Note: the module "R" cannot be unloaded because it was not loaded. WARNING: ignoring environment value of R_HOME R Under development (unstable) (2026-02-02 r89367) -- "Unsuffered Consequences" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > cargs <- commandArgs(trailingOnly=TRUE) > 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/2026-02-02/deps.csv", task.str = "1048", release = "/scratch/th798/data.table-revdeps/2026-02-02/data.table_release_1.18.2.1.tar.gz", master = "/scratch/th798/data.table-revdeps/2026-02-02/data.table_master_1.18.99.1bd88cbcc806bdaa2aa276e12c78fb4ba13cb645.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/26770126/R-devel/1048" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/26770126/R-devel/1048/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "pmparser" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/26770126/R-devel/1048/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] "2026-02-02 13:52:21 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/26770126/R-devel/1048/library' (as 'lib' is unspecified) also installing the dependencies 'xfun', 'yaml', 'RPostgres', 'knitr', 'rmarkdown' trying URL 'http://cloud.r-project.org/src/contrib/xfun_0.56.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/RPostgres_1.4.8.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/knitr_1.51.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/pmparser_1.0.23.tar.gz' * installing *source* package 'xfun' ... ** this is package 'xfun' version '0.56' ** 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/th798/26770126/R-devel/1048/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/th798/26770126/R-devel/1048/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 'RPostgres' ... ** this is package 'RPostgres' version '1.4.8' ** package 'RPostgres' successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs (libpq 14.5)! Using PKG_CFLAGS=-I/home/th798/.conda/envs/emacs1/include Using PKG_LIBS=-L/home/th798/.conda/envs/emacs1/lib -lpq Using PKG_PLOGR= /usr/bin/cp -f src/Makevars.new src/Makevars ** 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/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 DbColumn.cpp -o DbColumn.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 DbColumnDataSource.cpp -o DbColumnDataSource.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 DbColumnDataSourceFactory.cpp -o DbColumnDataSourceFactory.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 DbColumnStorage.cpp -o DbColumnStorage.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 DbConnection.cpp -o DbConnection.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 DbDataFrame.cpp -o DbDataFrame.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 DbResult.cpp -o DbResult.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 PqColumnDataSource.cpp -o PqColumnDataSource.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 PqColumnDataSourceFactory.cpp -o PqColumnDataSourceFactory.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 PqDataFrame.cpp -o PqDataFrame.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 PqResult.cpp -o PqResult.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 PqResultImpl.cpp -o PqResultImpl.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 PqResultSource.cpp -o PqResultSource.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 PqUtils.cpp -o PqUtils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 RPostgres-init.c -o RPostgres-init.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 connection.cpp -o connection.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 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/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 encode.cpp -o encode.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 encrypt.cpp -o encrypt.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 logging.cpp -o logging.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I'/projects/genomic-ml/R/R-devel/library/plogr/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 result.cpp -o result.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 RPostgres.so DbColumn.o DbColumnDataSource.o DbColumnDataSourceFactory.o DbColumnStorage.o DbConnection.o DbDataFrame.o DbResult.o PqColumnDataSource.o PqColumnDataSourceFactory.o PqDataFrame.o PqResult.o PqResultImpl.o PqResultSource.o PqUtils.o RPostgres-init.o connection.o cpp11.o encode.o encrypt.o logging.o result.o -L/home/th798/.conda/envs/emacs1/lib -lpq installing to /tmp/th798/26770126/R-devel/1048/library/00LOCK-RPostgres/00new/RPostgres/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 (RPostgres) * installing *source* package 'pmparser' ... ** this is package 'pmparser' version '1.0.23' ** package 'pmparser' successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 'pmparser' * removing '/tmp/th798/26770126/R-devel/1048/library/pmparser' * installing *source* package 'knitr' ... ** this is package 'knitr' version '1.51' ** package 'knitr' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (knitr) * installing *source* package '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) The downloaded source packages are in '/tmp/th798/26770126/RtmpPt6wXR/downloaded_packages' Warning message: In install.packages(rev.dep, dep = TRUE) : installation of package 'pmparser' had non-zero exit status > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 73.535 5.314 109.716 > print(Sys.time()) [1] "2026-02-02 13:54:11 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] "2026-02-02 13:54:11 MST" Installing package into '/tmp/th798/26770126/R-devel/1048/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.18.2.1' ** package 'data.table' successfully unpacked and MD5 sums checked ** using staged installation zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c assign.c -o assign.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c between.c -o between.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bmerge.c -o bmerge.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c chmatch.c -o chmatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cj.c -o cj.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c coalesce.c -o coalesce.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dogroups.c -o dogroups.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmean.c -o fastmean.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fcast.c -o fcast.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fifelse.c -o fifelse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fmelt.c -o fmelt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c forder.c -o forder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frank.c -o frank.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fread.c -o fread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c freadR.c -o freadR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c froll.c -o froll.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollR.c -o frollR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frolladaptive.c -o frolladaptive.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollapply.c -o frollapply.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fsort.c -o fsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwrite.c -o fwrite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwriteR.c -o fwriteR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c gsumm.c -o gsumm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c hash.c -o hash.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c idatetime.c -o idatetime.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ijoin.c -o ijoin.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c inrange.c -o inrange.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c mergelist.c -o mergelist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nafill.c -o nafill.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c negate.c -o negate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nqrecreateindices.c -o nqrecreateindices.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c openmp-utils.c -o openmp-utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c programming.c -o programming.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c quickselect.c -o quickselect.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rbindlist.c -o rbindlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c reorder.c -o reorder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shellsort.c -o shellsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shift.c -o shift.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c snprintf.c -o snprintf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c subset.c -o subset.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c transpose.c -o transpose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c types.c -o types.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uniqlist.c -o uniqlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.c -o utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vecseq.c -o vecseq.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wrappers.c -o wrappers.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o hash.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fvisibility=hidden -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fvisibility=hidden -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi installing to /tmp/th798/26770126/R-devel/1048/library/00LOCK-data.table/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) [1] "2026-02-02 13:54:43 MST" * using log directory '/tmp/th798/26770126/R-devel/1048/pmparser.Rcheck' * using R Under development (unstable) (2026-02-02 r89367) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * current time: 2026-02-02 20:54:43Z * checking for file 'pmparser/DESCRIPTION' ... OK * this is package 'pmparser' version '1.0.23' * 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 'pmparser' 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking 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: > library(testthat) > library(pmparser) > > test_check('pmparser') trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed26n1334.xml.gz.md5' Content type 'application/x-gzip' length 60 bytes ================================================== downloaded 60 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed26n1334.xml.gz' Content type 'application/x-gzip' length 13837691 bytes (13.2 MB) ================================================== downloaded 13.2 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed26n1335.xml.gz.md5' Content type 'application/x-gzip' length 60 bytes ================================================== downloaded 60 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed26n1335.xml.gz' Content type 'application/x-gzip' length 44629574 bytes (42.6 MB) ================================================== downloaded 42.6 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed26n1334.xml.gz.md5' Content type 'application/x-gzip' length 60 bytes ================================================== downloaded 60 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed26n1334.xml.gz' Content type 'application/x-gzip' length 13837691 bytes (13.2 MB) ================================================== downloaded 13.2 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed26n1335.xml.gz.md5' Content type 'application/x-gzip' length 60 bytes ================================================== downloaded 60 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed26n1335.xml.gz' Content type 'application/x-gzip' length 44629574 bytes (42.6 MB) ================================================== downloaded 42.6 MB [ FAIL 56 | WARN 48 | SKIP 4 | PASS 131 ] == Skipped tests (4) =========================================================== * On CRAN (4): 'test_get_citation.R:4:3', 'test_get_citation.R:13:3', 'test_get_pubmed_files.R:7:3', 'test_get_pubmed_files.R:20:3' == Failed tests ================================================================ -- Failure ('test_modify_pubmed_db_dup.R:76:5'): modifyPubmedDb update is unique -- data_bank not equal to 0L. 1/1 mismatches [1] 101 - 0 == 101 -- Failure ('test_modify_pubmed_db_dup.R:76:5'): modifyPubmedDb update is unique -- mesh_qualifier not equal to 0L. 1/1 mismatches [1] 405 - 0 == 405 -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- abstract not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (9603, 68) differ > Component "pmid": Numeric: lengths (9603, 68) differ Component "text": Lengths (9603, 68) differ (string compare on first 68) Component "text": 68 string mismatches Component "label": Lengths (9603, 68) differ (string compare on first 68) Component "label": 'is.NA' value mismatch: 15 in current 13 in target Component "nlm_category": Lengths (9603, 68) differ (string compare on first 68) Component "nlm_category": 'is.NA' value mismatch: 15 in current 13 in target Component "abstract_pos": Numeric: lengths (9603, 68) differ -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- abstract_copyright not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (3219, 22) differ > Component "pmid": Numeric: lengths (3219, 22) differ Component "copyright": Lengths (3219, 22) differ (string compare on first 22) Component "copyright": 22 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- article not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ > Component "pmid": Numeric: lengths (4989, 30) differ Component "title": Lengths (4989, 30) differ (string compare on first 30) Component "title": 30 string mismatches Component "language": Lengths (4989, 30) differ (string compare on first 30) Component "language": 2 string mismatches Component "vernacular_title": Lengths (4989, 30) differ (string compare on first 30) Component "vernacular_title": 'is.NA' value mismatch: 28 in current 30 in target Component "pub_model": Lengths (4989, 30) differ (string compare on first 30) ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- article_id not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (6359, 40) differ > Component "pmid": Numeric: lengths (6359, 40) differ Component "id_type": Lengths (6359, 40) differ (string compare on first 40) Component "id_type": 10 string mismatches Component "id_value": Lengths (6359, 40) differ (string compare on first 40) Component "id_value": 40 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (34978, 279) differ > Component "pmid": Numeric: lengths (34978, 279) differ Component "author_pos": Numeric: lengths (34978, 279) differ Component "last_name": Lengths (34978, 279) differ (string compare on first 279) Component "last_name": 'is.NA' value mismatch: 4 in current 0 in target Component "fore_name": Lengths (34978, 279) differ (string compare on first 279) Component "fore_name": 'is.NA' value mismatch: 5 in current 0 in target Component "initials": Lengths (34978, 279) differ (string compare on first 279) Component "initials": 'is.NA' value mismatch: 5 in current 0 in target ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author_affiliation not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (42448, 337) differ > Component "pmid": Numeric: lengths (42448, 337) differ Component "author_pos": Numeric: lengths (42448, 337) differ Component "affiliation_pos": Numeric: lengths (42448, 337) differ Component "affiliation": Lengths (42448, 337) differ (string compare on first 337) Component "affiliation": 337 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (989, 0) differ > Component "pmid": Numeric: lengths (989, 0) differ Component "author_pos": Numeric: lengths (989, 0) differ Component "affiliation_pos": Numeric: lengths (989, 0) differ Component "source": Lengths (989, 0) differ (string compare on first 0) Component "identifier": Lengths (989, 0) differ (string compare on first 0) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (7607, 29) differ > Component "pmid": Numeric: lengths (7607, 29) differ Component "author_pos": Numeric: lengths (7607, 29) differ Component "source": Lengths (7607, 29) differ (string compare on first 29) Component "identifier": Lengths (7607, 29) differ (string compare on first 29) Component "identifier": 29 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4932, 30) differ > Component "pmid": Numeric: lengths (4932, 30) differ Component "complete": Lengths (4932, 30) differ (string compare on first 30) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- chemical not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (1777, 5) differ > Component "pmid": Numeric: lengths (1777, 5) differ Component "registry_number": Lengths (1777, 5) differ (string compare on first 5) Component "registry_number": 3 string mismatches Component "substance_name": Lengths (1777, 5) differ (string compare on first 5) Component "substance_name": 5 string mismatches Component "substance_ui": Lengths (1777, 5) differ (string compare on first 5) Component "substance_ui": 5 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- comment not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (150, 3) differ > Component "pmid": Numeric: lengths (150, 3) differ Component "ref_type": Lengths (150, 3) differ (string compare on first 3) Component "ref_type": 1 string mismatch Component "ref_pmid": Numeric: lengths (150, 3) differ -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- data_bank not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (70, 4) differ > Component "pmid": Numeric: lengths (70, 4) differ Component "data_bank_name": Lengths (70, 4) differ (string compare on first 4) Component "accession_number": Lengths (70, 4) differ (string compare on first 4) Component "accession_number": 4 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- grant_item not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (2637, 35) differ > Component "pmid": Numeric: lengths (2637, 35) differ Component "grant_id": Lengths (2637, 35) differ (string compare on first 35) Component "grant_id": 'is.NA' value mismatch: 6 in current 8 in target Component "acronym": Lengths (2637, 35) differ (string compare on first 35) Component "acronym": 'is.NA' value mismatch: 20 in current 34 in target Component "agency": Lengths (2637, 35) differ (string compare on first 35) Component "agency": 35 string mismatches Component "country": Lengths (2637, 35) differ (string compare on first 35) ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- grant_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (909, 8) differ > Component "pmid": Numeric: lengths (909, 8) differ Component "complete": Lengths (909, 8) differ (string compare on first 8) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- investigator not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (2074, 80) differ > Component "pmid": Numeric: lengths (2074, 80) differ Component "investigator_pos": Numeric: lengths (2074, 80) differ Component "last_name": Lengths (2074, 80) differ (string compare on first 80) Component "last_name": 80 string mismatches Component "fore_name": Lengths (2074, 80) differ (string compare on first 80) Component "fore_name": 80 string mismatches Component "initials": Lengths (2074, 80) differ (string compare on first 80) Component "initials": 73 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (45, 53) differ > Component "pmid": Numeric: lengths (45, 53) differ Component "investigator_pos": Numeric: lengths (45, 53) differ Component "affiliation_pos": Numeric: lengths (45, 53) differ Component "affiliation": Lengths (45, 53) differ (string compare on first 45) Component "affiliation": 45 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- journal not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ > Component "pmid": Numeric: lengths (4989, 30) differ Component "journal_name": Lengths (4989, 30) differ (string compare on first 30) Component "journal_name": 30 string mismatches Component "journal_iso": Lengths (4989, 30) differ (string compare on first 30) Component "journal_iso": 30 string mismatches Component "pub_date": Numeric: lengths (4989, 30) differ Component "pub_year": Lengths (4989, 30) differ (string compare on first 30) Component "pub_year": 30 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- keyword_item not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (19167, 109) differ > Component "pmid": Numeric: lengths (19167, 109) differ Component "keyword_name": Lengths (19167, 109) differ (string compare on first 109) Component "keyword_name": 109 string mismatches Component "major_topic": Lengths (19167, 109) differ (string compare on first 109) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- keyword_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (3596, 21) differ > Component "pmid": Numeric: lengths (3596, 21) differ Component "list_owner": Lengths (3596, 21) differ (string compare on first 21) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (11460, 74) differ > Component "pmid": Numeric: lengths (11460, 74) differ Component "descriptor_pos": Lengths (11460, 74) differ (string compare on first 74) Component "descriptor_pos": 65 string mismatches Component "descriptor_name": Lengths (11460, 74) differ (string compare on first 74) Component "descriptor_name": 71 string mismatches Component "descriptor_ui": Lengths (11460, 74) differ (string compare on first 74) Component "descriptor_ui": 71 string mismatches Component "descriptor_major_topic": Lengths (11460, 74) differ (string compare on first 74) ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- mesh_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ > Component "pmid": Numeric: lengths (4989, 30) differ Component "indexing_method": Lengths (4989, 30) differ (string compare on first 30) Component "indexing_method": 1 string mismatch -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (7130, 39) differ > Component "pmid": Numeric: lengths (7130, 39) differ Component "descriptor_pos": Lengths (7130, 39) differ (string compare on first 39) Component "descriptor_pos": 35 string mismatches Component "qualifier_name": Lengths (7130, 39) differ (string compare on first 39) Component "qualifier_name": 38 string mismatches Component "qualifier_ui": Lengths (7130, 39) differ (string compare on first 39) Component "qualifier_ui": 38 string mismatches Component "qualifier_major_topic": Lengths (7130, 39) differ (string compare on first 39) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- other_abstract not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (147, 4) differ > Component "pmid": Numeric: lengths (147, 4) differ Component "text": Lengths (147, 4) differ (string compare on first 4) Component "text": 4 string mismatches Component "type": Lengths (147, 4) differ (string compare on first 4) Component "type": 2 string mismatches Component "language": Lengths (147, 4) differ (string compare on first 4) Component "language": 4 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- pmid_status not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ > Component "pmid": Numeric: lengths (4989, 30) differ Component "version": Numeric: lengths (4989, 30) differ Component "xml_filename": Lengths (4989, 30) differ (string compare on first 30) Component "xml_filename": 30 string mismatches Component "status": Lengths (4989, 30) differ (string compare on first 30) Component "status": 14 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- pub_history not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (22724, 143) differ > Component "pmid": Numeric: lengths (22724, 143) differ Component "pub_status": Lengths (22724, 143) differ (string compare on first 143) Component "pub_status": 100 string mismatches Component "pub_date": Numeric: lengths (22724, 143) differ -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- pub_type not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (6060, 37) differ > Component "pmid": Numeric: lengths (6060, 37) differ Component "type_name": Lengths (6060, 37) differ (string compare on first 37) Component "type_name": 12 string mismatches Component "type_id": Lengths (6060, 37) differ (string compare on first 37) Component "type_id": 12 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- readme not equal to DBI::dbReadTable(conExp, tableName). Component "text": 1 string mismatch -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- abstract not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (27961, 126) differ > Component "pmid": Numeric: lengths (27961, 126) differ Component "text": Lengths (27961, 126) differ (string compare on first 126) Component "text": 58 string mismatches Component "label": Lengths (27961, 126) differ (string compare on first 126) Component "label": 'is.NA' value mismatch: 34 in current 27 in target Component "nlm_category": Lengths (27961, 126) differ (string compare on first 126) Component "nlm_category": 'is.NA' value mismatch: 34 in current 50 in target Component "abstract_pos": Numeric: lengths (27961, 126) differ -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- abstract_copyright not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (9124, 43) differ > Component "pmid": Numeric: lengths (9124, 43) differ Component "copyright": Lengths (9124, 43) differ (string compare on first 43) Component "copyright": 21 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- article not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (14308, 60) differ > Component "pmid": Numeric: lengths (14308, 60) differ Component "title": Lengths (14308, 60) differ (string compare on first 60) Component "title": 30 string mismatches Component "language": Lengths (14308, 60) differ (string compare on first 60) Component "vernacular_title": Lengths (14308, 60) differ (string compare on first 60) Component "vernacular_title": 'is.NA' value mismatch: 57 in current 58 in target Component "pub_model": Lengths (14308, 60) differ (string compare on first 60) Component "pub_model": 19 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- article_id not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (16828, 76) differ > Component "pmid": Numeric: lengths (16828, 76) differ Component "id_type": Lengths (16828, 76) differ (string compare on first 76) Component "id_type": 10 string mismatches Component "id_value": Lengths (16828, 76) differ (string compare on first 76) Component "id_value": 36 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (101991, 490) differ > Component "pmid": Numeric: lengths (101991, 490) differ Component "author_pos": Numeric: lengths (101991, 490) differ Component "last_name": Lengths (101991, 490) differ (string compare on first 490) Component "last_name": 'is.NA' value mismatch: 6 in current 4 in target Component "fore_name": Lengths (101991, 490) differ (string compare on first 490) Component "fore_name": 'is.NA' value mismatch: 7 in current 5 in target Component "initials": Lengths (101991, 490) differ (string compare on first 490) Component "initials": 'is.NA' value mismatch: 7 in current 5 in target ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author_affiliation not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (121076, 614) differ > Component "pmid": Numeric: lengths (121076, 614) differ Component "author_pos": Numeric: lengths (121076, 614) differ Component "affiliation_pos": Numeric: lengths (121076, 614) differ Component "affiliation": Lengths (121076, 614) differ (string compare on first 614) Component "affiliation": 277 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (3559, 0) differ > Component "pmid": Numeric: lengths (3559, 0) differ Component "author_pos": Numeric: lengths (3559, 0) differ Component "affiliation_pos": Numeric: lengths (3559, 0) differ Component "source": Lengths (3559, 0) differ (string compare on first 0) Component "identifier": Lengths (3559, 0) differ (string compare on first 0) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (21074, 61) differ > Component "pmid": Numeric: lengths (21074, 61) differ Component "author_pos": Numeric: lengths (21074, 61) differ Component "source": Lengths (21074, 61) differ (string compare on first 61) Component "identifier": Lengths (21074, 61) differ (string compare on first 61) Component "identifier": 32 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (14209, 59) differ > Component "pmid": Numeric: lengths (14209, 59) differ Component "complete": Lengths (14209, 59) differ (string compare on first 59) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- chemical not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (9674, 16) differ > Component "pmid": Numeric: lengths (9674, 16) differ Component "registry_number": Lengths (9674, 16) differ (string compare on first 16) Component "registry_number": 8 string mismatches Component "substance_name": Lengths (9674, 16) differ (string compare on first 16) Component "substance_name": 11 string mismatches Component "substance_ui": Lengths (9674, 16) differ (string compare on first 16) Component "substance_ui": 11 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- comment not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (898, 6) differ > Component "pmid": Numeric: lengths (898, 6) differ Component "ref_type": Lengths (898, 6) differ (string compare on first 6) Component "ref_type": 3 string mismatches Component "ref_pmid": Numeric: lengths (898, 6) differ -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- data_bank not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (267, 6) differ > Component "pmid": Numeric: lengths (267, 6) differ Component "data_bank_name": Lengths (267, 6) differ (string compare on first 6) Component "data_bank_name": 1 string mismatch Component "accession_number": Lengths (267, 6) differ (string compare on first 6) Component "accession_number": 2 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- grant_item not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (8770, 57) differ > Component "pmid": Numeric: lengths (8770, 57) differ Component "grant_id": Lengths (8770, 57) differ (string compare on first 57) Component "grant_id": 'is.NA' value mismatch: 13 in current 8 in target Component "acronym": Lengths (8770, 57) differ (string compare on first 57) Component "acronym": 'is.NA' value mismatch: 42 in current 22 in target Component "agency": Lengths (8770, 57) differ (string compare on first 57) Component "agency": 22 string mismatches Component "country": Lengths (8770, 57) differ (string compare on first 57) ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- grant_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (3033, 17) differ > Component "pmid": Numeric: lengths (3033, 17) differ Component "complete": Lengths (3033, 17) differ (string compare on first 17) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- investigator not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (5842, 144) differ > Component "pmid": Numeric: lengths (5842, 144) differ Component "investigator_pos": Numeric: lengths (5842, 144) differ Component "last_name": Lengths (5842, 144) differ (string compare on first 144) Component "last_name": 64 string mismatches Component "fore_name": Lengths (5842, 144) differ (string compare on first 144) Component "fore_name": 64 string mismatches Component "initials": Lengths (5842, 144) differ (string compare on first 144) Component "initials": 59 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (227, 53) differ > Component "pmid": Numeric: lengths (227, 53) differ Component "investigator_pos": Numeric: lengths (227, 53) differ Component "affiliation_pos": Numeric: lengths (227, 53) differ Component "affiliation": Lengths (227, 53) differ (string compare on first 53) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- investigator_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (2, 0) differ > Component "pmid": Numeric: lengths (2, 0) differ Component "investigator_pos": Numeric: lengths (2, 0) differ Component "source": Lengths (2, 0) differ (string compare on first 0) Component "identifier": Lengths (2, 0) differ (string compare on first 0) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- journal not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (14308, 60) differ > Component "pmid": Numeric: lengths (14308, 60) differ Component "journal_name": Lengths (14308, 60) differ (string compare on first 60) Component "journal_name": 30 string mismatches Component "journal_iso": Lengths (14308, 60) differ (string compare on first 60) Component "journal_iso": 30 string mismatches Component "pub_date": Numeric: lengths (14308, 60) differ Component "pub_year": Lengths (14308, 60) differ (string compare on first 60) Component "pub_year": 30 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- keyword_item