Note: the module "R" cannot be unloaded because it was not loaded. WARNING: ignoring environment value of R_HOME R Under development (unstable) (2025-08-23 r88688) -- "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/2025-08-24/deps.csv", task.str = "1180", release = "/scratch/th798/data.table-revdeps/2025-08-24/data.table_release_1.17.8.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-08-24/data.table_master_1.17.99.55bbc3d1646a80ba1d5b2c073c17b9575e7c186a.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/21128216/R-devel/1180" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/21128216/R-devel/1180/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "readyomics" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/21128216/R-devel/1180/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] "2025-08-24 00:36:36 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/21128216/R-devel/1180/library' (as 'lib' is unspecified) trying URL 'http://cloud.r-project.org/src/contrib/readyomics_0.1.0.tar.gz' Content type 'application/x-gzip' length 238719 bytes (233 KB) ================================================== downloaded 233 KB * installing *source* package 'readyomics' ... ** this is package 'readyomics' version '0.1.0' ** package 'readyomics' 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 (readyomics) The downloaded source packages are in '/tmp/th798/21128216/Rtmpfsqt0Q/downloaded_packages' > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 5.622 0.727 8.817 > print(Sys.time()) [1] "2025-08-24 00:36:45 MST" > downloaded_packages <- file.path( + tempdir(), + "downloaded_packages") > dl.glob <- file.path( + downloaded_packages, + paste0(rev.dep,"_*.tar.gz")) > rev.dep.dl.row <- cbind(rev.dep, Sys.glob(dl.glob)) > colnames(rev.dep.dl.row) <- c("pkg","path") > rev.dep.release.tar.gz <- normalizePath(rev.dep.dl.row[,"path"], mustWork=TRUE) > pkg.Rcheck <- paste0(rev.dep, ".Rcheck") > > proj.dir <- "~/genomic-ml/data.table-revdeps" > source(file.path(proj.dir, "myStatus.R")) > Rvers <- gsub("[()]", "", gsub(" ", "_", R.version[["version.string"]])) > dir.create(Rvers, showWarnings=FALSE) > Rcheck.list <- list() > for(dt.version.short in c("release", "master")){ + dt.tar.gz <- cargs[[dt.version.short]] + dt.version <- gsub(".tar.gz|/.*?_", "", dt.tar.gz) + print(Sys.time()) + install.packages(dt.tar.gz, repos=NULL) + print(Sys.time()) + check.cmd <- get_check_cmd(rev.dep.release.tar.gz) + system(check.cmd) + print(Sys.time()) + dest.Rcheck <- file.path( + Rvers, + paste0(dt.version, ".Rcheck")) + unlink(dest.Rcheck, recursive=TRUE) + file.rename(pkg.Rcheck, dest.Rcheck) + Rcheck.list[[dt.version]] <- file.path(dest.Rcheck, "00check.log") + } [1] "2025-08-24 00:36:45 MST" Installing package into '/tmp/th798/21128216/R-devel/1180/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.17.8' ** package 'data.table' successfully unpacked and MD5 sums checked ** using staged installation zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c assign.c -o assign.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c between.c -o between.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bmerge.c -o bmerge.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c chmatch.c -o chmatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cj.c -o cj.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c coalesce.c -o coalesce.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dogroups.c -o dogroups.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmean.c -o fastmean.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fcast.c -o fcast.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fifelse.c -o fifelse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fmelt.c -o fmelt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c forder.c -o forder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frank.c -o frank.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fread.c -o fread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c freadR.c -o freadR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c froll.c -o froll.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollR.c -o frollR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frolladaptive.c -o frolladaptive.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fsort.c -o fsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwrite.c -o fwrite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwriteR.c -o fwriteR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c gsumm.c -o gsumm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c idatetime.c -o idatetime.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ijoin.c -o ijoin.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c inrange.c -o inrange.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nafill.c -o nafill.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c negate.c -o negate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nqrecreateindices.c -o nqrecreateindices.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c openmp-utils.c -o openmp-utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c programming.c -o programming.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c quickselect.c -o quickselect.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rbindlist.c -o rbindlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c reorder.c -o reorder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shift.c -o shift.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c snprintf.c -o snprintf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c subset.c -o subset.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c transpose.c -o transpose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c types.c -o types.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uniqlist.c -o uniqlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.c -o utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vecseq.c -o vecseq.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wrappers.c -o wrappers.