Note: the module "R" cannot be unloaded because it was not loaded. WARNING: ignoring environment value of R_HOME R Under development (unstable) (2025-08-24 r88696) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > cargs <- commandArgs(trailingOnly=TRUE) > if(length(cargs)==0){ + ## before running interactively, make sure to start emacs/R with + ## environment defined in /scratch/...check_one.sh, particularly + ## R_LIBS_USER=/tmp/... otherwise we get error when installing + ## data.table. + base <- "/scratch/th798/data.table-revdeps/*" + cargs <- c( + Sys.glob(file.path(base,"deps.csv")), + "349", + Sys.glob(file.path(base, "data.table_release_*tar.gz")), + Sys.glob(file.path(base, "data.table_master_*tar.gz")) + ) + } > names(cargs) <- c("deps.csv", "task.str", "release", "master") > dput(cargs) c(deps.csv = "/scratch/th798/data.table-revdeps/2025-08-25/deps.csv", task.str = "561", release = "/scratch/th798/data.table-revdeps/2025-08-25/data.table_release_1.17.8.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-08-25/data.table_master_1.17.99.55bbc3d1646a80ba1d5b2c073c17b9575e7c186a.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/21154706/R-devel/561" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/21154706/R-devel/561/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "goat" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/21154706/R-devel/561/library" [2] "/projects/genomic-ml/R/R-devel/library" > options(repos=c(#this should be in ~/.Rprofile too. + CRAN="http://cloud.r-project.org")) > print(Sys.time()) [1] "2025-08-25 00:29:07 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/21154706/R-devel/561/library' (as 'lib' is unspecified) Warning: dependencies 'org.Pt.eg.db', 'org.Mmu.eg.db' are not available also installing the dependency 'MonoPoly' trying URL 'http://cloud.r-project.org/src/contrib/MonoPoly_0.3-10.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/goat_1.1.2.tar.gz' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package 'goat' failed * installing *source* package 'MonoPoly' ... ** this is package 'MonoPoly' version '0.3-10' ** package 'MonoPoly' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using Fortran compiler: 'GNU Fortran (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gfortran -fvisibility=hidden -fpic -g -O2 -c beta_trans.f -o beta_trans.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o MonoPoly.so beta_trans.o init.o -lgfortran -lm -lquadmath installing to /tmp/th798/21154706/R-devel/561/library/00LOCK-MonoPoly/00new/MonoPoly/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MonoPoly) The downloaded source packages are in '/tmp/th798/21154706/RtmpIVQmH9/downloaded_packages' Warning messages: 1: In download.file(urls, destfiles, "libcurl", mode = "wb", ...) : cannot open URL 'http://cloud.r-project.org/src/contrib/goat_1.1.2.tar.gz': HTTP status was '404 Not Found' 2: In download.file(urls, destfiles, "libcurl", mode = "wb", ...) : some files were not downloaded > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 8.186 0.978 33.260 > print(Sys.time()) [1] "2025-08-25 00:29:40 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") Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent Calls: colnames<- Execution halted WARNING: ignoring environment value of R_HOME R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > cargs <- commandArgs(trailingOnly=TRUE) > if(length(cargs)==0){ + ## before running interactively, make sure to start emacs/R with + ## environment defined in /scratch/...check_one.sh, particularly + ## R_LIBS_USER=/tmp/... otherwise we get error when installing + ## data.table. + base <- "/scratch/th798/data.table-revdeps/*" + cargs <- c( + Sys.glob(file.path(base,"deps.csv")), + "349", + Sys.glob(file.path(base, "data.table_release_*tar.gz")), + Sys.glob(file.path(base, "data.table_master_*tar.gz")) + ) + } > names(cargs) <- c("deps.csv", "task.str", "release", "master") > dput(cargs) c(deps.csv = "/scratch/th798/data.table-revdeps/2025-08-25/deps.csv", task.str = "561", release = "/scratch/th798/data.table-revdeps/2025-08-25/data.table_release_1.17.8.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-08-25/data.table_master_1.17.99.55bbc3d1646a80ba1d5b2c073c17b9575e7c186a.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/21154706/R-release/561" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/21154706/R-release/561/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "goat" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/21154706/R-release/561/library" [2] "/projects/genomic-ml/R/R-release/library" > options(repos=c(#this should be in ~/.Rprofile too. + CRAN="http://cloud.r-project.org")) > print(Sys.time()) [1] "2025-08-25 00:29:46 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/21154706/R-release/561/library' (as 'lib' is unspecified) Warning: dependencies 'org.Pt.eg.db', 'org.Mmu.eg.db' are not available also installing the dependency 'MonoPoly' trying URL 'http://cloud.r-project.org/src/contrib/MonoPoly_0.3-10.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/goat_1.1.2.tar.gz' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package 'goat' failed * installing *source* package 'MonoPoly' ... ** this is package 'MonoPoly' version '0.3-10' ** package 'MonoPoly' successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' using Fortran compiler: 'GNU Fortran (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gfortran -fvisibility=hidden -fpic -g -O2 -c beta_trans.f -o beta_trans.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o MonoPoly.so beta_trans.o init.o -lgfortran -lm -lquadmath installing to /tmp/th798/21154706/R-release/561/library/00LOCK-MonoPoly/00new/MonoPoly/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MonoPoly) The downloaded source packages are in '/tmp/th798/21154706/Rtmp6MzAzE/downloaded_packages' Warning messages: 1: In download.file(urls, destfiles, "libcurl", mode = "wb", ...) : cannot open URL 'http://cloud.r-project.org/src/contrib/goat_1.1.2.tar.gz': HTTP status was '404 Not Found' 2: In download.file(urls, destfiles, "libcurl", mode = "wb", ...) : some files were not downloaded > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 8.359 0.942 16.106 > print(Sys.time()) [1] "2025-08-25 00:30:03 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") Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent Calls: colnames<- Execution halted