not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (57226, 229) differ > Component "pmid": Numeric: lengths (57226, 229) differ Component "keyword_name": Lengths (57226, 229) differ (string compare on first 229) Component "keyword_name": 120 string mismatches Component "major_topic": Lengths (57226, 229) differ (string compare on first 229) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- keyword_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (10762, 43) differ > Component "pmid": Numeric: lengths (10762, 43) differ Component "list_owner": Lengths (10762, 43) differ (string compare on first 43) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (72995, 140) differ > Component "pmid": Numeric: lengths (72995, 140) differ Component "descriptor_pos": Lengths (72995, 140) differ (string compare on first 140) Component "descriptor_pos": 51 string mismatches Component "descriptor_name": Lengths (72995, 140) differ (string compare on first 140) Component "descriptor_name": 66 string mismatches Component "descriptor_ui": Lengths (72995, 140) differ (string compare on first 140) Component "descriptor_ui": 66 string mismatches Component "descriptor_major_topic": Lengths (72995, 140) differ (string compare on first 140) ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- mesh_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (6973, 36) differ > Component "pmid": Numeric: lengths (6973, 36) differ Component "indexing_method": Lengths (6973, 36) differ (string compare on first 36) Component "indexing_method": 6 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (42278, 88) differ > Component "pmid": Numeric: lengths (42278, 88) differ Component "descriptor_pos": Lengths (42278, 88) differ (string compare on first 88) Component "descriptor_pos": 49 string mismatches Component "qualifier_name": Lengths (42278, 88) differ (string compare on first 88) Component "qualifier_name": 47 string mismatches Component "qualifier_ui": Lengths (42278, 88) differ (string compare on first 88) Component "qualifier_ui": 47 string mismatches Component "qualifier_major_topic": Lengths (42278, 88) differ (string compare on first 88) ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- other_abstract not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (417, 7) differ > Component "pmid": Numeric: lengths (417, 7) differ Component "text": Lengths (417, 7) differ (string compare on first 7) Component "text": 3 string mismatches Component "type": Lengths (417, 7) differ (string compare on first 7) Component "type": 2 string mismatches Component "language": Lengths (417, 7) differ (string compare on first 7) Component "language": 3 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- pmid_status not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (14327, 60) differ > Component "pmid": Numeric: lengths (14327, 60) differ Component "version": Numeric: lengths (14327, 60) differ Component "xml_filename": Lengths (14327, 60) differ (string compare on first 60) Component "xml_filename": 30 string mismatches Component "status": Lengths (14327, 60) differ (string compare on first 60) Component "status": 24 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- pub_history not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (70114, 293) differ > Component "pmid": Numeric: lengths (70114, 293) differ Component "pub_status": Lengths (70114, 293) differ (string compare on first 293) Component "pub_status": 114 string mismatches Component "pub_date": Numeric: lengths (70114, 293) differ -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- pub_type not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (19407, 74) differ > Component "pmid": Numeric: lengths (19407, 74) differ Component "type_name": Lengths (19407, 74) differ (string compare on first 74) Component "type_name": 27 string mismatches Component "type_id": Lengths (19407, 74) differ (string compare on first 74) Component "type_id": 27 string mismatches [ FAIL 56 | WARN 48 | SKIP 4 | PASS 131 ] Error: Test failures In addition: Warning message: call dbDisconnect() when finished working with a connection 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 See '/tmp/th798/26770126/R-devel/1048/pmparser.Rcheck/00check.log' for details. [1] "2026-02-02 14:07:59 MST" [1] "2026-02-02 14:07:59 MST" Installing package into '/tmp/th798/26770126/R-devel/1048/library' (as 'lib' is unspecified) Warning: invalid package '/scratch/th798/data.table-revdeps/2026-02-02/data.table_master_1.18.99.1bd88cbcc806bdaa2aa276e12c78fb4ba13cb645.tar.gz' Error: ERROR: no packages specified [1] "2026-02-02 14:08:00 MST" * using log directory '/tmp/th798/26770126/R-devel/1048/pmparser.Rcheck' * using R Under development (unstable) (2026-02-02 r89367) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Spack GCC) 12.2.0 GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII * current time: 2026-02-02 21:08:00Z * checking for file 'pmparser/DESCRIPTION' ... OK * this is package 'pmparser' version '1.0.23' * 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 'pmparser' 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking 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: > library(testthat) > library(pmparser) > > test_check('pmparser') trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed26n1334.xml.gz.md5' Content type 'application/x-gzip' length 60 bytes ================================================== downloaded 60 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed26n1334.xml.gz' Content type 'application/x-gzip' length 13837691 bytes (13.2 MB) ================================================== downloaded 13.2 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed26n1335.xml.gz.md5' Content type 'application/x-gzip' length 60 bytes ================================================== downloaded 60 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed26n1335.xml.gz' Content type 'application/x-gzip' length 44629574 bytes (42.6 MB) ================================================== downloaded 42.6 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed26n1334.xml.gz.md5' Content type 'application/x-gzip' length 60 bytes ================================================== downloaded 60 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed26n1334.xml.gz' Content type 'application/x-gzip' length 13837691 bytes (13.2 MB) ================================================== downloaded 13.2 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed26n1335.xml.gz.md5' Content type 'application/x-gzip' length 60 bytes ================================================== downloaded 60 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed26n1335.xml.gz' Content type 'application/x-gzip' length 44629574 bytes (42.6 MB) ================================================== downloaded 42.6 MB [ FAIL 56 | WARN 48 | SKIP 4 | PASS 131 ] == Skipped tests (4) =========================================================== * On CRAN (4): 'test_get_citation.R:4:3', 'test_get_citation.R:13:3', 'test_get_pubmed_files.R:7:3', 'test_get_pubmed_files.R:20:3' == Failed tests ================================================================ -- Failure ('test_modify_pubmed_db_dup.R:76:5'): modifyPubmedDb update is unique -- data_bank not equal to 0L. 1/1 mismatches [1] 101 - 0 == 101 -- Failure ('test_modify_pubmed_db_dup.R:76:5'): modifyPubmedDb update is unique -- mesh_qualifier not equal to 0L. 1/1 mismatches [1] 405 - 0 == 405 -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- abstract not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (9603, 68) differ > Component "pmid": Numeric: lengths (9603, 68) differ Component "text": Lengths (9603, 68) differ (string compare on first 68) Component "text": 68 string mismatches Component "label": Lengths (9603, 68) differ (string compare on first 68) Component "label": 'is.NA' value mismatch: 15 in current 13 in target Component "nlm_category": Lengths (9603, 68) differ (string compare on first 68) Component "nlm_category": 'is.NA' value mismatch: 15 in current 13 in target Component "abstract_pos": Numeric: lengths (9603, 68) differ -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- abstract_copyright not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (3219, 22) differ > Component "pmid": Numeric: lengths (3219, 22) differ Component "copyright": Lengths (3219, 22) differ (string compare on first 22) Component "copyright": 22 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- article not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ > Component "pmid": Numeric: lengths (4989, 30) differ Component "title": Lengths (4989, 30) differ (string compare on first 30) Component "title": 30 string mismatches Component "language": Lengths (4989, 30) differ (string compare on first 30) Component "language": 2 string mismatches Component "vernacular_title": Lengths (4989, 30) differ (string compare on first 30) Component "vernacular_title": 'is.NA' value mismatch: 28 in current 30 in target Component "pub_model": Lengths (4989, 30) differ (string compare on first 30) ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- article_id not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (6359, 40) differ > Component "pmid": Numeric: lengths (6359, 40) differ Component "id_type": Lengths (6359, 40) differ (string compare on first 40) Component "id_type": 10 string mismatches Component "id_value": Lengths (6359, 40) differ (string compare on first 40) Component "id_value": 40 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (34978, 279) differ > Component "pmid": Numeric: lengths (34978, 279) differ Component "author_pos": Numeric: lengths (34978, 279) differ Component "last_name": Lengths (34978, 279) differ (string compare on first 279) Component "last_name": 'is.NA' value mismatch: 4 in current 0 in target Component "fore_name": Lengths (34978, 279) differ (string compare on first 279) Component "fore_name": 'is.NA' value mismatch: 5 in current 0 in target Component "initials": Lengths (34978, 279) differ (string compare on first 279) Component "initials": 'is.NA' value mismatch: 5 in current 0 in target ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author_affiliation not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (42448, 337) differ > Component "pmid": Numeric: lengths (42448, 337) differ Component "author_pos": Numeric: lengths (42448, 337) differ Component "affiliation_pos": Numeric: lengths (42448, 337) differ Component "affiliation": Lengths (42448, 337) differ (string compare on first 337) Component "affiliation": 337 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (989, 0) differ > Component "pmid": Numeric: lengths (989, 0) differ Component "author_pos": Numeric: lengths (989, 0) differ Component "affiliation_pos": Numeric: lengths (989, 0) differ Component "source": Lengths (989, 0) differ (string compare on first 0) Component "identifier": Lengths (989, 0) differ (string compare on first 0) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (7607, 29) differ > Component "pmid": Numeric: lengths (7607, 29) differ Component "author_pos": Numeric: lengths (7607, 29) differ Component "source": Lengths (7607, 29) differ (string compare on first 29) Component "identifier": Lengths (7607, 29) differ (string compare on first 29) Component "identifier": 29 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4932, 30) differ > Component "pmid": Numeric: lengths (4932, 30) differ Component "complete": Lengths (4932, 30) differ (string compare on first 30) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- chemical not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (1777, 5) differ > Component "pmid": Numeric: lengths (1777, 5) differ Component "registry_number": Lengths (1777, 5) differ (string compare on first 5) Component "registry_number": 3 string mismatches Component "substance_name": Lengths (1777, 5) differ (string compare on first 5) Component "substance_name": 5 string mismatches Component "substance_ui": Lengths (1777, 5) differ (string compare on first 5) Component "substance_ui": 5 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- comment not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (150, 3) differ > Component "pmid": Numeric: lengths (150, 3) differ Component "ref_type": Lengths (150, 3) differ (string compare on first 3) Component "ref_type": 1 string mismatch Component "ref_pmid": Numeric: lengths (150, 3) differ -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- data_bank not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (70, 4) differ > Component "pmid": Numeric: lengths (70, 4) differ Component "data_bank_name": Lengths (70, 4) differ (string compare on first 4) Component "accession_number": Lengths (70, 4) differ (string compare on first 4) Component "accession_number": 4 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- grant_item not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (2637, 35) differ > Component "pmid": Numeric: lengths (2637, 35) differ Component "grant_id": Lengths (2637, 35) differ (string compare on first 35) Component "grant_id": 'is.NA' value mismatch: 6 in current 8 in target Component "acronym": Lengths (2637, 35) differ (string compare on first 35) Component "acronym": 'is.NA' value mismatch: 20 in current 34 in target Component "agency": Lengths (2637, 35) differ (string compare on first 35) Component "agency": 35 string mismatches Component "country": Lengths (2637, 35) differ (string compare on first 35) ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- grant_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (909, 8) differ > Component "pmid": Numeric: lengths (909, 8) differ Component "complete": Lengths (909, 8) differ (string compare on first 8) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- investigator not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (2074, 80) differ > Component "pmid": Numeric: lengths (2074, 80) differ Component "investigator_pos": Numeric: lengths (2074, 80) differ Component "last_name": Lengths (2074, 80) differ (string compare on first 80) Component "last_name": 80 string mismatches Component "fore_name": Lengths (2074, 80) differ (string compare on first 80) Component "fore_name": 80 string mismatches Component "initials": Lengths (2074, 80) differ (string compare on first 80) Component "initials": 73 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (45, 53) differ > Component "pmid": Numeric: lengths (45, 53) differ Component "investigator_pos": Numeric: lengths (45, 53) differ Component "affiliation_pos": Numeric: lengths (45, 53) differ Component "affiliation": Lengths (45, 53) differ (string compare on first 45) Component "affiliation": 45 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- journal not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ > Component "pmid": Numeric: lengths (4989, 30) differ Component "journal_name": Lengths (4989, 30) differ (string compare on first 30) Component "journal_name": 30 string mismatches Component "journal_iso": Lengths (4989, 30) differ (string compare on first 30) Component "journal_iso": 30 string mismatches Component "pub_date": Numeric: lengths (4989, 30) differ Component "pub_year": Lengths (4989, 30) differ (string compare on first 30) Component "pub_year": 30 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- keyword_item not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (19167, 109) differ > Component "pmid": Numeric: lengths (19167, 109) differ Component "keyword_name": Lengths (19167, 109) differ (string compare on first 109) Component "keyword_name": 109 string mismatches Component "major_topic": Lengths (19167, 109) differ (string compare on first 109) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- keyword_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (3596, 21) differ > Component "pmid": Numeric: lengths (3596, 21) differ Component "list_owner": Lengths (3596, 21) differ (string compare on first 21) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (11460, 74) differ > Component "pmid": Numeric: lengths (11460, 74) differ Component "descriptor_pos": Lengths (11460, 74) differ (string compare on first 74) Component "descriptor_pos": 65 string mismatches Component "descriptor_name": Lengths (11460, 74) differ (string compare on first 74) Component "descriptor_name": 