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi installing to /tmp/th798/21128216/R-devel/1180/library/00LOCK-data.table/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) [1] "2025-08-24 00:37:09 MST" * using log directory '/tmp/th798/21128216/R-devel/1180/readyomics.Rcheck' * using R Under development (unstable) (2025-08-23 r88688) * 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 'readyomics/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'readyomics' version '0.1.0' * 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 'readyomics' 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed build_phyloseq 8.378 0.349 8.899 dana 7.939 0.173 8.225 mva 6.709 0.247 7.049 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * 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: OK [1] "2025-08-24 00:40:20 MST" [1] "2025-08-24 00:40:20 MST" Installing package into '/tmp/th798/21128216/R-devel/1180/library' (as 'lib' is unspecified) Warning: invalid package '/scratch/th798/data.table-revdeps/2025-08-24/data.table_master_1.17.99.55bbc3d1646a80ba1d5b2c073c17b9575e7c186a.tar.gz' Error: ERROR: no packages specified [1] "2025-08-24 00:40:20 MST" * using log directory '/tmp/th798/21128216/R-devel/1180/readyomics.Rcheck' * using R Under development (unstable) (2025-08-23 r88688) * 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 'readyomics/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'readyomics' version '0.1.0' * 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 'readyomics' 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed build_phyloseq 8.250 0.350 8.784 dana 7.825 0.161 8.084 mva 6.616 0.215 6.929 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R' OK * 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: OK [1] "2025-08-24 00:43:29 MST" Warning message: In install.packages(dt.tar.gz, repos = NULL) : installation of package '/scratch/th798/data.table-revdeps/2025-08-24/data.table_master_1.17.99.55bbc3d1646a80ba1d5b2c073c17b9575e7c186a.tar.gz' had non-zero exit status > system(paste(c("diff -u", Rcheck.list), collapse=" ")) --- R_Under_development_unstable_2025-08-23_r88688/release_1.17.8.Rcheck/00check.log 2025-08-24 00:40:20.584707660 -0700 +++ R_Under_development_unstable_2025-08-23_r88688/master_1.17.99.55bbc3d1646a80ba1d5b2c073c17b9575e7c186a.Rcheck/00check.log 2025-08-24 00:43:29.700370599 -0700 @@ -53,9 +53,9 @@ * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed -build_phyloseq 8.378 0.349 8.899 -dana 7.939 0.173 8.225 -mva 6.709 0.247 7.049 +build_phyloseq 8.250 0.350 8.784 +dana 7.825 0.161 8.084 +mva 6.616 0.215 6.929 * checking for unstated dependencies in 'tests' ... OK * checking tests ... OK Running 'testthat.R' > 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") + 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) + } > 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/2025-08-24/deps.csv", task.str = "1180", release = "/scratch/th798/data.table-revdeps/2025-08-24/data.table_release_1.17.8.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-08-24/data.table_master_1.17.99.55bbc3d1646a80ba1d5b2c073c17b9575e7c186a.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/21128216/R-release/1180" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/21128216/R-release/1180/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "readyomics" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/21128216/R-release/1180/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] "2025-08-24 00:43:36 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/21128216/R-release/1180/library' (as 'lib' is unspecified) trying URL 'http://cloud.r-project.org/src/contrib/readyomics_0.1.0.tar.gz' Content type 'application/x-gzip' length 238719 bytes (233 KB) ================================================== downloaded 233 KB * installing *source* package 'readyomics' ... ** this is package 'readyomics' version '0.1.0' ** package 'readyomics' 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 (readyomics) The downloaded source packages are in '/tmp/th798/21128216/Rtmp6wGzph/downloaded_packages' > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 5.645 0.632 7.345 > print(Sys.time()) [1] "2025-08-24 00:43:43 MST" > downloaded_packages <- file.path( + tempdir(), + "downloaded_packages") > dl.glob <- file.path( + downloaded_packages, + paste0(rev.dep,"_*.tar.gz")) > rev.dep.dl.row <- cbind(rev.dep, Sys.glob(dl.glob)) > colnames(rev.dep.dl.row) <- c("pkg","path") > rev.dep.release.tar.gz <- normalizePath(rev.dep.dl.row[,"path"], mustWork=TRUE) > pkg.Rcheck <- paste0(rev.dep, ".Rcheck") > > proj.dir <- "~/genomic-ml/data.table-revdeps" > source(file.path(proj.dir, "myStatus.R")) > Rvers <- gsub("[()]", "", gsub(" ", "_", R.version[["version.string"]])) > dir.create(Rvers, showWarnings=FALSE) > Rcheck.list <- list() > for(dt.version.short in c("release", "master")){ + dt.tar.gz <- cargs[[dt.version.short]] + dt.version <- gsub(".tar.gz|/.*?_", "", dt.tar.gz) + print(Sys.time()) + install.packages(dt.tar.gz, repos=NULL) + print(Sys.time()) + check.cmd <- get_check_cmd(rev.dep.release.tar.gz) + system(check.cmd) + print(Sys.time()) + dest.Rcheck <- file.path( + Rvers, + paste0(dt.version, ".Rcheck")) + unlink(dest.Rcheck, recursive=TRUE) + file.rename(pkg.Rcheck, dest.Rcheck) + Rcheck.list[[dt.version]] <- file.path(dest.Rcheck, "00check.log") + } [1] "2025-08-24 00:43:43 MST" Installing package into '/tmp/th798/21128216/R-release/1180/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.17.8' ** package 'data.table' successfully unpacked and MD5 sums checked ** using staged installation zlib 1.2.13 is available ok * checking if R installation supports OpenMP without any extra hints... yes ** libs using C compiler: 'gcc (Spack GCC) 12.2.0' /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c assign.c -o assign.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c between.c -o between.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c bmerge.c -o bmerge.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c chmatch.c -o chmatch.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c cj.c -o cj.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c coalesce.c -o coalesce.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c dogroups.c -o dogroups.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fastmean.c -o fastmean.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fcast.c -o fcast.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fifelse.c -o fifelse.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fmelt.c -o fmelt.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c forder.c -o forder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frank.c -o frank.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fread.c -o fread.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c freadR.c -o freadR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c froll.c -o froll.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frollR.c -o frollR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c frolladaptive.c -o frolladaptive.