tcplPlot works for multiple m4id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Failure ('test-tcplPlot.R:233:3'): tcplPlot works for multiple m4id compared -- - `fn` has length 1, not length 2. + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:228:3'): tcplPlot works for multiple m4id compared -- + Expected `suppressWarnings(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:230:3'): tcplPlot works for multiple m4id compared -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:230:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:247:3'): tcplPlot works for single aeid compared mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Failure ('test-tcplPlot.R:253:3'): tcplPlot works for single aeid compared mc -- - `fn` has length 1, not length 2. + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:248:3'): tcplPlot works for single aeid compared mc -- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:250:3'): tcplPlot works for single aeid compared mc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:250:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:267:3'): tcplPlot works for multiple aeid compared mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Failure ('test-tcplPlot.R:273:3'): tcplPlot works for multiple aeid compared mc -- - `fn` has length 1, not length 2. + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:268:3'): tcplPlot works for multiple aeid compared mc -- + Expected `suppressWarnings(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:270:3'): tcplPlot works for multiple aeid compared mc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:270:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:287:3'): tcplPlot works for single spid/aeid compared mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:288:3'): tcplPlot works for single spid/aeid compared mc -- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:289:3'): tcplPlot works for single spid/aeid compared mc -- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:291:3'): tcplPlot works for single spid/aeid compared mc -- - `fn` has length 1, not length 2. + `fn` has length 0, not length 2. -- Failure ('test-tcplPlot.R:305:3'): tcplPlot works for multiple spid/aeid compared mc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Failure ('test-tcplPlot.R:311:3'): tcplPlot works for multiple spid/aeid compared mc -- - `fn` has length 1, not length 2. + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:306:3'): tcplPlot works for multiple spid/aeid compared mc -- + Expected `suppressWarnings(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:308:3'): tcplPlot works for multiple spid/aeid compared mc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:308:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) + -- Failure ('test-tcplPlot.R:325:3'): tcplPlot works for large comparisons greater than group.threshold mc -- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:326:3'): tcplPlot works for large comparisons greater than group.threshold mc -- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:328:3'): tcplPlot works for large comparisons greater than group.threshold mc -- + `fn` has length 0, not length 2. + -- Failure ('test-tcplPlot.R:342:3'): tcplPlot works for large comparisons greater than group.threshold sc -- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:343:3'): tcplPlot works for large comparisons greater than group.threshold sc -- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:345:3'): tcplPlot works for large comparisons greater than group.threshold sc -- + `fn` has length 0, not length 2. + -- Error ('test-tcplPlot.R:359:3'): tcplPlot errors if 'compare' or 'by' are not fields in 'dat' -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:359:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) + -- Failure ('test-tcplPlot.R:378:3'): tcplPlot works for single s2id ----------- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:379:3'): tcplPlot works for single s2id ----------- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:380:3'): tcplPlot works for single s2id ----------- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:382:3'): tcplPlot works for single s2id ----------- + `fn` has length 0, not length 2. + -- Failure ('test-tcplPlot.R:396:3'): tcplPlot works for multiple s2id --------- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:397:3'): tcplPlot works for multiple s2id --------- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:399:3'): tcplPlot works for multiple s2id ----------- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:399:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(...) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) + -- Failure ('test-tcplPlot.R:416:3'): tcplPlot works for single aeid sc -------- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:417:3'): tcplPlot works for single aeid sc -------- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:419:3'): tcplPlot works for single aeid sc ---------- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:419:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(...) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) + -- Failure ('test-tcplPlot.R:436:3'): tcplPlot works for multiple aeid sc ------ + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:437:3'): tcplPlot works for multiple aeid sc ------ + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:438:3'): tcplPlot works for multiple aeid sc ------ + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:440:3'): tcplPlot works for multiple aeid sc -------- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:440:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(...) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) + -- Failure ('test-tcplPlot.R:457:3'): tcplPlot works for single spid/aeid sc --- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:458:3'): tcplPlot works for single spid/aeid sc --- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:459:3'): tcplPlot works for single spid/aeid sc --- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:461:3'): tcplPlot works for single spid/aeid sc --- + `fn` has length 0, not length 2. + -- Failure ('test-tcplPlot.R:475:3'): tcplPlot works for multiple spid/aeid sc -- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:476:3'): tcplPlot works for multiple spid/aeid sc -- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:478:3'): tcplPlot works for multiple spid/aeid sc --- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:478:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(...) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) -- Failure ('test-tcplPlot.R:495:3'): tcplPlot works for single s2id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:496:3'): tcplPlot works for single s2id compared -- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:497:3'): tcplPlot works for single s2id compared -- + Expected `tcplPlot(...)` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. -- Failure ('test-tcplPlot.R:499:3'): tcplPlot works for single s2id compared -- - `fn` has length 1, not length 2. + `fn` has length 0, not length 2. -- Failure ('test-tcplPlot.R:513:3'): tcplPlot works for multiple s2id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Failure ('test-tcplPlot.R:519:3'): tcplPlot works for multiple s2id compared -- - `fn` has length 1, not length 2. - -- Failure ('test-tcplPlot.R:533:3'): tcplPlot works for single aeid compared sc -- + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:514:3'): tcplPlot works for multiple s2id compared -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Failure ('test-tcplPlot.R:539:3'): tcplPlot works for single aeid compared sc -- - `fn` has length 1, not length 2. - -- Failure ('test-tcplPlot.R:553:3'): tcplPlot works for multiple aeid compared sc -- + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:516:3'): tcplPlot works for multiple s2id compared -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:516:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(...) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) + -- Failure ('test-tcplPlot.R:533:3'): tcplPlot works for single aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Failure ('test-tcplPlot.R:559:3'): tcplPlot works for multiple aeid compared sc -- - `fn` has length 1, not length 2. - -- Failure ('test-tcplPlot.R:573:3'): tcplPlot works for single spid/aeid compared sc -- + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:534:3'): tcplPlot works for single aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Failure ('test-tcplPlot.R:577:3'): tcplPlot works for single spid/aeid compared sc -- - `fn` has length 1, not length 2. - -- Failure ('test-tcplPlot.R:591:3'): tcplPlot works for multiple spid/aeid compared sc -- + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:536:3'): tcplPlot works for single aeid compared sc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:536:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(...) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) + -- Failure ('test-tcplPlot.R:553:3'): tcplPlot works for multiple aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Failure ('test-tcplPlot.R:597:3'): tcplPlot works for multiple spid/aeid compared sc -- - `fn` has length 1, not length 2. - -- Failure ('test-tcplPlot.R:632:3'): standalone advanced comparison plotting works in mc -- + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:554:3'): tcplPlot works for multiple aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Failure ('test-tcplPlot.R:634:3'): standalone advanced comparison plotting works in mc -- + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:556:3'): tcplPlot works for multiple aeid compared sc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:556:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(...) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) + -- Failure ('test-tcplPlot.R:573:3'): tcplPlot works for single spid/aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Failure ('test-tcplPlot.R:636:3'): standalone advanced comparison plotting works in mc -- - `fn` has length 0, not length 2. - -- Failure ('test-tcplPlot.R:668:3'): standalone advanced comparison plotting works in sc -- + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:574:3'): tcplPlot works for single spid/aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Failure ('test-tcplPlot.R:670:3'): standalone advanced comparison plotting works in sc -- + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:575:3'): tcplPlot works for single spid/aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Failure ('test-tcplPlot.R:672:3'): standalone advanced comparison plotting works in sc -- + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:577:3'): tcplPlot works for single spid/aeid compared sc -- `fn` has length 0, not length 2. - -- Failure ('test-tcplPlot.R:798:3'): loec plotting works for small comparison plot -- + -- Failure ('test-tcplPlot.R:591:3'): tcplPlot works for multiple spid/aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Failure ('test-tcplPlot.R:800:3'): loec plotting works for small comparison plot -- - `fn` has length 0, not length 1. - -- Failure ('test-tcplPlot.R:820:3'): loec plotting works for large comparison plot -- + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Failure ('test-tcplPlot.R:592:3'): tcplPlot works for multiple spid/aeid compared sc -- Expected `tcplPlot(...)` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Failure ('test-tcplPlot.R:826:3'): loec plotting works for large comparison plot -- - `fn` has length 2, not length 3. - -- Error ('test-tcplggplot2.R:82:3'): tcplggplot2 works for verbose mc small comparison plot -- - Error in `as_gtable(anno_tbl)`: could not find function "as_gtable" + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:594:3'): tcplPlot works for multiple spid/aeid compared sc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:594:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(...) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplPlot.R:614:3'): standalone plotting works in mc ------------ + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplPlot.R:614:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplPlot.R:631:3'): standalone advanced comparison plotting works in mc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplPlot.R:631:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplPlot.R:650:3'): standalone plotting works in sc ------------ + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "s2id", val = mocked$s2id) at test-tcplPlot.R:650:3 + 2. \-tcpl::tcplLoadData(...) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplPlot.R:667:3'): standalone advanced comparison plotting works in sc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x - 1. +-testthat::expect_false(...) at test-tcplggplot2.R:82:3 + 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "s2id", val = mocked$s2id) at test-tcplPlot.R:667:3 + 2. \-tcpl::tcplLoadData(...) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Failure ('test-tcplPlot.R:689:3'): ggplot output works in mc ---------------- + Expected `... <- NULL` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:690:3'): ggplot output works in mc ------------------ + Error in `eval(code, test_env)`: object 'otpt' not found + Backtrace: + x + 1. +-testthat::expect_true(ggplot2::is_ggplot(otpt)) at test-tcplPlot.R:690:3 2. | \-testthat::quasi_label(enquo(object), label, arg = "object") 3. | \-rlang::eval_bare(expr, quo_get_env(quo)) - 4. +-ggplot2::is_ggplot(...) - 5. | \-S7::S7_inherits(x, class_ggplot) - 6. \-tcpl:::tcplggplot2(dat = dat, compare = "conc_unit", verbose = TRUE) - 7. \-tcpl:::get_verbose_tables(dat, type, compare, flags) - -- Error ('test-tcplggplot2.R:185:3'): tcplggplot2 works for verbose sc small comparison plot -- - Error in `as_gtable(anno_tbl)`: could not find function "as_gtable" + 4. \-ggplot2::is_ggplot(otpt) + 5. \-S7::S7_inherits(x, class_ggplot) + -- Failure ('test-tcplPlot.R:705:3'): ggplot output comparison plotting works in mc -- + Expected `... <- NULL` to run without any errors. + i Actually got a with text: + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:706:3'): ggplot output comparison plotting works in mc -- + Error in `eval(code, test_env)`: object 'otpt' not found Backtrace: x - 1. +-testthat::expect_false(...) at test-tcplggplot2.R:185:3 + 1. +-testthat::expect_true(ggplot2::is_ggplot(otpt)) at test-tcplPlot.R:706:3 2. | \-testthat::quasi_label(enquo(object), label, arg = "object") 3. | \-rlang::eval_bare(expr, quo_get_env(quo)) - 4. +-ggplot2::is_ggplot(...) - 5. | \-S7::S7_inherits(x, class_ggplot) - 6. \-tcpl:::tcplggplot2(...) - 7. \-tcpl:::get_verbose_tables(dat, type, compare, flags) - -- Failure ('test-tcplggplot2Utils.R:344:3'): get_verbose_tables returns two tables small compare mc -- + 4. \-ggplot2::is_ggplot(otpt) + 5. \-S7::S7_inherits(x, class_ggplot) + -- Failure ('test-tcplPlot.R:721:3'): ggplot output works in sc ---------------- Expected `... <- NULL` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Error ('test-tcplggplot2Utils.R:345:3'): get_verbose_tables returns two tables small compare mc -- - Error in `eval(code, test_env)`: object 'tbls' not found + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:722:3'): ggplot output works in sc ------------------ + Error in `eval(code, test_env)`: object 'otpt' not found Backtrace: x - 1. \-testthat::expect_length(tbls, 2) at test-tcplggplot2Utils.R:345:3 - 2. \-testthat::quasi_label(enquo(object), arg = "object") - 3. \-rlang::eval_bare(expr, quo_get_env(quo)) - -- Failure ('test-tcplggplot2Utils.R:367:3'): get_verbose_tables returns two tables large compare mc -- + 1. +-testthat::expect_true(ggplot2::is_ggplot(otpt)) at test-tcplPlot.R:722:3 + 2. | \-testthat::quasi_label(enquo(object), label, arg = "object") + 3. | \-rlang::eval_bare(expr, quo_get_env(quo)) + 4. \-ggplot2::is_ggplot(otpt) + 5. \-S7::S7_inherits(x, class_ggplot) + -- Failure ('test-tcplPlot.R:737:3'): ggplot output comparison plotting works in sc -- Expected `... <- NULL` to run without any errors. i Actually got a with text: - could not find function "as_gtable" - -- Error ('test-tcplggplot2Utils.R:368:3'): get_verbose_tables returns two tables large compare mc -- - Error in `eval(code, test_env)`: object 'tbls' not found + Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + -- Error ('test-tcplPlot.R:738:3'): ggplot output comparison plotting works in sc -- + Error in `eval(code, test_env)`: object 'otpt' not found Backtrace: x - 1. \-testthat::expect_length(tbls, 2) at test-tcplggplot2Utils.R:368:3 - 2. \-testthat::quasi_label(enquo(object), arg = "object") - 3. \-rlang::eval_bare(expr, quo_get_env(quo)) - -- Failure ('test-tcplggplot2Utils.R:390:3'): get_verbose_tables returns two tables small compare sc -- - Expected `tbls <- get_verbose_tables(dat = dat, type = "sc", compare = "normalized_data_type")` to run without any errors. - i Actually got a with text: - could not find function "as_gtable" - -- Error ('test-tcplggplot2Utils.R:391:3'): get_verbose_tables returns two tables small compare sc -- - Error in `eval(code, test_env)`: object 'tbls' not found + 1. +-testthat::expect_true(ggplot2::is_ggplot(otpt)) at test-tcplPlot.R:738:3 + 2. | \-testthat::quasi_label(enquo(object), label, arg = "object") + 3. | \-rlang::eval_bare(expr, quo_get_env(quo)) + 4. \-ggplot2::is_ggplot(otpt) + 5. \-S7::S7_inherits(x, class_ggplot) + -- Error ('test-tcplPlot.R:753:3'): ggplot output returns specific warnings and errors -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. +-testthat::expect_error(...) at test-tcplPlot.R:753:3 + 2. | \-testthat:::expect_condition_matching(...) + 3. | \-testthat:::quasi_capture(...) + 4. | +-testthat (local) .capture(...) + 5. | | \-base::withCallingHandlers(...) + 6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) + 7. \-tcpl::tcplPlot(...) + 8. \-tcpl::tcplPlotLoadData(type = type, fld = fld, val = val, flags = flags) + 9. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 10. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 11. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplPlot.R:776:3'): loec plotting works for single plot -------- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x - 1. \-testthat::expect_length(tbls, 2) at test-tcplggplot2Utils.R:391:3 - 2. \-testthat::quasi_label(enquo(object), arg = "object") - 3. \-rlang::eval_bare(expr, quo_get_env(quo)) - -- Failure ('test-tcplggplot2Utils.R:409:3'): get_verbose_tables returns two tables large compare sc -- - Expected `tbls <- get_verbose_tables(dat = dat, type = "sc", compare = "normalized_data_type")` to run without any errors. - i Actually got a with text: - could not find function "as_gtable" - -- Error ('test-tcplggplot2Utils.R:410:3'): get_verbose_tables returns two tables large compare sc -- - Error in `eval(code, test_env)`: object 'tbls' not found + 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplPlot.R:776:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplPlot.R:795:3'): loec plotting works for small comparison plot -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplPlot.R:795:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplPlot.R:814:3'): loec plotting works for large comparison plot -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplPlot.R:814:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplPlotLoadData.R:30:3'): tcplPlotLoadData loads all necessary mc data -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplPlotLoadData.R:30:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplPlotLoadData.R:57:3'): tcplPlotLoadData loads all necessary sc data -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplPlotLoadData.R:57:3 + 2. \-tcpl::tcplLoadData(...) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplPlotUtils.R:57:3'): tcplPlotValidate properly validates 'by' -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplPlotUtils.R:57:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplPlotUtils.R:75:3'): tcplPlotValidate properly validates 'dat' as a list or a data.table -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplPlotUtils.R:75:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplPlotUtils.R:135:3'): tcplPlotSetYRange correctly sets yrange for mc data -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplPlotUtils.R:135:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplPlotUtils.R:170:3'): tcplPlotSetYRange correctly sets yrange for sc data -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplPlotUtils.R:170:3 + 2. \-tcpl::tcplLoadData(...) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplPlotUtils.R:194:3'): tcplPlotLoadWllt replaces NA dtxsid and chnm with well type description -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplPlotUtils.R:194:3 + 2. \-tcpl::tcplLoadData(lvl = "agg", fld = "m4id", val = dat$m4id) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2.R:32:3'): tcplggplot2 works for mc single plot ----- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplggplot2.R:32:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2.R:48:3'): tcplggplot2 works for verbose mc single plot -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplggplot2.R:48:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2.R:64:3'): tcplggplot2 works for mc small comparison plot -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2.R:64:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2.R:81:3'): tcplggplot2 works for verbose mc small comparison plot -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2.R:81:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2.R:97:3'): tcplggplot2 works for mc large comparison plot -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2.R:97:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2.R:114:3'): tcplggplot2 works for verbose (flags table) mc large comparison plot -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2.R:114:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2.R:136:3'): tcplggplot2 works for sc single plot ---- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "s2id", val = mocked$s2id) at test-tcplggplot2.R:136:3 + 2. \-tcpl::tcplLoadData(...) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2.R:152:3'): tcplggplot2 works for verbose sc single plot -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "s2id", val = mocked$s2id) at test-tcplggplot2.R:152:3 + 2. \-tcpl::tcplLoadData(...) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2.R:168:3'): tcplggplot2 works for sc small comparison plot -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplggplot2.R:168:3 + 2. \-tcpl::tcplLoadData(...) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2.R:184:3'): tcplggplot2 works for verbose sc small comparison plot -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplggplot2.R:184:3 + 2. \-tcpl::tcplLoadData(...) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2.R:200:3'): tcplggplot2 works for sc large comparison plot -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplggplot2.R:200:3 + 2. \-tcpl::tcplLoadData(...) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2.R:217:3'): tcplggplot2 correctly performs checks and validates parameters -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2.R:217:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2Utils.R:46:3'): tcplfit2_fun works ------------------ + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplggplot2Utils.R:46:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2Utils.R:86:3'): get_plot_title creates full title for single plot mc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplggplot2Utils.R:86:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2Utils.R:108:3'): get_plot_title creates full title for aeid compare plot mc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplggplot2Utils.R:108:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2Utils.R:126:3'): get_plot_title creates full title for chem compare plot mc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2Utils.R:126:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2Utils.R:149:3'): get_plot_title creates full title for other compare plot mc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2Utils.R:149:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2Utils.R:172:3'): get_plot_title creates full title for single plot sc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "s2id", val = mocked$s2id) at test-tcplggplot2Utils.R:172:3 + 2. \-tcpl::tcplLoadData(...) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2Utils.R:194:3'): get_plot_title creates full title for aeid compare plot sc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "s2id", val = mocked$s2id) at test-tcplggplot2Utils.R:194:3 + 2. \-tcpl::tcplLoadData(...) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2Utils.R:212:3'): get_plot_title creates full title for chem compare plot sc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplggplot2Utils.R:212:3 + 2. \-tcpl::tcplLoadData(...) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2Utils.R:235:3'): get_plot_title creates full title for other compare plot sc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplggplot2Utils.R:235:3 + 2. \-tcpl::tcplLoadData(...) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2Utils.R:262:3'): get_plot_caption returns list of flags for a single plot -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(val = mocked$m4id, flags = TRUE) at test-tcplggplot2Utils.R:262:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2Utils.R:278:3'): get_plot_caption returns list of flags for a compare plot -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2Utils.R:278:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2Utils.R:341:3'): get_verbose_tables returns two tables small compare mc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2Utils.R:341:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2Utils.R:364:3'): get_verbose_tables returns two tables large compare mc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(fld = "aeid", val = mocked$aeid, flags = TRUE) at test-tcplggplot2Utils.R:364:3 + 2. \-tcpl::tcplLoadData(lvl = lvl, fld = fld, val = val, type = type) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2Utils.R:387:3'): get_verbose_tables returns two tables small compare sc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. + Backtrace: + x + 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplggplot2Utils.R:387:3 + 2. \-tcpl::tcplLoadData(...) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) + -- Error ('test-tcplggplot2Utils.R:406:3'): get_verbose_tables returns two tables large compare sc -- + Error in ``[.data.table`(dat, , `:=`(which(duplicated(names(dat))), NULL))`: Internal error in R_resizeVector_: attempt to resize a non-resizable vector. Please report to the data.table issues tracker. Backtrace: x - 1. \-testthat::expect_length(tbls, 2) at test-tcplggplot2Utils.R:410:3 - 2. \-testthat::quasi_label(enquo(object), arg = "object") - 3. \-rlang::eval_bare(expr, quo_get_env(quo)) + 1. \-tcpl::tcplPlotLoadData(type = "sc", fld = "aeid", val = mocked$aeid) at test-tcplggplot2Utils.R:406:3 + 2. \-tcpl::tcplLoadData(...) + 3. +-dat[, `:=`(which(duplicated(names(dat))), NULL)] + 4. \-data.table:::`[.data.table`(...) - [ FAIL 44 | WARN 859 | SKIP 5 | PASS 681 ] + [ FAIL 157 | WARN 705 | SKIP 5 | PASS 453 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK > 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") + unlink(dt.git, recursive=TRUE, force=TRUE) + system(paste("cd ~/R/data.table && git fetch --tags")) + system(paste("git clone ~/R/data.table", dt.git)) + release.tag <- gsub(".tar.gz|.*_", "", cargs[["release"]]) + rev.parse.cmd <- paste( + "cd", dt.git, "&& git rev-parse master") + master.sha <- system(rev.parse.cmd, intern=TRUE) + merge.base.cmd <- paste( + "cd", dt.git, "&& git merge-base master", release.tag) + merge.base.sha <- system(merge.base.cmd, intern=TRUE) + old.sha <- merge.base.sha + run_R <- file.path(proj.dir, "install_dt_then_check_dep.R") + sig.diff.dt[, first.bad.commit := NA_character_] + sig.diff.dt[, comments := NA_character_] + for(diff.i in 1:nrow(sig.diff.dt)){ + sig.diff.row <- sig.diff.dt[diff.i] + bisect.cmd <- paste( + "cd", dt.git, "&&", + "git bisect start &&", + "git bisect old", old.sha, "&&", + "git bisect new master &&", + "git bisect run", + R.home('bin/Rscript'), + run_R, + shQuote(sig.diff.row$checking), + sig.diff.row$release, + rev.dep.release.tar.gz, + release.tag) + print(bisect.cmd) + bisect.out <- system(bisect.cmd, intern=TRUE) + cat(bisect.out,sep="\n") + if(is.null(attr(bisect.out,"status"))){ + first.bad.sha <- nc::capture_all_str( + bisect.out, + sha="[0-9a-f]+", + " is the first new commit")$sha + parent.cmd <- paste( + "cd ~/R/data.table && git log --pretty=%P -n 1", + first.bad.sha) + parent.sha <- system(parent.cmd, intern=TRUE) + sig.diff.dt[diff.i, first.bad.commit := first.bad.sha] + parent.msg <- paste0("parent=", parent.sha) + this.comment <- if(parent.sha==old.sha){ + paste(parent.msg, "same as git bisect old") + }else if(first.bad.sha==master.sha){ + paste("same as git bisect new=master,", parent.msg) + }else{ + parent.msg + } + sig.diff.dt[diff.i, comments := this.comment] + } + } + ## add CRAN column. + sig.diff.dt[, CRAN := { + flavor <- get_flavor(Rvers) + details <- data.table(flavor=unique(flavor))[, { + base <- "https://www.r-project.org/nosvn/R.check/" + u <- paste0(base, flavor, "/", rev.dep, "-00check.txt") + check.txt <- tempfile() + tryCatch({ + download.file(u, check.txt, quiet=TRUE) + }, error=function(e){ + NULL + }) + check.lines <- if(file.exists(check.txt)){ + readLines(check.txt,encoding="UTF-8") + }else{ + "" + } + repl.lines <- gsub("[\u2018\u2019]", "'", check.lines) + ##gsub("[‘’]", "'", check.lines) does not work with LC_ALL=C. + myStatus(line.vec=repl.lines) + }, by=flavor] + select.dt <- data.table(flavor, checking) + details[select.dt, msg, on=.(flavor, checking)] + }] + dir.create(file.path(job.dir, Rvers)) + diffs.csv <- file.path(job.dir, Rvers, "significant_differences.csv") + data.table::fwrite(sig.diff.dt, diffs.csv) + print(sig.diff.dt) + } >