71 string mismatches Component "descriptor_ui": Lengths (11460, 74) differ (string compare on first 74) Component "descriptor_ui": 71 string mismatches Component "descriptor_major_topic": Lengths (11460, 74) differ (string compare on first 74) ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- mesh_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ > Component "pmid": Numeric: lengths (4989, 30) differ Component "indexing_method": Lengths (4989, 30) differ (string compare on first 30) Component "indexing_method": 1 string mismatch -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (7130, 39) differ > Component "pmid": Numeric: lengths (7130, 39) differ Component "descriptor_pos": Lengths (7130, 39) differ (string compare on first 39) Component "descriptor_pos": 35 string mismatches Component "qualifier_name": Lengths (7130, 39) differ (string compare on first 39) Component "qualifier_name": 38 string mismatches Component "qualifier_ui": Lengths (7130, 39) differ (string compare on first 39) Component "qualifier_ui": 38 string mismatches Component "qualifier_major_topic": Lengths (7130, 39) differ (string compare on first 39) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- other_abstract not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (147, 4) differ > Component "pmid": Numeric: lengths (147, 4) differ Component "text": Lengths (147, 4) differ (string compare on first 4) Component "text": 4 string mismatches Component "type": Lengths (147, 4) differ (string compare on first 4) Component "type": 2 string mismatches Component "language": Lengths (147, 4) differ (string compare on first 4) Component "language": 4 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- pmid_status not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ > Component "pmid": Numeric: lengths (4989, 30) differ Component "version": Numeric: lengths (4989, 30) differ Component "xml_filename": Lengths (4989, 30) differ (string compare on first 30) Component "xml_filename": 30 string mismatches Component "status": Lengths (4989, 30) differ (string compare on first 30) Component "status": 14 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- pub_history not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (22724, 143) differ > Component "pmid": Numeric: lengths (22724, 143) differ Component "pub_status": Lengths (22724, 143) differ (string compare on first 143) Component "pub_status": 100 string mismatches Component "pub_date": Numeric: lengths (22724, 143) differ -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- pub_type not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (6060, 37) differ > Component "pmid": Numeric: lengths (6060, 37) differ Component "type_name": Lengths (6060, 37) differ (string compare on first 37) Component "type_name": 12 string mismatches Component "type_id": Lengths (6060, 37) differ (string compare on first 37) Component "type_id": 12 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- readme not equal to DBI::dbReadTable(conExp, tableName). Component "text": 1 string mismatch -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- abstract not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (27961, 126) differ > Component "pmid": Numeric: lengths (27961, 126) differ Component "text": Lengths (27961, 126) differ (string compare on first 126) Component "text": 58 string mismatches Component "label": Lengths (27961, 126) differ (string compare on first 126) Component "label": 'is.NA' value mismatch: 34 in current 27 in target Component "nlm_category": Lengths (27961, 126) differ (string compare on first 126) Component "nlm_category": 'is.NA' value mismatch: 34 in current 50 in target Component "abstract_pos": Numeric: lengths (27961, 126) differ -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- abstract_copyright not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (9124, 43) differ > Component "pmid": Numeric: lengths (9124, 43) differ Component "copyright": Lengths (9124, 43) differ (string compare on first 43) Component "copyright": 21 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- article not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (14308, 60) differ > Component "pmid": Numeric: lengths (14308, 60) differ Component "title": Lengths (14308, 60) differ (string compare on first 60) Component "title": 30 string mismatches Component "language": Lengths (14308, 60) differ (string compare on first 60) Component "vernacular_title": Lengths (14308, 60) differ (string compare on first 60) Component "vernacular_title": 'is.NA' value mismatch: 57 in current 58 in target Component "pub_model": Lengths (14308, 60) differ (string compare on first 60) Component "pub_model": 19 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- article_id not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (16828, 76) differ > Component "pmid": Numeric: lengths (16828, 76) differ Component "id_type": Lengths (16828, 76) differ (string compare on first 76) Component "id_type": 10 string mismatches Component "id_value": Lengths (16828, 76) differ (string compare on first 76) Component "id_value": 36 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (101991, 490) differ > Component "pmid": Numeric: lengths (101991, 490) differ Component "author_pos": Numeric: lengths (101991, 490) differ Component "last_name": Lengths (101991, 490) differ (string compare on first 490) Component "last_name": 'is.NA' value mismatch: 6 in current 4 in target Component "fore_name": Lengths (101991, 490) differ (string compare on first 490) Component "fore_name": 'is.NA' value mismatch: 7 in current 5 in target Component "initials": Lengths (101991, 490) differ (string compare on first 490) Component "initials": 'is.NA' value mismatch: 7 in current 5 in target ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author_affiliation not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (121076, 614) differ > Component "pmid": Numeric: lengths (121076, 614) differ Component "author_pos": Numeric: lengths (121076, 614) differ Component "affiliation_pos": Numeric: lengths (121076, 614) differ Component "affiliation": Lengths (121076, 614) differ (string compare on first 614) Component "affiliation": 277 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (3559, 0) differ > Component "pmid": Numeric: lengths (3559, 0) differ Component "author_pos": Numeric: lengths (3559, 0) differ Component "affiliation_pos": Numeric: lengths (3559, 0) differ Component "source": Lengths (3559, 0) differ (string compare on first 0) Component "identifier": Lengths (3559, 0) differ (string compare on first 0) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (21074, 61) differ > Component "pmid": Numeric: lengths (21074, 61) differ Component "author_pos": Numeric: lengths (21074, 61) differ Component "source": Lengths (21074, 61) differ (string compare on first 61) Component "identifier": Lengths (21074, 61) differ (string compare on first 61) Component "identifier": 32 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (14209, 59) differ > Component "pmid": Numeric: lengths (14209, 59) differ Component "complete": Lengths (14209, 59) differ (string compare on first 59) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- chemical not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (9674, 16) differ > Component "pmid": Numeric: lengths (9674, 16) differ Component "registry_number": Lengths (9674, 16) differ (string compare on first 16) Component "registry_number": 8 string mismatches Component "substance_name": Lengths (9674, 16) differ (string compare on first 16) Component "substance_name": 11 string mismatches Component "substance_ui": Lengths (9674, 16) differ (string compare on first 16) Component "substance_ui": 11 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- comment not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (898, 6) differ > Component "pmid": Numeric: lengths (898, 6) differ Component "ref_type": Lengths (898, 6) differ (string compare on first 6) Component "ref_type": 3 string mismatches Component "ref_pmid": Numeric: lengths (898, 6) differ -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- data_bank not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (267, 6) differ > Component "pmid": Numeric: lengths (267, 6) differ Component "data_bank_name": Lengths (267, 6) differ (string compare on first 6) Component "data_bank_name": 1 string mismatch Component "accession_number": Lengths (267, 6) differ (string compare on first 6) Component "accession_number": 2 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- grant_item not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (8770, 57) differ > Component "pmid": Numeric: lengths (8770, 57) differ Component "grant_id": Lengths (8770, 57) differ (string compare on first 57) Component "grant_id": 'is.NA' value mismatch: 13 in current 8 in target Component "acronym": Lengths (8770, 57) differ (string compare on first 57) Component "acronym": 'is.NA' value mismatch: 42 in current 22 in target Component "agency": Lengths (8770, 57) differ (string compare on first 57) Component "agency": 22 string mismatches Component "country": Lengths (8770, 57) differ (string compare on first 57) ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- grant_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (3033, 17) differ > Component "pmid": Numeric: lengths (3033, 17) differ Component "complete": Lengths (3033, 17) differ (string compare on first 17) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- investigator not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (5842, 144) differ > Component "pmid": Numeric: lengths (5842, 144) differ Component "investigator_pos": Numeric: lengths (5842, 144) differ Component "last_name": Lengths (5842, 144) differ (string compare on first 144) Component "last_name": 64 string mismatches Component "fore_name": Lengths (5842, 144) differ (string compare on first 144) Component "fore_name": 64 string mismatches Component "initials": Lengths (5842, 144) differ (string compare on first 144) Component "initials": 59 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (227, 53) differ > Component "pmid": Numeric: lengths (227, 53) differ Component "investigator_pos": Numeric: lengths (227, 53) differ Component "affiliation_pos": Numeric: lengths (227, 53) differ Component "affiliation": Lengths (227, 53) differ (string compare on first 53) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- investigator_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (2, 0) differ > Component "pmid": Numeric: lengths (2, 0) differ Component "investigator_pos": Numeric: lengths (2, 0) differ Component "source": Lengths (2, 0) differ (string compare on first 0) Component "identifier": Lengths (2, 0) differ (string compare on first 0) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- journal not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (14308, 60) differ > Component "pmid": Numeric: lengths (14308, 60) differ Component "journal_name": Lengths (14308, 60) differ (string compare on first 60) Component "journal_name": 30 string mismatches Component "journal_iso": Lengths (14308, 60) differ (string compare on first 60) Component "journal_iso": 30 string mismatches Component "pub_date": Numeric: lengths (14308, 60) differ Component "pub_year": Lengths (14308, 60) differ (string compare on first 60) Component "pub_year": 30 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- keyword_item not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (57226, 229) differ > Component "pmid": Numeric: lengths (57226, 229) differ Component "keyword_name": Lengths (57226, 229) differ (string compare on first 229) Component "keyword_name": 120 string mismatches Component "major_topic": Lengths (57226, 229) differ (string compare on first 229) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- keyword_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (10762, 43) differ > Component "pmid": Numeric: lengths (10762, 43) differ Component "list_owner": Lengths (10762, 43) differ (string compare on first 43) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (72995, 140) differ > Component "pmid": Numeric: lengths (72995, 140) differ Component "descriptor_pos": Lengths (72995, 140) differ (string compare on first 140) Component "descriptor_pos": 51 string mismatches Component "descriptor_name": Lengths (72995, 140) differ (string compare on first 140) Component "descriptor_name": 66 string mismatches Component "descriptor_ui": Lengths (72995, 140) differ (string compare on first 140) Component "descriptor_ui": 66 string mismatches Component "descriptor_major_topic": Lengths (72995, 140) differ (string compare on first 140) ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- mesh_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (6973, 36) differ > Component "pmid": Numeric: lengths (6973, 36) differ Component "indexing_method": Lengths (6973, 36) differ (string compare on first 36) Component "indexing_method": 6 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (42278, 88) differ > Component "pmid": Numeric: lengths (42278, 88) differ Component "descriptor_pos": Lengths (42278, 88) differ (string compare on first 88) Component "descriptor_pos": 49 string mismatches Component "qualifier_name": Lengths (42278, 88) differ (string compare on first 88) Component "qualifier_name": 47 string mismatches Component "qualifier_ui": Lengths (42278, 88) differ (string compare on first 88) Component "qualifier_ui": 47 string mismatches Component "qualifier_major_topic": Lengths (42278, 88) differ (string compare on first 88) ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- other_abstract not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (417, 7) differ > Component "pmid": Numeric: lengths (417, 7) differ Component "text": Lengths (417, 7) differ (string compare on first 7) Component "text": 3 string mismatches Component "type": Lengths (417, 7) differ (string compare on first 7) Component "type": 2 string mismatches Component "language": Lengths (417, 7) differ (string compare on first 7) Component "language": 3 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- pmid_status not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (14327, 60) differ > Component "pmid": Numeric: lengths (14327, 60) differ Component "version": Numeric: lengths (14327, 60) differ Component "xml_filename": Lengths (14327, 60) differ (string compare on first 60) Component "xml_filename": 30 string mismatches Component "status": Lengths (14327, 60) differ (string compare on first 60) Component "status": 24 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- pub_history not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (70114, 293) differ > Component "pmid": Numeric: lengths (70114, 293) differ Component "pub_status": Lengths (70114, 293) differ (string compare on first 293) Component "pub_status": 114 string mismatches Component "pub_date": Numeric: lengths (70114, 293) differ -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- pub_type not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (19407, 74) differ > Component "pmid": Numeric: lengths (19407, 74) differ Component "type_name": Lengths (19407, 74) differ (string compare on first 74) Component "type_name": 27 string mismatches Component "type_id": Lengths (19407, 74) differ (string compare on first 74) Component "type_id": 27 string mismatches [ FAIL 56 | WARN 48 | SKIP 4 | PASS 131 ] Error: Test failures In addition: Warning message: call dbDisconnect() when finished working with a connection 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 See '/tmp/th798/26770126/R-devel/1048/pmparser.Rcheck/00check.log' for details. [1] "2026-02-02 14:21:17 MST" Warning message: In install.packages(dt.tar.gz, repos = NULL) : installation of package '/scratch/th798/data.table-revdeps/2026-02-02/data.table_master_1.18.99.1bd88cbcc806bdaa2aa276e12c78fb4ba13cb645.tar.gz' had non-zero exit status > system(paste(c("diff -u", Rcheck.list), collapse=" ")) --- R_Under_development_unstable_2026-02-02_r89367/release_1.18.2.1.Rcheck/00check.log 2026-02-02 14:07:59.624705660 -0700 +++ R_Under_development_unstable_2026-02-02_r89367/master_1.18.99.1bd88cbcc806bdaa2aa276e12c78fb4ba13cb645.Rcheck/00check.log 2026-02-02 14:21:17.596004035 -0700 @@ -6,7 +6,7 @@ GNU Fortran (Spack GCC) 12.2.0 * running under: Red Hat Enterprise Linux 8.10 (Ootpa) * using session charset: ASCII -* current time: 2026-02-02 20:54:43Z +* current time: 2026-02-02 21:08:00Z * checking for file 'pmparser/DESCRIPTION' ... OK * this is package 'pmparser' version '1.0.23' * package encoding: UTF-8 > 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/2026-02-02/deps.csv", task.str = "1048", release = "/scratch/th798/data.table-revdeps/2026-02-02/data.table_release_1.18.2.1.tar.gz", master = "/scratch/th798/data.table-revdeps/2026-02-02/data.table_master_1.18.99.1bd88cbcc806bdaa2aa276e12c78fb4ba13cb645.