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fsort.c -o fsort.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwrite.c -o fwrite.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c fwriteR.c -o fwriteR.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c gsumm.c -o gsumm.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c idatetime.c -o idatetime.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c ijoin.c -o ijoin.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c init.c -o init.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c inrange.c -o inrange.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nafill.c -o nafill.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c negate.c -o negate.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c nqrecreateindices.c -o nqrecreateindices.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c openmp-utils.c -o openmp-utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c programming.c -o programming.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c quickselect.c -o quickselect.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c rbindlist.c -o rbindlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c reorder.c -o reorder.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c shift.c -o shift.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c snprintf.c -o snprintf.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c subset.c -o subset.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c transpose.c -o transpose.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c types.c -o types.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c uniqlist.c -o uniqlist.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c utils.c -o utils.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c vecseq.c -o vecseq.o /packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include -c wrappers.c -o wrappers.o /packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi installing to /tmp/th798/21128216/R-release/1180/library/00LOCK-data.table/00new/data.table/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (data.table) [1] "2025-08-24 00:44:07 MST" * using log directory '/tmp/th798/21128216/R-release/1180/readyomics.Rcheck' * using R version 4.5.1 (2025-06-13) * 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 'readyomics/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'readyomics' version '0.1.0' * 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 'readyomics' 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 ...sh: line 1: 1107470 Segmentation fault (core dumped) LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/home/th798/R/R-release/bin/R' --vanilla > 'readyomics-Ex.Rout' 2>&1 < 'readyomics-Ex.R' ERROR Running examples in 'readyomics-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: dana > ### Title: Differential analysis (dana) > ### Aliases: dana > > ### ** Examples > > mock_X <- matrix( + rnorm(50 * 10) + + rep(c(rep(0, 25), rep(2, 25)), each = 10) * rep(1:10 %in% 1:3, each = 50), + nrow = 50 + ) > > rownames(mock_X) <- paste0("sample", 1:50) > colnames(mock_X) <- paste0("feat", 1:10) > > sample_data <- data.frame( + sample_id = rownames(mock_X), + group = factor(rep(c("A", "B"), each = 25)), + subject = factor(rep(1:25, each = 2)), + row.names = rownames(mock_X) + ) > > # Example with parallel computation setup (not run) > # future::plan(multisession) > # progressr::handlers(global = TRUE) > # progressr::with_progress({ > result <- dana(X = mock_X, + sample_data = sample_data, + formula_rhs = ~ group + (1 | subject), + term_LRT = c("group", "1 | subject"), # Multiple terms allowed + platform = "ms", + assay = "lipidomics", + verbose = FALSE + ) Warning in check_dep_version() : ABI version mismatch: lme4 was built with Matrix ABI version 1 Current Matrix ABI version is 2 Please re-install lme4 from source or restore original 'Matrix' package *** caught segfault *** address (nil), cause 'unknown' Traceback: 1: .Call(merPredDCreate, as(X, "matrix"), Lambdat, LamtUt, Lind, RZX, Ut, Utr, V, VtV, Vtr, Xwts, Zt, beta0, delb, delu, theta, u0) 2: initializePtr() 3: .Object$initialize(...) 4: initialize(value, ...) 5: initialize(value, ...) 6: methods::new(def, ...) 7: (new("refMethodDef", .Data = function (...) { methods::new(def, ...)}, mayCall = c("methods", "new"), name = "new", refClassName = "refGeneratorSlot", superClassMethod = ""))(Zt = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L), p = 0:50, Dim = c(25L, 50L), Dimnames = list( c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25"), c("sample1", "sample2", "sample3", "sample4", "sample5", "sample6", "sample7", "sample8", "sample9", "sample10", "sample11", "sample12", "sample13", "sample14", "sample15", "sample16", "sample17", "sample18", "sample19", "sample20", "sample21", "sample22", "sample23", "sample24", "sample25", "sample26", "sample27", "sample28", "sample29", "sample30", "sample31", "sample32", "sample33", "sample34", "sample35", "sample36", "sample37", "sample38", "sample39", "sample40", "sample41", "sample42", "sample43", "sample44", "sample45", "sample46", "sample47", "sample48", "sample49", "sample50")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), theta = 1, Lambdat = new("dgCMatrix", i = 0:24, p = 0:25, Dim = c(25L, 25L), Dimnames = list(NULL, NULL), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), Lind = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), n = 50L, X = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)) 8: do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")], n = nrow(X), list(X = X))) 9: (function (fr, X, reTrms, REML = TRUE, start = NULL, verbose = 0, control = lmerControl(), ...) { p <- ncol(X) rho <- new.env(parent = parent.env(environment())) rho$pp <- do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")], n = nrow(X), list(X = X))) REMLpass <- if (REML) p else 0L rho$resp <- if (missing(fr)) mkRespMod(REML = REMLpass, ...) else mkRespMod(fr, REML = REMLpass) pp <- resp <- NULL rho$lmer_Deviance <- lmer_Deviance devfun <- function(theta) .Call(lmer_Deviance, pp$ptr(), resp$ptr(), as.double(theta)) environment(devfun) <- rho if (is.null(start) && all(reTrms$cnms == "(Intercept)") && length(reTrms$flist) == length(reTrms$lower) && !is.null(y <- model.response(fr))) { v <- sapply(reTrms$flist, function(f) var(ave(y, f))) v.e <- var(y) - sum(v) if (!is.na(v.e) && v.e > 0) { v.rel <- v/v.e if (all(v.rel >= reTrms$lower^2)) rho$pp$setTheta(sqrt(v.rel)) } } if (length(rho$resp$y) > 