Note: the module "R" cannot be unloaded because it was not loaded. WARNING: ignoring environment value of R_HOME R Under development (unstable) (2025-03-29 r88074) -- "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/2025-03-30/deps.csv", task.str = "1216", release = "/scratch/th798/data.table-revdeps/2025-03-30/data.table_release_1.17.0.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-03-30/data.table_master_1.17.99.2cb03162a21328cc5f68a8c3b0e554f5edfcb5b9.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/16190241/R-devel/1216" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/16190241/R-devel/1216/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "RITCH" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/16190241/R-devel/1216/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] "2025-03-30 01:01:18 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/16190241/R-devel/1216/library' (as 'lib' is unspecified) also installing the dependency 'tinytest' trying URL 'http://cloud.r-project.org/src/contrib/tinytest_1.4.1.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/RITCH_0.1.26.tar.gz' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package 'RITCH' failed * installing *source* package 'tinytest' ... ** this is package 'tinytest' version '1.4.1' ** package 'tinytest' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tinytest) The downloaded source packages are in '/tmp/th798/16190241/Rtmpa8B3kZ/downloaded_packages' Warning messages: 1: In download.file(urls, destfiles, "libcurl", mode = "wb", ...) : cannot open URL 'http://cloud.r-project.org/src/contrib/RITCH_0.1.26.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 3.936 2.494 66.830 > print(Sys.time()) [1] "2025-03-30 01:02:25 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 4.4.3 (2025-02-28) -- "Trophy Case" 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/2025-03-30/deps.csv", task.str = "1216", release = "/scratch/th798/data.table-revdeps/2025-03-30/data.table_release_1.17.0.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-03-30/data.table_master_1.17.99.2cb03162a21328cc5f68a8c3b0e554f5edfcb5b9.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/16190241/R-release/1216" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/16190241/R-release/1216/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "RITCH" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/16190241/R-release/1216/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] "2025-03-30 01:02:33 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/16190241/R-release/1216/library' (as 'lib' is unspecified) also installing the dependency 'tinytest' trying URL 'http://cloud.r-project.org/src/contrib/tinytest_1.4.1.tar.gz' Content type 'application/x-gzip' length 587352 bytes (573 KB) ================================================== downloaded 573 KB trying URL 'http://cloud.r-project.org/src/contrib/RITCH_0.1.26.tar.gz' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://cloud.r-project.org/src/contrib/RITCH_0.1.26.tar.gz' In addition: Warning messages: 1: In download.file(url, destfile, method, mode = "wb", ...) : downloaded length 0 != reported length 279 2: In download.file(url, destfile, method, mode = "wb", ...) : cannot open URL 'http://cloud.r-project.org/src/contrib/RITCH_0.1.26.tar.gz': HTTP status was '404 Not Found' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package 'RITCH' failed * installing *source* package 'tinytest' ... ** package 'tinytest' successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tinytest) The downloaded source packages are in '/tmp/th798/16190241/Rtmp6Nq76k/downloaded_packages' > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 4.266 0.948 154.422 > print(Sys.time()) [1] "2025-03-30 01:05:07 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