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/26770126/R-release/1048" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/26770126/R-release/1048/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "pmparser" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/26770126/R-release/1048/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] "2026-02-02 14:21:23 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/26770126/R-release/1048/library' (as 'lib' is unspecified) also installing the dependency 'RPostgres' trying URL 'http://cloud.r-project.org/src/contrib/RPostgres_1.4.8.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/pmparser_1.0.23.tar.gz' * installing *source* package 'RPostgres' ... ** this is package 'RPostgres' version '1.4.8' ** package 'RPostgres' successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs (libpq 14.5)! Using PKG_CFLAGS=-I/home/th798/.conda/envs/emacs1/include Using PKG_LIBS=-L/home/th798/.conda/envs/emacs1/lib -lpq Using PKG_PLOGR= /usr/bin/cp -f src/Makevars.new src/Makevars ** 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-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 DbColumn.cpp -o DbColumn.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 DbColumnDataSource.cpp -o DbColumnDataSource.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 DbColumnDataSourceFactory.cpp -o DbColumnDataSourceFactory.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 DbColumnStorage.cpp -o DbColumnStorage.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 DbConnection.cpp -o DbConnection.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 DbDataFrame.cpp -o DbDataFrame.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 DbResult.cpp -o DbResult.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 PqColumnDataSource.cpp -o PqColumnDataSource.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 PqColumnDataSourceFactory.cpp -o PqColumnDataSourceFactory.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 PqDataFrame.cpp -o PqDataFrame.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 PqResult.cpp -o PqResult.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 PqResultImpl.cpp -o PqResultImpl.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 PqResultSource.cpp -o PqResultSource.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 PqUtils.cpp -o PqUtils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 RPostgres-init.c -o RPostgres-init.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 connection.cpp -o connection.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 cpp11.cpp -o cpp11.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 encode.cpp -o encode.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 encrypt.cpp -o encrypt.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 logging.cpp -o logging.o /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -Ivendor -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I'/projects/genomic-ml/R/R-release/library/cpp11/include' -I'/projects/genomic-ml/R/R-release/library/plogr/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 result.cpp -o result.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 RPostgres.so DbColumn.o DbColumnDataSource.o DbColumnDataSourceFactory.o DbColumnStorage.o DbConnection.o DbDataFrame.o DbResult.o PqColumnDataSource.o PqColumnDataSourceFactory.o PqDataFrame.o PqResult.o PqResultImpl.o PqResultSource.o PqUtils.o RPostgres-init.o connection.o cpp11.o encode.o encrypt.o logging.o result.o -L/home/th798/.conda/envs/emacs1/lib -lpq installing to /tmp/th798/26770126/R-release/1048/library/00LOCK-RPostgres/00new/RPostgres/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 (RPostgres) * installing *source* package 'pmparser' ... ** this is package 'pmparser' version '1.0.23' ** package 'pmparser' 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 (pmparser) The downloaded source packages are in '/tmp/th798/26770126/RtmpmFSutk/downloaded_packages' > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 43.337 4.088 50.684 > print(Sys.time()) [1] "2026-02-02 14:22:14 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] "2026-02-02 14:22:14 MST" Installing package into '/tmp/th798/26770126/R-release/1048/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.18.2.1' ** package 'data.table' successfully unpacked and MD5 sums checked ** using staged installation zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c assign.c -o assign.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c between.c -o between.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bmerge.c -o bmerge.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c chmatch.c -o chmatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cj.c -o cj.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c coalesce.c -o coalesce.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dogroups.c -o dogroups.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmean.c -o fastmean.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fcast.c -o fcast.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fifelse.c -o fifelse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fmelt.c -o fmelt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c forder.c -o forder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frank.c -o frank.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fread.c -o fread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c freadR.c -o freadR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c froll.c -o froll.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollR.c -o frollR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frolladaptive.c -o frolladaptive.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollapply.c -o frollapply.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fsort.c -o fsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwrite.c -o fwrite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwriteR.c -o fwriteR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c gsumm.c -o gsumm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c hash.c -o hash.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c idatetime.c -o idatetime.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ijoin.c -o ijoin.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c inrange.c -o inrange.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c mergelist.c -o mergelist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nafill.c -o nafill.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c negate.c -o negate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nqrecreateindices.c -o nqrecreateindices.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c openmp-utils.c -o openmp-utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c programming.c -o programming.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c quickselect.c -o quickselect.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rbindlist.c -o rbindlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c reorder.c -o reorder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shellsort.c -o shellsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shift.c -o shift.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c snprintf.c -o snprintf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c subset.c -o subset.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c transpose.c -o transpose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c types.c -o types.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uniqlist.c -o uniqlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.c -o utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vecseq.c -o vecseq.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wrappers.c -o wrappers.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o frollapply.o fsort.o fwrite.o fwriteR.o gsumm.o hash.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shellsort.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fvisibility=hidden -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fvisibility=hidden -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fvisibility=hidden -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi installing to /tmp/th798/26770126/R-release/1048/library/00LOCK-data.table/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) [1] "2026-02-02 14:22:43 MST" * using log directory '/tmp/th798/26770126/R-release/1048/pmparser.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 'pmparser/DESCRIPTION' ... OK * this is package 'pmparser' version '1.0.23' * 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 'pmparser' 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking 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: > library(testthat) > library(pmparser) > > test_check('pmparser') trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed26n1334.xml.gz.md5' Content type 'application/x-gzip' length 60 bytes ================================================== downloaded 60 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed26n1334.xml.gz' Content type 'application/x-gzip' length 13837691 bytes (13.2 MB) ================================================== downloaded 13.2 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed26n1335.xml.gz.md5' Content type 'application/x-gzip' length 60 bytes ================================================== downloaded 60 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed26n1335.xml.gz' Content type 'application/x-gzip' length 44629574 bytes (42.6 MB) ================================================== downloaded 42.6 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed26n1334.xml.gz.md5' Content type 'application/x-gzip' length 60 bytes ================================================== downloaded 60 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed26n1334.xml.gz' Content type 'application/x-gzip' length 13837691 bytes (13.2 MB) ================================================== downloaded 13.2 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed26n1335.xml.gz.md5' Content type 'application/x-gzip' length 60 bytes ================================================== downloaded 60 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed26n1335.xml.gz' Content type 'application/x-gzip' length 44629574 bytes (42.6 MB) ================================================== downloaded 42.6 MB [ FAIL 56 | WARN 48 | SKIP 4 | PASS 131 ] == Skipped tests (4) =========================================================== * On CRAN (4): 'test_get_citation.R:4:3', 'test_get_citation.R:13:3', 'test_get_pubmed_files.R:7:3', 'test_get_pubmed_files.R:20:3' == Failed tests ================================================================ -- Failure ('test_modify_pubmed_db_dup.R:76:5'): modifyPubmedDb update is unique -- data_bank not equal to 0L. 1/1 mismatches [1] 101 - 0 == 101 -- Failure ('test_modify_pubmed_db_dup.R:76:5'): modifyPubmedDb update is unique -- mesh_qualifier not equal to 0L. 1/1 mismatches [1] 405 - 0 == 405 -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- abstract not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (9603, 68) differ > Component "pmid": Numeric: lengths (9603, 68) differ Component "text": Lengths (9603, 68) differ (string compare on first 68) Component "text": 68 string mismatches Component "label": Lengths (9603, 68) differ (string compare on first 68) Component "label": 'is.NA' value mismatch: 15 in current 13 in target Component "nlm_category": Lengths (9603, 68) differ (string compare on first 68) Component "nlm_category": 'is.NA' value mismatch: 15 in current 13 in target Component "abstract_pos": Numeric: lengths (9603, 68) differ -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- abstract_copyright not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (3219, 22) differ > Component "pmid": Numeric: lengths (3219, 22) differ Component "copyright": Lengths (3219, 22) differ (string compare on first 22) Component "copyright": 22 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- article not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ > Component "pmid": Numeric: lengths (4989, 30) differ Component "title": Lengths (4989, 30) differ (string compare on first 30) Component "title": 30 string mismatches Component "language": Lengths (4989, 30) differ (string compare on first 30) Component "language": 2 string mismatches Component "vernacular_title": Lengths (4989, 30) differ (string compare on first 30) Component "vernacular_title": 'is.NA' value mismatch: 28 in current 30 in target Component "pub_model": Lengths (4989, 30) differ (string compare on first 30) ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- article_id not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (6359, 40) differ > Component "pmid": Numeric: lengths (6359, 40) differ Component "id_type": Lengths (6359, 40) differ (string compare on first 40) Component "id_type": 10 string mismatches Component "id_value": Lengths (6359, 40) differ (string compare on first 40) Component "id_value": 40 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (34978, 279) differ > Component "pmid": Numeric: lengths (34978, 279) differ Component "author_pos": Numeric: lengths (34978, 279) differ Component "last_name": Lengths (34978, 279) differ (string compare on first 279) Component "last_name": 'is.NA' value mismatch: 4 in current 0 in target Component "fore_name": Lengths (34978, 279) differ (string compare on first 279) Component "fore_name": 'is.NA' value mismatch: 5 in current 0 in target Component "initials": Lengths (34978, 279) differ (string compare on first 279) Component "initials": 'is.NA' value mismatch: 5 in current 0 in target ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author_affiliation not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (42448, 337) differ > Component "pmid": Numeric: lengths (42448, 337) differ Component "author_pos": Numeric: lengths (42448, 337) differ Component "affiliation_pos": Numeric: lengths (42448, 337) differ Component "affiliation": Lengths (42448, 337) differ (string compare on first 337) Component "affiliation": 337 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (989, 0) differ > Component "pmid": Numeric: lengths (989, 0) differ Component "author_pos": Numeric: lengths (989, 0) differ Component "affiliation_pos": Numeric: lengths (989, 0) differ Component "source": Lengths (989, 0) differ (string compare on first 0) Component "identifier": Lengths (989, 0) differ (string compare on first 0) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (7607, 29) differ > Component "pmid": Numeric: lengths (7607, 29) differ Component "author_pos": Numeric: lengths (7607, 29) differ Component "source": Lengths (7607, 29) differ (string compare on first 29) Component "identifier": Lengths (7607, 29) differ (string compare on first 29) Component "identifier": 29 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4932, 30) differ > Component "pmid": Numeric: lengths (4932, 30) differ Component "complete": Lengths (4932, 30) differ (string compare on first 30) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- chemical not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (1777, 5) differ > Component "pmid": Numeric: lengths (1777, 5) differ Component "registry_number": Lengths (1777, 5) differ (string compare on first 5) Component "registry_number": 3 string mismatches Component "substance_name": Lengths (1777, 5) differ (string compare on first 5) Component "substance_name": 5 string mismatches Component "substance_ui": Lengths (1777, 5) differ (string compare on first 5) Component "substance_ui": 5 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- comment