Note: the module "R" cannot be unloaded because it was not loaded. WARNING: ignoring environment value of R_HOME R Under development (unstable) (2026-01-29 r89354) -- "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/2026-01-30/deps.csv", task.str = "949", release = "/scratch/th798/data.table-revdeps/2026-01-30/data.table_release_1.18.2.1.tar.gz", master = "/scratch/th798/data.table-revdeps/2026-01-30/data.table_master_1.18.99.1bd88cbcc806bdaa2aa276e12c78fb4ba13cb645.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/26735107/R-devel/949" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/26735107/R-devel/949/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "numbat" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/26735107/R-devel/949/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] "2026-01-30 02:55:51 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/26735107/R-devel/949/library' (as 'lib' is unspecified) Warning message: package 'numbat' is not available for this version of R A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 0.750 0.032 0.889 > print(Sys.time()) [1] "2026-01-30 02:55:52 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 4.5.2 (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/2026-01-30/deps.csv", task.str = "949", release = "/scratch/th798/data.table-revdeps/2026-01-30/data.table_release_1.18.2.1.tar.gz", master = "/scratch/th798/data.table-revdeps/2026-01-30/data.table_master_1.18.99.1bd88cbcc806bdaa2aa276e12c78fb4ba13cb645.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/26735107/R-release/949" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/26735107/R-release/949/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "numbat" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/26735107/R-release/949/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] "2026-01-30 02:55:58 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/26735107/R-release/949/library' (as 'lib' is unspecified) Warning message: package 'numbat' is not available for this version of R A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 0.710 0.019 0.837 > print(Sys.time()) [1] "2026-01-30 02:55:59 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