0) devfun(rho$pp$theta) rho$lower <- reTrms$lower devfun})(fr = list(feat1 = c(-0.626453810742332, 0.183643324222082, -0.835628612410047, 1.59528080213779, 0.329507771815361, -0.820468384118015, 0.487429052428485, 0.738324705129217, 0.575781351653492, -0.305388387156356, 1.51178116845085, 0.389843236411431, -0.621240580541804, -2.2146998871775, 1.12493091814311, -0.0449336090152309, -0.0161902630989461, 0.943836210685299, 0.821221195098089, 0.593901321217509, 0.918977371608218, 0.782136300731067, 0.0745649833651906, -1.98935169586337, 0.61982574789471, -0.0561287395290008, -0.155795506705329, -1.47075238389927, -0.47815005510862, 0.417941560199702, 1.35867955152904, -0.102787727342996, 0.387671611559369, -0.0538050405829051, -1.37705955682861, -0.41499456329968, -0.394289953710349, -0.0593133967111857, 1.10002537198388, 0.763175748457544, -0.164523596253587, -0.253361680136508, 0.696963375404737, 0.556663198673657, -0.68875569454952, -0.70749515696212, 0.36458196213683, 0.768532924515416, -0.112346212150228, 0.881107726454215), group = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), subject = c(1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L, 25L, 25L)), X = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), reTrms = list(Zt = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L), p = 0:50, Dim = c(25L, 50L), Dimnames = list( c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25"), c("sample1", "sample2", "sample3", "sample4", "sample5", "sample6", "sample7", "sample8", "sample9", "sample10", "sample11", "sample12", "sample13", "sample14", "sample15", "sample16", "sample17", "sample18", "sample19", "sample20", "sample21", "sample22", "sample23", "sample24", "sample25", "sample26", "sample27", "sample28", "sample29", "sample30", "sample31", "sample32", "sample33", "sample34", "sample35", "sample36", "sample37", "sample38", "sample39", "sample40", "sample41", "sample42", "sample43", "sample44", "sample45", "sample46", "sample47", "sample48", "sample49", "sample50")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), theta = 1, Lind = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L ), Gp = c(0L, 25L), lower = 0, Lambdat = new("dgCMatrix", i = 0:24, p = 0:25, Dim = c(25L, 25L), Dimnames = list( NULL, NULL), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), flist = list(subject = c(1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L, 25L, 25L)), cnms = list(subject = "(Intercept)"), Ztlist = list(`1 | subject` = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L), p = 0:50, Dim = c(25L, 50L), Dimnames = list(c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25"), c("sample1", "sample2", "sample3", "sample4", "sample5", "sample6", "sample7", "sample8", "sample9", "sample10", "sample11", "sample12", "sample13", "sample14", "sample15", "sample16", "sample17", "sample18", "sample19", "sample20", "sample21", "sample22", "sample23", "sample24", "sample25", "sample26", "sample27", "sample28", "sample29", "sample30", "sample31", "sample32", "sample33", "sample34", "sample35", "sample36", "sample37", "sample38", "sample39", "sample40", "sample41", "sample42", "sample43", "sample44", "sample45", "sample46", "sample47", "sample48", "sample49", "sample50")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list())), nl = c(subject = 25L)), REML = TRUE, wmsgs = character(0), start = NULL, verbose = 0L, control = list(optimizer = "nloptwrap", restart_edge = TRUE, boundary.tol = 1e-05, calc.derivs = TRUE, use.last.params = FALSE, checkControl = list(check.nobs.vs.rankZ = "ignore", check.nobs.vs.nlev = "stop", check.nlev.gtreq.5 = "ignore", check.nlev.gtr.1 = "stop", check.nobs.vs.nRE = "stop", check.rankX = "message+drop.cols", check.scaleX = "warning", check.formula.LHS = "stop"), checkConv = list(check.conv.grad = list(action = "warning", tol = 0.002, relTol = NULL), check.conv.singular = list( action = "message", tol = 1e-04), check.conv.hess = list( action = "warning", tol = 1e-06)), optCtrl = list())) 10: do.call(mkLmerDevfun, c(lmod, list(start = start, verbose = verbose, control = control))) 11: lme4::lmer(formula = feat1 ~ group + (1 | subject), data = list( sample_id = c("sample1", "sample2", "sample3", "sample4", "sample5", "sample6", "sample7", "sample8", "sample9", "sample10", "sample11", "sample12", "sample13", "sample14", "sample15", "sample16", "sample17", "sample18", "sample19", "sample20", "sample21", "sample22", "sample23", "sample24", "sample25", "sample26", "sample27", "sample28", "sample29", "sample30", "sample31", "sample32", "sample33", "sample34", "sample35", "sample36", "sample37", "sample38", "sample39", "sample40", "sample41", "sample42", "sample43", "sample44", "sample45", "sample46", "sample47", "sample48", "sample49", "sample50" ), group = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), subject = c(1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L, 25L, 25L), feat1 = c(-0.626453810742332, 0.183643324222082, -0.835628612410047, 1.59528080213779, 0.329507771815361, -0.820468384118015, 0.487429052428485, 0.738324705129217, 0.575781351653492, -0.305388387156356, 1.51178116845085, 0.389843236411431, -0.621240580541804, -2.2146998871775, 1.12493091814311, -0.0449336090152309, -0.0161902630989461, 0.943836210685299, 0.821221195098089, 0.593901321217509, 0.918977371608218, 0.782136300731067, 0.0745649833651906, -1.98935169586337, 0.61982574789471, -0.0561287395290008, -0.155795506705329, -1.47075238389927, -0.47815005510862, 0.417941560199702, 1.35867955152904, -0.102787727342996, 0.387671611559369, -0.0538050405829051, -1.37705955682861, -0.41499456329968, -0.394289953710349, -0.0593133967111857, 1.10002537198388, 0.763175748457544, -0.164523596253587, -0.253361680136508, 0.696963375404737, 0.556663198673657, -0.68875569454952, -0.70749515696212, 0.36458196213683, 0.768532924515416, -0.112346212150228, 0.881107726454215))) 12: eval(expr, p) 13: eval(expr, p) 14: eval.parent(mc) 15: (function (formula, data = NULL, REML = TRUE, control = lmerControl(), start = NULL, verbose = 0L, subset, weights, na.action, offset, contrasts = NULL, devFunOnly = FALSE) { orig_call <- mc <- match.call() mc[[1L]] <- quote(lme4::lmer) model <- eval.parent(mc) if (devFunOnly) return(model) args <- as.list(mc) args$devFunOnly <- TRUE if (!"control" %in% names(as.list(mc))) args$control <- lme4::lmerControl(check.rankX = "silent.drop.cols") Call <- as.call(c(list(quote(lme4::lmer)), args[-1])) devfun <- eval.parent(Call) res <- as_lmerModLT(model, devfun) res@call <- orig_call return(res)})(formula = feat1 ~ group + (1 | subject), data = list(sample_id = c("sample1", "sample2", "sample3", "sample4", "sample5", "sample6", "sample7", "sample8", "sample9", "sample10", "sample11", "sample12", "sample13", "sample14", "sample15", "sample16", "sample17", "sample18", "sample19", "sample20", "sample21", "sample22", "sample23", "sample24", "sample25", "sample26", "sample27", "sample28", "sample29", "sample30", "sample31", "sample32", "sample33", "sample34", "sample35", "sample36", "sample37", "sample38", "sample39", "sample40", "sample41", "sample42", "sample43", "sample44", "sample45", "sample46", "sample47", "sample48", "sample49", "sample50"), group = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), subject = c(1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L, 25L, 25L), feat1 = c(-0.626453810742332, 0.183643324222082, -0.835628612410047, 1.59528080213779, 0.329507771815361, -0.820468384118015, 0.487429052428485, 0.738324705129217, 0.575781351653492, -0.305388387156356, 1.51178116845085, 0.389843236411431, -0.621240580541804, -2.2146998871775, 1.12493091814311, -0.0449336090152309, -0.0161902630989461, 0.943836210685299, 0.821221195098089, 0.593901321217509, 0.918977371608218, 0.782136300731067, 0.0745649833651906, -1.98935169586337, 0.61982574789471, -0.0561287395290008, -0.155795506705329, -1.47075238389927, -0.47815005510862, 0.417941560199702, 1.35867955152904, -0.102787727342996, 0.387671611559369, -0.0538050405829051, -1.37705955682861, -0.41499456329968, -0.394289953710349, -0.0593133967111857, 1.10002537198388, 0.763175748457544, -0.164523596253587, -0.253361680136508, 0.696963375404737, 0.556663198673657, -0.68875569454952, -0.70749515696212, 0.36458196213683, 0.768532924515416, -0.112346212150228, 0.881107726454215))) 16: do.call(fit_model, model_args_temp) 17: doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, classes, parentenv, handlers) 20: tryCatch({ data_temp <- cbind(sdata_matched, X_matched[, i, drop = FALSE]) y_temp <- colnames(X_matched)[i] formula_temp <- stats::update(formula_rhs, paste(y_temp, "~ .")) model_args_temp <- utils::modifyList(model_control, list(formula = formula_temp, data = data_temp)) model_temp <- do.call(fit_model, model_args_temp) coeff_temp <- summary(model_temp)$coefficients confint_temp <- if (inherits(model_temp, "lm")) { stats::confint(model_temp) } else { lme4::confint.merMod(model_temp, parm = "beta_") } fit_df <- data.frame(Coefficient = rownames(coeff_temp), coeff_temp, confint_temp, feat_id = y_temp, check.names = FALSE, row.names = NULL) ranef_varcor <- if (inherits(model_temp, "lm")) { NULL } else { df <- as.data.frame(lme4::VarCorr(model_temp)) df$feat_id <- y_temp df } lrt_result <- if (is.null(term_LRT)) { NULL } else { lrt_temp <- lapply(term_LRT, function(z) { if (grepl("\\|", z)) { term_temp <- paste0("(", z, ")") } else { term_temp <- z } formula_null <- stats::update(formula_temp, paste(". ~ . -", term_temp)) model_args_null <- utils::modifyList(model_args_temp, list(formula = formula_null)) rand_eff_null <- lme4::findbars(formula_null) has_ranef_null <- length(rand_eff_null) > 0 fit_model_null <- if (has_ranef_null) lmerTest::lmer else stats::lm model_null <- do.call(fit_model_null, model_args_null) lrt_stats <- if (inherits(model_null, "lm") && inherits(model_temp, "lmerModLmerTest")) { stats::anova(model_temp, model_null) } else { stats::anova(model_null, model_temp) } lrt_stats$term <- z lrt_stats }) df <- do.call(rbind, lrt_temp) df$feat_id <- y_temp df } list(fit = fit_df, ranef = ranef_varcor, lrt = lrt_result, error = NULL)}, error = function(e) { warning(paste("Model failed for feature", i, ":", e$message)) list(fit = NULL, ranef = NULL, lrt = NULL, error = data.frame(feat_id = colnames(X_matched)[i], error = e$message))}) 21: ...future.FUN(...future.X_jj, ...) 22: FUN(X[[i]], ...) 23: lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...)}) 24: (function (...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) }})() 25: do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) }}, args = future.call.arguments) 26: eval(quote({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments)}), new.env()) 27: eval(quote({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments)}), new.env()) 28: eval(expr, p) 29: eval(expr, p) 30: eval.parent(substitute(eval(quote(expr), envir))) 31: base::local({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments)}) 32: base::withVisible(base::local({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments)})) 33: base::withCallingHandlers({ ...future.value <- base::withVisible(base::local({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments) })) future::FutureResult(value = ...future.value$value, visible = ...future.value$visible, rng = !identical(base::globalenv()$.Random.seed, ...future.rng), globalenv = if (FALSE) list(added = base::setdiff(base::names(base::.GlobalEnv), ...future.globalenv.names)) else NULL, started = ...future.startTime, version = "1.8")}, condition = base::local({ c <- base::c inherits <- base::inherits invokeRestart <- base::invokeRestart length <- base::length list <- base::list seq.int <- base::seq.int signalCondition <- base::signalCondition sys.calls <- base::sys.calls `[[` <- base::`[[` `+` <- base::`+` `<<-` <- base::`<<-` sysCalls <- function(calls = sys.calls(), from = 1L) { calls[seq.int(from = from + 12L, to = length(calls) - 3L)] } function(cond) { is_error <- inherits(cond, "error") ignore <- !is_error && !is.null(NULL) && inherits(cond, NULL) if (is_error) { sessionInformation <- function() { list(r = base::R.Version(), locale = base::Sys.getlocale(), rngkind = base::RNGkind(), namespaces = base::loadedNamespaces(), search = base::search(), system = base::Sys.info()) } ...future.conditions[[length(...future.conditions) + 1L]] <<- list(condition = cond, calls = c(sysCalls(from = ...future.frame), cond$call), session = sessionInformation(), timestamp = base::Sys.time(), signaled = 0L) signalCondition(cond) } else if (!ignore && TRUE && inherits(cond, c("condition", "immediateCondition"))) { signal <- TRUE && inherits(cond, "immediateCondition") ...future.conditions[[length(...future.conditions) + 1L]] <<- list(condition = cond, signaled = base::as.integer(signal)) if (TRUE && !signal) { muffleCondition <- function (cond, pattern = "^muffle") { inherits <- base::inherits invokeRestart <- base::invokeRestart is.null <- base::is.null muffled <- FALSE if (inherits(cond, "message")) { muffled <- grepl(pattern, "muffleMessage") if (muffled) invokeRestart("muffleMessage") } else if (inherits(cond, "warning")) { muffled <- grepl(pattern, "muffleWarning") if (muffled) invokeRestart("muffleWarning") } else if (inherits(cond, "condition")) { if (!is.null(pattern)) { computeRestarts <- base::computeRestarts grepl <- base::grepl restarts <- computeRestarts(cond) for (restart in restarts) { name <- restart$name if (is.null(name)) next if (!grepl(pattern, name)) next invokeRestart(restart) muffled <- TRUE break } } } invisible(muffled) } muffleCondition(cond, pattern = "^muffle") } } else { if (TRUE) { muffleCondition <- function (cond, pattern = "^muffle") { inherits <- base::inherits invokeRestart <- base::invokeRestart is.null <- base::is.null muffled <- FALSE if (inherits(cond, "message")) { muffled <- grepl(pattern, "muffleMessage") if (muffled) invokeRestart("muffleMessage") } else if (inherits(cond, "warning")) { muffled <- grepl(pattern, "muffleWarning") if (muffled) invokeRestart("muffleWarning") } else if (inherits(cond, "condition")) { if (!is.null(pattern)) { computeRestarts <- base::computeRestarts grepl <- base::grepl restarts <- computeRestarts(cond) for (restart in restarts) { name <- restart$name if (is.null(name)) next if (!grepl(pattern, name)) next invokeRestart(restart) muffled <- TRUE break } } } invisible(muffled) } muffleCondition(cond, pattern = "^muffle") } } }})) 34: doTryCatch(return(expr), name, parentenv, handler) 35: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 36: tryCatchList(expr, classes, parentenv, handlers) 37: base::tryCatch({ base::withCallingHandlers({ ...future.value <- base::withVisible(base::local({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments) })) future::FutureResult(value = ...future.value$value, visible = ...future.value$visible, rng = !identical(base::globalenv()$.Random.seed, ...future.rng), globalenv = if (FALSE) list(added = base::setdiff(base::names(base::.GlobalEnv), ...future.globalenv.names)) else NULL, started = ...future.startTime, version = "1.8") }, condition = base::local({ c <- base::c inherits <- base::inherits invokeRestart <- base::invokeRestart length <- base::length list <- base::list seq.int <- base::seq.int signalCondition <- base::signalCondition sys.calls <- base::sys.calls `[[` <- base::`[[` `+` <- base::`+` `<<-` <- base::`<<-` sysCalls <- function(calls = sys.calls(), from = 1L) { calls[seq.int(from = from + 12L, to = length(calls) - 3L)] } function(cond) { is_error <- inherits(cond, "error") ignore <- !is_error && !is.null(NULL) && inherits(cond, NULL) if (is_error) { sessionInformation <- function() { list(r = base::R.Version(), locale = base::Sys.getlocale(), rngkind = base::RNGkind(), namespaces = base::loadedNamespaces(), search = base::search(), system = base::Sys.info()) } ...future.conditions[[length(...future.conditions) + 1L]] <<- list(condition = cond, calls = c(sysCalls(from = ...future.frame), cond$call), session = sessionInformation(), timestamp = base::Sys.time(), signaled = 0L) signalCondition(cond) } else if (!ignore && TRUE && inherits(cond, c("condition", "immediateCondition"))) { signal <- TRUE && inherits(cond, "immediateCondition") ...future.conditions[[length(...future.conditions) + 1L]] <<- list(condition = cond, signaled = base::as.integer(signal)) if (TRUE && !signal) { muffleCondition <- function (cond, pattern = "^muffle") { inherits <- base::inherits invokeRestart <- base::invokeRestart is.null <- base::is.null muffled <- FALSE if (inherits(cond, "message")) { muffled <- grepl(pattern, "muffleMessage") if (muffled) invokeRestart("muffleMessage") } else if (inherits(cond, "warning")) { muffled <- grepl(pattern, "muffleWarning") if (muffled) invokeRestart("muffleWarning") } else if (inherits(cond, "condition")) { if (!is.null(pattern)) { computeRestarts <- base::computeRestarts grepl <- base::grepl restarts <- computeRestarts(cond) for (restart in restarts) { name <- restart$name if (is.null(name)) next if (!grepl(pattern, name)) next invokeRestart(restart) muffled <- TRUE break } } } invisible(muffled) } muffleCondition(cond, pattern = "^muffle") } } else { if (TRUE) { muffleCondition <- function (cond, pattern = "^muffle") { inherits <- base::inherits invokeRestart <- base::invokeRestart is.null <- base::is.null muffled <- FALSE if (inherits(cond, "message")) { muffled <- grepl(pattern, "muffleMessage") if (muffled) invokeRestart("muffleMessage") } else if (inherits(cond, "warning")) { muffled <- grepl(pattern, "muffleWarning") if (muffled) invokeRestart("muffleWarning") } else if (inherits(cond, "condition")) { if (!is.null(pattern)) { computeRestarts <- base::computeRestarts grepl <- base::grepl restarts <- computeRestarts(cond) for (restart in restarts) { name <- restart$name if (is.null(name)) next if (!grepl(pattern, name)) next invokeRestart(restart) muffled <- TRUE break } } } invisible(muffled) } muffleCondition(cond, pattern = "^muffle") } } } }))}, error = function(ex) { base::structure(base::list(value = NULL, visible = NULL, conditions = ...future.conditions, rng = !identical(base::globalenv()$.Random.seed, ...future.rng), started = ...future.startTime, finished = Sys.time(), session_uuid = NA_character_, version = "1.8"), class = "FutureResult")}, finally = { if (!identical(...future.workdir, getwd())) setwd(...future.workdir) { if (identical(getOption("nwarnings"), ...future.oldOptions$nwarnings)) { ...future.oldOptions$nwarnings <- NULL } base::options(...future.oldOptions) if (.Platform$OS.type == "windows") { old_names <- names(...future.oldEnvVars) envs <- base::Sys.getenv() names <- names(envs) common <- intersect(names, old_names) added <- setdiff(names, old_names) removed <- setdiff(old_names, names) changed <- common[...future.oldEnvVars[common] != envs[common]] NAMES <- toupper(changed) args <- list() for (kk in seq_along(NAMES)) { name <- changed[[kk]] NAME <- NAMES[[kk]] if (name != NAME && is.element(NAME, old_names)) next args[[name]] <- ...future.oldEnvVars[[name]] } NAMES <- toupper(added) for (kk in seq_along(NAMES)) { name <- added[[kk]] NAME <- NAMES[[kk]] if (name != NAME && is.element(NAME, old_names)) next args[[name]] <- "" } NAMES <- toupper(removed) for (kk in seq_along(NAMES)) { name <- removed[[kk]] NAME <- NAMES[[kk]] if (name != NAME && is.element(NAME, old_names)) next args[[name]] <- ...future.oldEnvVars[[name]] } if (length(args) > 0) base::do.call(base::Sys.setenv, args = args) args <- names <- old_names <- NAMES <- envs <- common <- added <- removed <- NULL } else { base::do.call(base::Sys.setenv, args = base::as.list(...future.oldEnvVars)) } { if (base::length(...future.futureOptionsAdded) > 0L) { opts <- base::vector("list", length = base::length(...future.futureOptionsAdded)) base::names(opts) <- ...future.futureOptionsAdded base::options(opts) } { { base::assign(".Random.seed", c(10403L, 378L, 1980538363L, -125047968L, -820381145L, -1073960099L, -33499050L, 1164085917L, 1218464490L, -1045685882L, -1933699935L, 795942478L, 495210185L, 1943097543L, -229514104L, -1232480817L, 352489432L, 351006324L, -867325393L, -1442019852L, 629147155L, 966152721L, 1616591578L, 200016369L, 1339052126L, -225299422L, -1512315715L, 103118938L, 1508496509L, 226325507L, 1531586180L, 1851232347L, -180012444L, 1939719752L, 1161394291L, 1375986488L, -1867206193L, -269449371L, 1080036398L, 1121658053L, 1200423730L, -1114719938L, 1019413465L, 699098406L, -2049351935L, -216610673L, 1752238736L, -1881625753L, 1183034576L, 289280140L, -1743926729L, -243822724L, -1713104501L, 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1981426537L, 176783780L, 523648218L, -589977567L, 1914642721L, -1871760254L, -1586947104L, -346442695L, 703798945L, 732710968L, -165412766L, 1888428821L, 1893337521L, -743130742L, -1050505356L, 471691885L, -1581648751L, 1125688788L, 2098523018L, 358039561L, -1567651463L, 597627866L, 1346302752L, -160376471L, 1063411465L, -623243680L, 897524434L, 995310533L, -1124453319L, -1103252830L, -1708500724L, -983918331L, 324701481L, -1224973676L, -1261295304L, -2057610510L ), envir = base::globalenv(), inherits = FALSE) NULL } options(future.plan = NULL) if (is.na(NA_character_)) Sys.unsetenv("R_FUTURE_PLAN") else Sys.setenv(R_FUTURE_PLAN = NA_character_) future::plan(...future.strategy.old, .cleanup = FALSE, .init = FALSE) } } }}) 38: eval(expr, envir = envir, enclos = baseenv()) 39: eval(expr, envir = envir, enclos = baseenv()) 40: run.UniprocessFuture(future) 41: run(future) 42: run.Future(future) 43: run(future) 44: future(expr, substitute = FALSE, envir = future.envir, stdout = future.stdout, conditions = future.conditions, globals = globals_ii, packages = packages_ii, seed = future.seed, label = labels[ii]) 45: future_xapply(FUN = FUN, nX = nX, chunk_args = X, args = list(...), get_chunk = `chunkWith[[`, expr = expr, envir = envir, future.envir = future.envir, future.globals = future.globals, future.packages = future.packages, future.scheduling = future.scheduling, future.chunk.size = future.chunk.size, future.stdout = future.stdout, future.conditions = future.conditions, future.seed = future.seed, future.label = future.label, fcn_name = fcn_name, args_name = args_name, debug = debug) 46: future.apply::future_lapply(seq_len(feat_num), function(i) { if (report(i)) p(sprintf("Processed %d of %d", i, feat_num)) tryCatch({ data_temp <- cbind(sdata_matched, X_matched[, i, drop = FALSE]) y_temp <- colnames(X_matched)[i] formula_temp <- stats::update(formula_rhs, paste(y_temp, "~ .")) model_args_temp <- utils::modifyList(model_control, list(formula = formula_temp, data = data_temp)) model_temp <- do.call(fit_model, model_args_temp) coeff_temp <- summary(model_temp)$coefficients confint_temp <- if (inherits(model_temp, "lm")) { stats::confint(model_temp) } else { lme4::confint.merMod(model_temp, parm = "beta_") } fit_df <- data.frame(Coefficient = rownames(coeff_temp), coeff_temp, confint_temp, feat_id = y_temp, check.names = FALSE, row.names = NULL) ranef_varcor <- if (inherits(model_temp, "lm")) { NULL } else { df <- as.data.frame(lme4::VarCorr(model_temp)) df$feat_id <- y_temp df } lrt_result <- if (is.null(term_LRT)) { NULL } else { lrt_temp <- lapply(term_LRT, function(z) { if (grepl("\\|", z)) { term_temp <- paste0("(", z, ")") } else { term_temp <- z } formula_null <- stats::update(formula_temp, paste(". ~ . -", term_temp)) model_args_null <- utils::modifyList(model_args_temp, list(formula = formula_null)) rand_eff_null <- lme4::findbars(formula_null) has_ranef_null <- length(rand_eff_null) > 0 fit_model_null <- if (has_ranef_null) lmerTest::lmer else stats::lm model_null <- do.call(fit_model_null, model_args_null) lrt_stats <- if (inherits(model_null, "lm") && inherits(model_temp, "lmerModLmerTest")) { stats::anova(model_temp, model_null) } else { stats::anova(model_null, model_temp) } lrt_stats$term <- z lrt_stats }) df <- do.call(rbind, lrt_temp) df$feat_id <- y_temp df } list(fit = fit_df, ranef = ranef_varcor, lrt = lrt_result, error = NULL) }, error = function(e) { warning(paste("Model failed for feature", i, ":", e$message)) list(fit = NULL, ranef = NULL, lrt = NULL, error = data.frame(feat_id = colnames(X_matched)[i], error = e$message)) })}, future.seed = TRUE) 47: dana(X = mock_X, sample_data = sample_data, formula_rhs = ~group + (1 | subject), term_LRT = c("group", "1 | subject"), platform = "ms", assay = "lipidomics", verbose = FALSE) An irrecoverable exception occurred. R is aborting now ... Examples with CPU (user + system) or elapsed time > 5s user system elapsed build_phyloseq 8.585 0.392 9.156 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R'/home/th798/R/R-release/bin/BATCH: line 60: 1108412 Segmentation fault (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 ERROR Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(readyomics) > > test_check("readyomics") Error in smooth.spline(lambda, pi0, df = smooth.df) : missing or infinite values in inputs are not allowed 2 samples found in common between 2 rows in 'X' and 2 rows in 'sample_data'. *** caught segfault *** address (nil), cause 'unknown' Traceback: 1: .Call(merPredDCreate, as(X, "matrix"), Lambdat, LamtUt, Lind, RZX, Ut, Utr, V, VtV, Vtr, Xwts, Zt, beta0, delb, delu, theta, u0) 2: initializePtr() 3: .Object$initialize(...) 4: initialize(value, ...) 5: initialize(value, ...) 6: methods::new(def, ...) 7: (new("refMethodDef", .Data = function (...) { methods::new(def, ...)