not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (150, 3) differ > Component "pmid": Numeric: lengths (150, 3) differ Component "ref_type": Lengths (150, 3) differ (string compare on first 3) Component "ref_type": 1 string mismatch Component "ref_pmid": Numeric: lengths (150, 3) differ -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- data_bank not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (70, 4) differ > Component "pmid": Numeric: lengths (70, 4) differ Component "data_bank_name": Lengths (70, 4) differ (string compare on first 4) Component "accession_number": Lengths (70, 4) differ (string compare on first 4) Component "accession_number": 4 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- grant_item not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (2637, 35) differ > Component "pmid": Numeric: lengths (2637, 35) differ Component "grant_id": Lengths (2637, 35) differ (string compare on first 35) Component "grant_id": 'is.NA' value mismatch: 6 in current 8 in target Component "acronym": Lengths (2637, 35) differ (string compare on first 35) Component "acronym": 'is.NA' value mismatch: 20 in current 34 in target Component "agency": Lengths (2637, 35) differ (string compare on first 35) Component "agency": 35 string mismatches Component "country": Lengths (2637, 35) differ (string compare on first 35) ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- grant_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (909, 8) differ > Component "pmid": Numeric: lengths (909, 8) differ Component "complete": Lengths (909, 8) differ (string compare on first 8) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- investigator not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (2074, 80) differ > Component "pmid": Numeric: lengths (2074, 80) differ Component "investigator_pos": Numeric: lengths (2074, 80) differ Component "last_name": Lengths (2074, 80) differ (string compare on first 80) Component "last_name": 80 string mismatches Component "fore_name": Lengths (2074, 80) differ (string compare on first 80) Component "fore_name": 80 string mismatches Component "initials": Lengths (2074, 80) differ (string compare on first 80) Component "initials": 73 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (45, 53) differ > Component "pmid": Numeric: lengths (45, 53) differ Component "investigator_pos": Numeric: lengths (45, 53) differ Component "affiliation_pos": Numeric: lengths (45, 53) differ Component "affiliation": Lengths (45, 53) differ (string compare on first 45) Component "affiliation": 45 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- journal not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ > Component "pmid": Numeric: lengths (4989, 30) differ Component "journal_name": Lengths (4989, 30) differ (string compare on first 30) Component "journal_name": 30 string mismatches Component "journal_iso": Lengths (4989, 30) differ (string compare on first 30) Component "journal_iso": 30 string mismatches Component "pub_date": Numeric: lengths (4989, 30) differ Component "pub_year": Lengths (4989, 30) differ (string compare on first 30) Component "pub_year": 30 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- keyword_item not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (19167, 109) differ > Component "pmid": Numeric: lengths (19167, 109) differ Component "keyword_name": Lengths (19167, 109) differ (string compare on first 109) Component "keyword_name": 109 string mismatches Component "major_topic": Lengths (19167, 109) differ (string compare on first 109) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- keyword_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (3596, 21) differ > Component "pmid": Numeric: lengths (3596, 21) differ Component "list_owner": Lengths (3596, 21) differ (string compare on first 21) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (11460, 74) differ > Component "pmid": Numeric: lengths (11460, 74) differ Component "descriptor_pos": Lengths (11460, 74) differ (string compare on first 74) Component "descriptor_pos": 65 string mismatches Component "descriptor_name": Lengths (11460, 74) differ (string compare on first 74) Component "descriptor_name": 71 string mismatches Component "descriptor_ui": Lengths (11460, 74) differ (string compare on first 74) Component "descriptor_ui": 71 string mismatches Component "descriptor_major_topic": Lengths (11460, 74) differ (string compare on first 74) ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- mesh_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ > Component "pmid": Numeric: lengths (4989, 30) differ Component "indexing_method": Lengths (4989, 30) differ (string compare on first 30) Component "indexing_method": 1 string mismatch -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (7130, 39) differ > Component "pmid": Numeric: lengths (7130, 39) differ Component "descriptor_pos": Lengths (7130, 39) differ (string compare on first 39) Component "descriptor_pos": 35 string mismatches Component "qualifier_name": Lengths (7130, 39) differ (string compare on first 39) Component "qualifier_name": 38 string mismatches Component "qualifier_ui": Lengths (7130, 39) differ (string compare on first 39) Component "qualifier_ui": 38 string mismatches Component "qualifier_major_topic": Lengths (7130, 39) differ (string compare on first 39) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- other_abstract not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (147, 4) differ > Component "pmid": Numeric: lengths (147, 4) differ Component "text": Lengths (147, 4) differ (string compare on first 4) Component "text": 4 string mismatches Component "type": Lengths (147, 4) differ (string compare on first 4) Component "type": 2 string mismatches Component "language": Lengths (147, 4) differ (string compare on first 4) Component "language": 4 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- pmid_status not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ > Component "pmid": Numeric: lengths (4989, 30) differ Component "version": Numeric: lengths (4989, 30) differ Component "xml_filename": Lengths (4989, 30) differ (string compare on first 30) Component "xml_filename": 30 string mismatches Component "status": Lengths (4989, 30) differ (string compare on first 30) Component "status": 14 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- pub_history not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (22724, 143) differ > Component "pmid": Numeric: lengths (22724, 143) differ Component "pub_status": Lengths (22724, 143) differ (string compare on first 143) Component "pub_status": 100 string mismatches Component "pub_date": Numeric: lengths (22724, 143) differ -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- pub_type not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (6060, 37) differ > Component "pmid": Numeric: lengths (6060, 37) differ Component "type_name": Lengths (6060, 37) differ (string compare on first 37) Component "type_name": 12 string mismatches Component "type_id": Lengths (6060, 37) differ (string compare on first 37) Component "type_id": 12 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- readme not equal to DBI::dbReadTable(conExp, tableName). Component "text": 1 string mismatch -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- abstract not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (27961, 126) differ > Component "pmid": Numeric: lengths (27961, 126) differ Component "text": Lengths (27961, 126) differ (string compare on first 126) Component "text": 58 string mismatches Component "label": Lengths (27961, 126) differ (string compare on first 126) Component "label": 'is.NA' value mismatch: 34 in current 27 in target Component "nlm_category": Lengths (27961, 126) differ (string compare on first 126) Component "nlm_category": 'is.NA' value mismatch: 34 in current 50 in target Component "abstract_pos": Numeric: lengths (27961, 126) differ -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- abstract_copyright not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (9124, 43) differ > Component "pmid": Numeric: lengths (9124, 43) differ Component "copyright": Lengths (9124, 43) differ (string compare on first 43) Component "copyright": 21 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- article not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (14308, 60) differ > Component "pmid": Numeric: lengths (14308, 60) differ Component "title": Lengths (14308, 60) differ (string compare on first 60) Component "title": 30 string mismatches Component "language": Lengths (14308, 60) differ (string compare on first 60) Component "vernacular_title": Lengths (14308, 60) differ (string compare on first 60) Component "vernacular_title": 'is.NA' value mismatch: 57 in current 58 in target Component "pub_model": Lengths (14308, 60) differ (string compare on first 60) Component "pub_model": 19 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- article_id not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (16828, 76) differ > Component "pmid": Numeric: lengths (16828, 76) differ Component "id_type": Lengths (16828, 76) differ (string compare on first 76) Component "id_type": 10 string mismatches Component "id_value": Lengths (16828, 76) differ (string compare on first 76) Component "id_value": 36 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (101991, 490) differ > Component "pmid": Numeric: lengths (101991, 490) differ Component "author_pos": Numeric: lengths (101991, 490) differ Component "last_name": Lengths (101991, 490) differ (string compare on first 490) Component "last_name": 'is.NA' value mismatch: 6 in current 4 in target Component "fore_name": Lengths (101991, 490) differ (string compare on first 490) Component "fore_name": 'is.NA' value mismatch: 7 in current 5 in target Component "initials": Lengths (101991, 490) differ (string compare on first 490) Component "initials": 'is.NA' value mismatch: 7 in current 5 in target ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author_affiliation not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (121076, 614) differ > Component "pmid": Numeric: lengths (121076, 614) differ Component "author_pos": Numeric: lengths (121076, 614) differ Component "affiliation_pos": Numeric: lengths (121076, 614) differ Component "affiliation": Lengths (121076, 614) differ (string compare on first 614) Component "affiliation": 277 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (3559, 0) differ > Component "pmid": Numeric: lengths (3559, 0) differ Component "author_pos": Numeric: lengths (3559, 0) differ Component "affiliation_pos": Numeric: lengths (3559, 0) differ Component "source": Lengths (3559, 0) differ (string compare on first 0) Component "identifier": Lengths (3559, 0) differ (string compare on first 0) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (21074, 61) differ > Component "pmid": Numeric: lengths (21074, 61) differ Component "author_pos": Numeric: lengths (21074, 61) differ Component "source": Lengths (21074, 61) differ (string compare on first 61) Component "identifier": Lengths (21074, 61) differ (string compare on first 61) Component "identifier": 32 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (14209, 59) differ > Component "pmid": Numeric: lengths (14209, 59) differ Component "complete": Lengths (14209, 59) differ (string compare on first 59) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- chemical not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (9674, 16) differ > Component "pmid": Numeric: lengths (9674, 16) differ Component "registry_number": Lengths (9674, 16) differ (string compare on first 16) Component "registry_number": 8 string mismatches Component "substance_name": Lengths (9674, 16) differ (string compare on first 16) Component "substance_name": 11 string mismatches Component "substance_ui": Lengths (9674, 16) differ (string compare on first 16) Component "substance_ui": 11 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- comment not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (898, 6) differ > Component "pmid": Numeric: lengths (898, 6) differ Component "ref_type": Lengths (898, 6) differ (string compare on first 6) Component "ref_type": 3 string mismatches Component "ref_pmid": Numeric: lengths (898, 6) differ -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- data_bank not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (267, 6) differ > Component "pmid": Numeric: lengths (267, 6) differ Component "data_bank_name": Lengths (267, 6) differ (string compare on first 6) Component "data_bank_name": 1 string mismatch Component "accession_number": Lengths (267, 6) differ (string compare on first 6) Component "accession_number": 2 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- grant_item not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (8770, 57) differ > Component "pmid": Numeric: lengths (8770, 57) differ Component "grant_id": Lengths (8770, 57) differ (string compare on first 57) Component "grant_id": 'is.NA' value mismatch: 13 in current 8 in target Component "acronym": Lengths (8770, 57) differ (string compare on first 57) Component "acronym": 'is.NA' value mismatch: 42 in current 22 in target Component "agency": Lengths (8770, 57) differ (string compare on first 57) Component "agency": 22 string mismatches Component "country": Lengths (8770, 57) differ (string compare on first 57) ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- grant_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (3033, 17) differ > Component "pmid": Numeric: lengths (3033, 17) differ Component "complete": Lengths (3033, 17) differ (string compare on first 17) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- investigator not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (5842, 144) differ > Component "pmid": Numeric: lengths (5842, 144) differ Component "investigator_pos": Numeric: lengths (5842, 144) differ Component "last_name": Lengths (5842, 144) differ (string compare on first 144) Component "last_name": 64 string mismatches Component "fore_name": Lengths (5842, 144) differ (string compare on first 144) Component "fore_name": 64 string mismatches Component "initials": Lengths (5842, 144) differ (string compare on first 144) Component "initials": 59 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (227, 53) differ > Component "pmid": Numeric: lengths (227, 53) differ Component "investigator_pos": Numeric: lengths (227, 53) differ Component "affiliation_pos": Numeric: lengths (227, 53) differ Component "affiliation": Lengths (227, 53) differ (string compare on first 53) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- investigator_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (2, 0) differ > Component "pmid": Numeric: lengths (2, 0) differ Component "investigator_pos": Numeric: lengths (2, 0) differ Component "source": Lengths (2, 0) differ (string compare on first 0) Component "identifier": Lengths (2, 0) differ (string compare on first 0) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- journal not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (14308, 60) differ > Component "pmid": Numeric: lengths (14308, 60) differ Component "journal_name": Lengths (14308, 60) differ (string compare on first 60) Component "journal_name": 30 string mismatches Component "journal_iso": Lengths (14308, 60) differ (string compare on first 60) Component "journal_iso": 30 string mismatches Component "pub_date": Numeric: lengths (14308, 60) differ Component "pub_year": Lengths (14308, 60) differ (string compare on first 60) Component "pub_year": 30 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- keyword_item not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (57226, 229) differ > Component "pmid": Numeric: lengths (57226, 229) differ Component "keyword_name": Lengths (57226, 229) differ (string compare on first 229) Component "keyword_name": 120 string mismatches Component "major_topic": Lengths (57226, 229) differ (string compare on first 229) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- keyword_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (10762, 43) differ > Component "pmid": Numeric: lengths (10762, 43) differ Component "list_owner": Lengths (10762, 43) differ (string compare on first 43) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (72995, 140) differ > Component "pmid": Numeric: lengths (72995, 140) differ Component "descriptor_pos": Lengths (72995, 140) differ (string compare on first 140) Component "descriptor_pos": 51 string mismatches Component "descriptor_name": Lengths (72995, 140) differ (string compare on first 140) Component "descriptor_name": 66 string mismatches Component "descriptor_ui": Lengths (72995, 140) differ (string compare on first 140) Component "descriptor_ui": 66 string mismatches Component "descriptor_major_topic": Lengths (72995, 140) differ (string compare on first 140) ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- mesh_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (6973, 36) differ > Component "pmid": Numeric: lengths (6973, 36) differ Component "indexing_method": Lengths (6973, 36) differ (string compare on first 36) Component "indexing_method": 6 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (42278, 88) differ > Component "pmid": Numeric: lengths (42278, 88) differ Component "descriptor_pos": Lengths (42278, 88) differ (string compare on first 88) Component "descriptor_pos": 49 string mismatches Component "qualifier_name": Lengths (42278, 88) differ (string compare on first 88) Component "qualifier_name": 47 string mismatches Component "qualifier_ui": Lengths (42278, 88) differ (string compare on first 88) Component "qualifier_ui": 47 string mismatches Component "qualifier_major_topic": Lengths (42278, 88) differ (string compare on first 88) ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- other_abstract not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (417, 7) differ > Component "pmid": Numeric: lengths (417, 7) differ Component "text": Lengths (417, 7) differ (string compare on first 7) Component "text": 3 string mismatches Component "type": Lengths (417, 7) differ (string compare on first 7) Component "type": 2 string mismatches Component "language": Lengths (417, 7) differ (string compare on first 7) Component "language": 3 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- pmid_status not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (14327, 60) differ > Component "pmid": Numeric: lengths (14327, 60) differ Component "version": Numeric: lengths (14327, 60) differ Component "xml_filename": Lengths (14327, 60) differ (string compare on first 60) Component "xml_filename": 30 string mismatches Component "status": Lengths (14327, 60) differ (string compare on first 60) Component "status": 24 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- pub_history not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (70114, 293) differ > Component "pmid": Numeric: lengths (70114, 293) differ Component "pub_status": Lengths (70114, 293) differ (string compare on first 293) Component "pub_status": 114 string mismatches Component "pub_date": Numeric: lengths (70114, 293) differ -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- pub_type not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (19407, 74) differ > Component "pmid": Numeric: lengths (19407, 74) differ Component "type_name": Lengths (19407, 74) differ (string compare on first 74) Component "type_name": 27 string mismatches Component "type_id": Lengths (19407, 74) differ (string compare on first 74) Component "type_id": 27 string mismatches [ FAIL 56 | WARN 48 | SKIP 4 | PASS 131 ] Error: Test failures In addition: Warning message: call dbDisconnect() when finished working with a connection 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 See '/tmp/th798/26770126/R-release/1048/pmparser.Rcheck/00check.log' for details. [1] "2026-02-02 14:34:46 MST" [1] "2026-02-02 14:34:46 MST" Installing package into '/tmp/th798/26770126/R-release/1048/library' (as 'lib' is unspecified) Warning: invalid package '/scratch/th798/data.table-revdeps/2026-02-02/data.table_master_1.18.99.1bd88cbcc806bdaa2aa276e12c78fb4ba13cb645.tar.gz' Error: ERROR: no packages specified [1] "2026-02-02 14:34:47 MST" * using log directory '/tmp/th798/26770126/R-release/1048/pmparser.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 'pmparser/DESCRIPTION' ... OK * this is package 'pmparser' version '1.0.23' * 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 'pmparser' 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 dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking 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: > library(testthat) > library(pmparser) > > test_check('pmparser') trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed26n1334.xml.gz.md5' Content type 'application/x-gzip' length 60 bytes ================================================== downloaded 60 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed26n1334.xml.gz' Content type 'application/x-gzip' length 13837691 bytes (13.2 MB) ================================================== downloaded 13.2 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed26n1335.xml.gz.md5' Content type 'application/x-gzip' length 60 bytes ================================================== downloaded 60 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed26n1335.xml.gz' Content type 'application/x-gzip' length 44629574 bytes (42.6 MB) ================================================== downloaded 42.6 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//baseline/pubmed26n1334.xml.gz.md5' Content type 'application/x-gzip' length 60 bytes ================================================== downloaded 60 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/pubmed26n1334.xml.gz' Content type 'application/x-gzip' length 13837691 bytes (13.2 MB) ================================================== downloaded 13.2 MB trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed//updatefiles/pubmed26n1335.xml.gz.md5' Content type 'application/x-gzip' length 60 bytes ================================================== downloaded 60 bytes trying URL 'https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/pubmed26n1335.xml.gz' Content type 'application/x-gzip' length 44629574 bytes (42.6 MB) ================================================== downloaded 42.6 MB [ FAIL 56 | WARN 48 | SKIP 4 | PASS 131 ] == Skipped tests (4) =========================================================== * On CRAN (4): 'test_get_citation.R:4:3', 'test_get_citation.R:13:3', 'test_get_pubmed_files.R:7:3', 'test_get_pubmed_files.R:20:3' == Failed tests ================================================================ -- Failure ('test_modify_pubmed_db_dup.R:76:5'): modifyPubmedDb update is unique -- data_bank not equal to 0L. 1/1 mismatches [1] 101 - 0 == 101 -- Failure ('test_modify_pubmed_db_dup.R:76:5'): modifyPubmedDb update is unique -- mesh_qualifier not equal to 0L. 1/1 mismatches [1] 405 - 0 == 405 -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- abstract not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (9603, 68) differ > Component "pmid": Numeric: lengths (9603, 68) differ Component "text": Lengths (9603, 68) differ (string compare on first 68) Component "text": 68 string mismatches Component "label": Lengths (9603, 68) differ (string compare on first 68) Component "label": 'is.NA' value mismatch: 15 in current 13 in target Component "nlm_category": Lengths (9603, 68) differ (string compare on first 68) Component "nlm_category": 'is.NA' value mismatch: 15 in current 13 in target Component "abstract_pos": Numeric: lengths (9603, 68) differ -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- abstract_copyright not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (3219, 22) differ > Component "pmid": Numeric: lengths (3219, 22) differ Component "copyright": Lengths (3219, 22) differ (string compare on first 22) Component "copyright": 22 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- article not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ > Component "pmid": Numeric: lengths (4989, 30) differ Component "title": Lengths (4989, 30) differ (string compare on first 30) Component "title": 30 string mismatches Component "language": Lengths (4989, 30) differ (string compare on first 30) Component "language": 2 string mismatches Component "vernacular_title": Lengths (4989, 30) differ (string compare on first 30) Component "vernacular_title": 'is.NA' value mismatch: 28 in current 30 in target Component "pub_model": Lengths (4989, 30) differ (string compare on first 30) ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- article_id not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (6359, 40) differ > Component "pmid": Numeric: lengths (6359, 40) differ Component "id_type": Lengths (6359, 40) differ (string compare on first 40) Component "id_type": 10 string mismatches Component "id_value": Lengths (6359, 40) differ (string compare on first 40) Component "id_value": 40 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (34978, 279) differ > Component "pmid": Numeric: lengths (34978, 279) differ Component "author_pos": Numeric: lengths (34978, 279) differ Component "last_name": Lengths (34978, 279) differ (string compare on first 279) Component "last_name": 'is.NA' value mismatch: 4 in current 0 in target Component "fore_name": Lengths (34978, 279) differ (string compare on first 279) Component "fore_name": 'is.NA' value mismatch: 5 in current 0 in target Component "initials": Lengths (34978, 279) differ (string compare on first 279) Component "initials": 'is.NA' value mismatch: 5 in current 0 in target ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author_affiliation not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (42448, 337) differ > Component "pmid": Numeric: lengths (42448, 337) differ Component "author_pos": Numeric: lengths (42448, 337) differ Component "affiliation_pos": Numeric: lengths (42448, 337) differ Component "affiliation": Lengths (42448, 337) differ (string compare on first 337) Component "affiliation": 337 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (989, 0) differ > Component "pmid": Numeric: lengths (989, 0) differ Component "author_pos": Numeric: lengths (989, 0) differ Component "affiliation_pos": Numeric: lengths (989, 0) differ Component "source": Lengths (989, 0) differ (string compare on first 0) Component "identifier": Lengths (989, 0) differ (string compare on first 0) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (7607, 29) differ > Component "pmid": Numeric: lengths (7607, 29) differ Component "author_pos": Numeric: lengths (7607, 29) differ Component "source": Lengths (7607, 29) differ (string compare on first 29) Component "identifier": Lengths (7607, 29) differ (string compare on first 29) Component "identifier": 29 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- author_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4932, 30) differ > Component "pmid": Numeric: lengths (4932, 30) differ Component "complete": Lengths (4932, 30) differ (string compare on first 30) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- chemical not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (1777, 5) differ > Component "pmid": Numeric: lengths (1777, 5) differ Component "registry_number": Lengths (1777, 5) differ (string compare on first 5) Component "registry_number": 3 string mismatches Component "substance_name": Lengths (1777, 5) differ (string compare on first 5) Component "substance_name": 5 string mismatches Component "substance_ui": Lengths (1777, 5) differ (string compare on first 5) Component "substance_ui": 5 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- comment not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (150, 3) differ > Component "pmid": Numeric: lengths (150, 3) differ Component "ref_type": Lengths (150, 3) differ (string compare on first 3) Component "ref_type": 1 string mismatch Component "ref_pmid": Numeric: lengths (150, 3) differ -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- data_bank not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (70, 4) differ > Component "pmid": Numeric: lengths (70, 4) differ Component "data_bank_name": Lengths (70, 4) differ (string compare on first 4) Component "accession_number": Lengths (70, 4) differ (string compare on first 4) Component "accession_number": 4 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- grant_item not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (2637, 35) differ > Component "pmid": Numeric: lengths (2637, 35) differ Component "grant_id": Lengths (2637, 35) differ (string compare on first 35) Component "grant_id": 'is.NA' value mismatch: 6 in current 8 in target Component "acronym": Lengths (2637, 35) differ (string compare on first 35) Component "acronym": 'is.NA' value mismatch: 20 in current 34 in target Component "agency": Lengths (2637, 35) differ (string compare on first 35) Component "agency": 35 string mismatches Component "country": Lengths (2637, 35) differ (string compare on first 35) ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- grant_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (909, 8) differ > Component "pmid": Numeric: lengths (909, 8) differ Component "complete": Lengths (909, 8) differ (string compare on first 8) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- investigator not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (2074, 80) differ > Component "pmid": Numeric: lengths (2074, 80) differ Component "investigator_pos": Numeric: lengths (2074, 80) differ Component "last_name": Lengths (2074, 80) differ (string compare on first 80) Component "last_name": 80 string mismatches Component "fore_name": Lengths (2074, 80) differ (string compare on first 80) Component "fore_name": 80 string mismatches Component "initials": Lengths (2074, 80) differ (string compare on first 80) Component "initials": 73 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (45, 53) differ > Component "pmid": Numeric: lengths (45, 53) differ Component "investigator_pos": Numeric: lengths (45, 53) differ Component "affiliation_pos": Numeric: lengths (45, 53) differ Component "affiliation": Lengths (45, 53) differ (string compare on first 45) Component "affiliation": 45 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- journal not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ > Component "pmid": Numeric: lengths (4989, 30) differ Component "journal_name": Lengths (4989, 30) differ (string compare on first 30) Component "journal_name": 30 string mismatches Component "journal_iso": Lengths (4989, 30) differ (string compare on first 30) Component "journal_iso": 30 string mismatches Component "pub_date": Numeric: lengths (4989, 30) differ Component "pub_year": Lengths (4989, 30) differ (string compare on first 30) Component "pub_year": 30 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- keyword_item not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (19167, 109) differ > Component "pmid": Numeric: lengths (19167, 109) differ Component "keyword_name": Lengths (19167, 109) differ (string compare on first 109) Component "keyword_name": 109 string mismatches Component "major_topic": Lengths (19167, 109) differ (string compare on first 109) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- keyword_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (3596, 21) differ > Component "pmid": Numeric: lengths (3596, 21) differ Component "list_owner": Lengths (3596, 21) differ (string compare on first 21) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (11460, 74) differ > Component "pmid": Numeric: lengths (11460, 74) differ Component "descriptor_pos": Lengths (11460, 74) differ (string compare on first 74) Component "descriptor_pos": 65 string mismatches Component "descriptor_name": Lengths (11460, 74) differ (string compare on first 74) Component "descriptor_name": 71 string mismatches Component "descriptor_ui": Lengths (11460, 74) differ (string compare on first 74) Component "descriptor_ui": 71 string mismatches Component "descriptor_major_topic": Lengths (11460, 74) differ (string compare on first 74) ... -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- mesh_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ > Component "pmid": Numeric: lengths (4989, 30) differ Component "indexing_method": Lengths (4989, 30) differ (string compare on first 30) Component "indexing_method": 1 string mismatch -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (7130, 39) differ > Component "pmid": Numeric: lengths (7130, 39) differ Component "descriptor_pos": Lengths (7130, 39) differ (string compare on first 39) Component "descriptor_pos": 35 string mismatches Component "qualifier_name": Lengths (7130, 39) differ (string compare on first 39) Component "qualifier_name": 38 string mismatches Component "qualifier_ui": Lengths (7130, 39) differ (string compare on first 39) Component "qualifier_ui": 38 string mismatches Component "qualifier_major_topic": Lengths (7130, 39) differ (string compare on first 39) -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- other_abstract not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (147, 4) differ > Component "pmid": Numeric: lengths (147, 4) differ Component "text": Lengths (147, 4) differ (string compare on first 4) Component "text": 4 string mismatches Component "type": Lengths (147, 4) differ (string compare on first 4) Component "type": 2 string mismatches Component "language": Lengths (147, 4) differ (string compare on first 4) Component "language": 4 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- pmid_status not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (4989, 30) differ > Component "pmid": Numeric: lengths (4989, 30) differ Component "version": Numeric: lengths (4989, 30) differ Component "xml_filename": Lengths (4989, 30) differ (string compare on first 30) Component "xml_filename": 30 string mismatches Component "status": Lengths (4989, 30) differ (string compare on first 30) Component "status": 14 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- pub_history not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (22724, 143) differ > Component "pmid": Numeric: lengths (22724, 143) differ Component "pub_status": Lengths (22724, 143) differ (string compare on first 143) Component "pub_status": 100 string mismatches Component "pub_date": Numeric: lengths (22724, 143) differ -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- pub_type not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (6060, 37) differ > Component "pmid": Numeric: lengths (6060, 37) differ Component "type_name": Lengths (6060, 37) differ (string compare on first 37) Component "type_name": 12 string mismatches Component "type_id": Lengths (6060, 37) differ (string compare on first 37) Component "type_id": 12 string mismatches -- Failure ('test_modify_pubmed_db_std.R:32:5'): modifyPubmedDb create matches standard -- readme not equal to DBI::dbReadTable(conExp, tableName). Component "text": 1 string mismatch -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- abstract not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (27961, 126) differ > Component "pmid": Numeric: lengths (27961, 126) differ Component "text": Lengths (27961, 126) differ (string compare on first 126) Component "text": 58 string mismatches Component "label": Lengths (27961, 126) differ (string compare on first 126) Component "label": 'is.NA' value mismatch: 34 in current 27 in target Component "nlm_category": Lengths (27961, 126) differ (string compare on first 126) Component "nlm_category": 'is.NA' value mismatch: 34 in current 50 in target Component "abstract_pos": Numeric: lengths (27961, 126) differ -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- abstract_copyright not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (9124, 43) differ > Component "pmid": Numeric: lengths (9124, 43) differ Component "copyright": Lengths (9124, 43) differ (string compare on first 43) Component "copyright": 21 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- article not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (14308, 60) differ > Component "pmid": Numeric: lengths (14308, 60) differ Component "title": Lengths (14308, 60) differ (string compare on first 60) Component "title": 30 string mismatches Component "language": Lengths (14308, 60) differ (string compare on first 60) Component "vernacular_title": Lengths (14308, 60) differ (string compare on first 60) Component "vernacular_title": 'is.NA' value mismatch: 57 in current 58 in target Component "pub_model": Lengths (14308, 60) differ (string compare on first 60) Component "pub_model": 19 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- article_id not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (16828, 76) differ > Component "pmid": Numeric: lengths (16828, 76) differ Component "id_type": Lengths (16828, 76) differ (string compare on first 76) Component "id_type": 10 string mismatches Component "id_value": Lengths (16828, 76) differ (string compare on first 76) Component "id_value": 36 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (101991, 490) differ > Component "pmid": Numeric: lengths (101991, 490) differ Component "author_pos": Numeric: lengths (101991, 490) differ Component "last_name": Lengths (101991, 490) differ (string compare on first 490) Component "last_name": 'is.NA' value mismatch: 6 in current 4 in target Component "fore_name": Lengths (101991, 490) differ (string compare on first 490) Component "fore_name": 'is.NA' value mismatch: 7 in current 5 in target Component "initials": Lengths (101991, 490) differ (string compare on first 490) Component "initials": 'is.NA' value mismatch: 7 in current 5 in target ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author_affiliation not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (121076, 614) differ > Component "pmid": Numeric: lengths (121076, 614) differ Component "author_pos": Numeric: lengths (121076, 614) differ Component "affiliation_pos": Numeric: lengths (121076, 614) differ Component "affiliation": Lengths (121076, 614) differ (string compare on first 614) Component "affiliation": 277 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author_affiliation_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (3559, 0) differ > Component "pmid": Numeric: lengths (3559, 0) differ Component "author_pos": Numeric: lengths (3559, 0) differ Component "affiliation_pos": Numeric: lengths (3559, 0) differ Component "source": Lengths (3559, 0) differ (string compare on first 0) Component "identifier": Lengths (3559, 0) differ (string compare on first 0) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (21074, 61) differ > Component "pmid": Numeric: lengths (21074, 61) differ Component "author_pos": Numeric: lengths (21074, 61) differ Component "source": Lengths (21074, 61) differ (string compare on first 61) Component "identifier": Lengths (21074, 61) differ (string compare on first 61) Component "identifier": 32 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- author_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (14209, 59) differ > Component "pmid": Numeric: lengths (14209, 59) differ Component "complete": Lengths (14209, 59) differ (string compare on first 59) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- chemical not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (9674, 16) differ > Component "pmid": Numeric: lengths (9674, 16) differ Component "registry_number": Lengths (9674, 16) differ (string compare on first 16) Component "registry_number": 8 string mismatches Component "substance_name": Lengths (9674, 16) differ (string compare on first 16) Component "substance_name": 11 string mismatches Component "substance_ui": Lengths (9674, 16) differ (string compare on first 16) Component "substance_ui": 11 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- comment not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (898, 6) differ > Component "pmid": Numeric: lengths (898, 6) differ Component "ref_type": Lengths (898, 6) differ (string compare on first 6) Component "ref_type": 3 string mismatches Component "ref_pmid": Numeric: lengths (898, 6) differ -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- data_bank not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (267, 6) differ > Component "pmid": Numeric: lengths (267, 6) differ Component "data_bank_name": Lengths (267, 6) differ (string compare on first 6) Component "data_bank_name": 1 string mismatch Component "accession_number": Lengths (267, 6) differ (string compare on first 6) Component "accession_number": 2 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- grant_item not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (8770, 57) differ > Component "pmid": Numeric: lengths (8770, 57) differ Component "grant_id": Lengths (8770, 57) differ (string compare on first 57) Component "grant_id": 'is.NA' value mismatch: 13 in current 8 in target Component "acronym": Lengths (8770, 57) differ (string compare on first 57) Component "acronym": 'is.NA' value mismatch: 42 in current 22 in target Component "agency": Lengths (8770, 57) differ (string compare on first 57) Component "agency": 22 string mismatches Component "country": Lengths (8770, 57) differ (string compare on first 57) ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- grant_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (3033, 17) differ > Component "pmid": Numeric: lengths (3033, 17) differ Component "complete": Lengths (3033, 17) differ (string compare on first 17) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- investigator not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (5842, 144) differ > Component "pmid": Numeric: lengths (5842, 144) differ Component "investigator_pos": Numeric: lengths (5842, 144) differ Component "last_name": Lengths (5842, 144) differ (string compare on first 144) Component "last_name": 64 string mismatches Component "fore_name": Lengths (5842, 144) differ (string compare on first 144) Component "fore_name": 64 string mismatches Component "initials": Lengths (5842, 144) differ (string compare on first 144) Component "initials": 59 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- investigator_affiliation not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (227, 53) differ > Component "pmid": Numeric: lengths (227, 53) differ Component "investigator_pos": Numeric: lengths (227, 53) differ Component "affiliation_pos": Numeric: lengths (227, 53) differ Component "affiliation": Lengths (227, 53) differ (string compare on first 53) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- investigator_identifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (2, 0) differ > Component "pmid": Numeric: lengths (2, 0) differ Component "investigator_pos": Numeric: lengths (2, 0) differ Component "source": Lengths (2, 0) differ (string compare on first 0) Component "identifier": Lengths (2, 0) differ (string compare on first 0) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- journal not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (14308, 60) differ > Component "pmid": Numeric: lengths (14308, 60) differ Component "journal_name": Lengths (14308, 60) differ (string compare on first 60) Component "journal_name": 30 string mismatches Component "journal_iso": Lengths (14308, 60) differ (string compare on first 60) Component "journal_iso": 30 string mismatches Component "pub_date": Numeric: lengths (14308, 60) differ Component "pub_year": Lengths (14308, 60) differ (string compare on first 60) Component "pub_year": 30 string mismatches ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- keyword_item not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (57226, 229) differ > Component "pmid": Numeric: lengths (57226, 229) differ Component "keyword_name": Lengths (57226, 229) differ (string compare on first 229) Component "keyword_name": 120 string mismatches Component "major_topic": Lengths (57226, 229) differ (string compare on first 229) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- keyword_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (10762, 43) differ > Component "pmid": Numeric: lengths (10762, 43) differ Component "list_owner": Lengths (10762, 43) differ (string compare on first 43) -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- mesh_descriptor not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (72995, 140) differ > Component "pmid": Numeric: lengths (72995, 140) differ Component "descriptor_pos": Lengths (72995, 140) differ (string compare on first 140) Component "descriptor_pos": 51 string mismatches Component "descriptor_name": Lengths (72995, 140) differ (string compare on first 140) Component "descriptor_name": 66 string mismatches Component "descriptor_ui": Lengths (72995, 140) differ (string compare on first 140) Component "descriptor_ui": 66 string mismatches Component "descriptor_major_topic": Lengths (72995, 140) differ (string compare on first 140) ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- mesh_list not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (6973, 36) differ > Component "pmid": Numeric: lengths (6973, 36) differ Component "indexing_method": Lengths (6973, 36) differ (string compare on first 36) Component "indexing_method": 6 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- mesh_qualifier not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (42278, 88) differ > Component "pmid": Numeric: lengths (42278, 88) differ Component "descriptor_pos": Lengths (42278, 88) differ (string compare on first 88) Component "descriptor_pos": 49 string mismatches Component "qualifier_name": Lengths (42278, 88) differ (string compare on first 88) Component "qualifier_name": 47 string mismatches Component "qualifier_ui": Lengths (42278, 88) differ (string compare on first 88) Component "qualifier_ui": 47 string mismatches Component "qualifier_major_topic": Lengths (42278, 88) differ (string compare on first 88) ... -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- other_abstract not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (417, 7) differ > Component "pmid": Numeric: lengths (417, 7) differ Component "text": Lengths (417, 7) differ (string compare on first 7) Component "text": 3 string mismatches Component "type": Lengths (417, 7) differ (string compare on first 7) Component "type": 2 string mismatches Component "language": Lengths (417, 7) differ (string compare on first 7) Component "language": 3 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- pmid_status not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (14327, 60) differ > Component "pmid": Numeric: lengths (14327, 60) differ Component "version": Numeric: lengths (14327, 60) differ Component "xml_filename": Lengths (14327, 60) differ (string compare on first 60) Component "xml_filename": 30 string mismatches Component "status": Lengths (14327, 60) differ (string compare on first 60) Component "status": 24 string mismatches -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- pub_history not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (70114, 293) differ > Component "pmid": Numeric: lengths (70114, 293) differ Component "pub_status": Lengths (70114, 293) differ (string compare on first 293) Component "pub_status": 114 string mismatches Component "pub_date": Numeric: lengths (70114, 293) differ -- Failure ('test_modify_pubmed_db_std.R:52:5'): modifyPubmedDb update matches standard -- pub_type not equal to DBI::dbReadTable(conExp, tableName). Attributes: < Component "row.names": Numeric: lengths (19407, 74) differ > Component "pmid": Numeric: lengths (19407, 74) differ Component "type_name": Lengths (19407, 74) differ (string compare on first 74) Component "type_name": 27 string mismatches Component "type_id": Lengths (19407, 74) differ (string compare on first 74) Component "type_id": 27 string mismatches [ FAIL 56 | WARN 48 | SKIP 4 | PASS 131 ] Error: Test failures In addition: Warning message: call dbDisconnect() when finished working with a connection 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 See '/tmp/th798/26770126/R-release/1048/pmparser.Rcheck/00check.log' for details. [1] "2026-02-02 14:47:01 MST" Warning message: In install.packages(dt.tar.gz, repos = NULL) : installation of package '/scratch/th798/data.table-revdeps/2026-02-02/data.table_master_1.18.99.1bd88cbcc806bdaa2aa276e12c78fb4ba13cb645.tar.gz' had non-zero exit status > system(paste(c("diff -u", Rcheck.list), collapse=" ")) > library(data.table, lib.loc=R.home("library")) > (sig.diff.dt <- myDiff(Rvers)) Key: Empty data.table (0 rows and 3 cols): checking,master,release > > ## If there are significant differences, use git bisect to find when > ## they started. > if(nrow(sig.diff.dt)){ + dt.git <- file.path(task.dir, "data.table.git") + 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) + } >