}, mayCall = c("methods", "new"), name = "new", refClassName = "refGeneratorSlot", superClassMethod = ""))(Zt = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L), p = 0:5, Dim = c(3L, 5L), Dimnames = list(c("1", "2", "3"), c("id1", "id2", "id3", "id4", "id5")), x = c(1, 1, 1, 1, 1), factors = list()), theta = 1, Lambdat = new("dgCMatrix", i = 0:2, p = 0:3, Dim = c(3L, 3L), Dimnames = list(NULL, NULL), x = c(1, 1, 1), factors = list()), Lind = c(1L, 1L, 1L), n = 5L, X = c(1, 1, 1, 1, 1, 0, 0, 1, 1, 1)) 8: do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")], n = nrow(X), list(X = X))) 9: (function (fr, X, reTrms, REML = TRUE, start = NULL, verbose = 0, control = lmerControl(), ...) { p <- ncol(X) rho <- new.env(parent = parent.env(environment())) rho$pp <- do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")], n = nrow(X), list(X = X))) REMLpass <- if (REML) p else 0L rho$resp <- if (missing(fr)) mkRespMod(REML = REMLpass, ...) else mkRespMod(fr, REML = REMLpass) pp <- resp <- NULL rho$lmer_Deviance <- lmer_Deviance devfun <- function(theta) .Call(lmer_Deviance, pp$ptr(), resp$ptr(), as.double(theta)) environment(devfun) <- rho if (is.null(start) && all(reTrms$cnms == "(Intercept)") && length(reTrms$flist) == length(reTrms$lower) && !is.null(y <- model.response(fr))) { v <- sapply(reTrms$flist, function(f) var(ave(y, f))) v.e <- var(y) - sum(v) if (!is.na(v.e) && v.e > 0) { v.rel <- v/v.e if (all(v.rel >= reTrms$lower^2)) rho$pp$setTheta(sqrt(v.rel)) } } if (length(rho$resp$y) > 0) devfun(rho$pp$theta) rho$lower <- reTrms$lower devfun})(fr = list(feat1 = c(-0.217974914658295, -1.02600444830724, -0.72889122929114, -0.625039267849257, -1.68669331074241), group = c(1L, 1L, 2L, 2L, 2L), subject = c(1L, 1L, 2L, 2L, 3L)), X = c(1, 1, 1, 1, 1, 0, 0, 1, 1, 1), reTrms = list(Zt = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L), p = 0:5, Dim = c(3L, 5L), Dimnames = list( c("1", "2", "3"), c("id1", "id2", "id3", "id4", "id5" )), x = c(1, 1, 1, 1, 1), factors = list()), theta = 1, Lind = c(1L, 1L, 1L), Gp = c(0L, 3L), lower = 0, Lambdat = new("dgCMatrix", i = 0:2, p = 0:3, Dim = c(3L, 3L), Dimnames = list(NULL, NULL), x = c(1, 1, 1), factors = list()), flist = list( subject = c(1L, 1L, 2L, 2L, 3L)), cnms = list(subject = "(Intercept)"), Ztlist = list(`1 | subject` = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L), p = 0:5, Dim = c(3L, 5L), Dimnames = list( c("1", "2", "3"), c("id1", "id2", "id3", "id4", "id5" )), x = c(1, 1, 1, 1, 1), factors = list())), nl = c(subject = 3L)), REML = TRUE, wmsgs = character(0), start = NULL, verbose = 0L, control = list(optimizer = "nloptwrap", restart_edge = TRUE, boundary.tol = 1e-05, calc.derivs = TRUE, use.last.params = FALSE, checkControl = list(check.nobs.vs.rankZ = "ignore", check.nobs.vs.nlev = "stop", check.nlev.gtreq.5 = "ignore", check.nlev.gtr.1 = "stop", check.nobs.vs.nRE = "stop", check.rankX = "message+drop.cols", check.scaleX = "warning", check.formula.LHS = "stop"), checkConv = list(check.conv.grad = list(action = "warning", tol = 0.002, relTol = NULL), check.conv.singular = list( action = "message", tol = 1e-04), check.conv.hess = list( action = "warning", tol = 1e-06)), optCtrl = list())) 10: do.call(mkLmerDevfun, c(lmod, list(start = start, verbose = verbose, control = control))) 11: lme4::lmer(formula = feat1 ~ group + (1 | subject), data = list( sample_id = c("id1", "id2", "id3", "id4", "id5"), group = c(1L, 1L, 2L, 2L, 2L), subject = c(1L, 1L, 2L, 2L, 3L), feat1 = c(-0.217974914658295, -1.02600444830724, -0.72889122929114, -0.625039267849257, -1.68669331074241))) 12: eval(expr, p) 13: eval(expr, p) 14: eval.parent(mc) 15: (function (formula, data = NULL, REML = TRUE, control = lmerControl(), start = NULL, verbose = 0L, subset, weights, na.action, offset, contrasts = NULL, devFunOnly = FALSE) { orig_call <- mc <- match.call() mc[[1L]] <- quote(lme4::lmer) model <- eval.parent(mc) if (devFunOnly) return(model) args <- as.list(mc) args$devFunOnly <- TRUE if (!"control" %in% names(as.list(mc))) args$control <- lme4::lmerControl(check.rankX = "silent.drop.cols") Call <- as.call(c(list(quote(lme4::lmer)), args[-1])) devfun <- eval.parent(Call) res <- as_lmerModLT(model, devfun) res@call <- orig_call return(res)})(formula = feat1 ~ group + (1 | subject), data = list(sample_id = c("id1", "id2", "id3", "id4", "id5"), group = c(1L, 1L, 2L, 2L, 2L), subject = c(1L, 1L, 2L, 2L, 3L), feat1 = c(-0.217974914658295, -1.02600444830724, -0.72889122929114, -0.625039267849257, -1.68669331074241))) 16: do.call(fit_model, model_args_temp) 17: doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, classes, parentenv, handlers) 20: tryCatch({ data_temp <- cbind(sdata_matched, X_matched[, i, drop = FALSE]) y_temp <- colnames(X_matched)[i] formula_temp <- stats::update(formula_rhs, paste(y_temp, "~ .")) model_args_temp <- utils::modifyList(model_control, list(formula = formula_temp, data = data_temp)) model_temp <- do.call(fit_model, model_args_temp) coeff_temp <- summary(model_temp)$coefficients confint_temp <- if (inherits(model_temp, "lm")) { stats::confint(model_temp) } else { lme4::confint.merMod(model_temp, parm = "beta_") } fit_df <- data.frame(Coefficient = rownames(coeff_temp), coeff_temp, confint_temp, feat_id = y_temp, check.names = FALSE, row.names = NULL) ranef_varcor <- if (inherits(model_temp, "lm")) { NULL } else { df <- as.data.frame(lme4::VarCorr(model_temp)) df$feat_id <- y_temp df } lrt_result <- if (is.null(term_LRT)) { NULL } else { lrt_temp <- lapply(term_LRT, function(z) { if (grepl("\\|", z)) { term_temp <- paste0("(", z, ")") } else { term_temp <- z } formula_null <- stats::update(formula_temp, paste(". ~ . -", term_temp)) model_args_null <- utils::modifyList(model_args_temp, list(formula = formula_null)) rand_eff_null <- lme4::findbars(formula_null) has_ranef_null <- length(rand_eff_null) > 0 fit_model_null <- if (has_ranef_null) lmerTest::lmer else stats::lm model_null <- do.call(fit_model_null, model_args_null) lrt_stats <- if (inherits(model_null, "lm") && inherits(model_temp, "lmerModLmerTest")) { stats::anova(model_temp, model_null) } else { stats::anova(model_null, model_temp) } lrt_stats$term <- z lrt_stats }) df <- do.call(rbind, lrt_temp) df$feat_id <- y_temp df } list(fit = fit_df, ranef = ranef_varcor, lrt = lrt_result, error = NULL)}, error = function(e) { warning(paste("Model failed for feature", i, ":", e$message)) list(fit = NULL, ranef = NULL, lrt = NULL, error = data.frame(feat_id = colnames(X_matched)[i], error = e$message))}) 21: ...future.FUN(...future.X_jj, ...) 22: FUN(X[[i]], ...) 23: lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...)}) 24: (function (...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) }})() 25: do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) }}, args = future.call.arguments) 26: eval(quote({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments)}), new.env()) 27: eval(quote({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments)}), new.env()) 28: eval(expr, p) 29: eval(expr, p) 30: eval.parent(substitute(eval(quote(expr), envir))) 31: base::local({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments)}) 32: base::withVisible(base::local({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments)})) 33: base::withCallingHandlers({ ...future.value <- base::withVisible(base::local({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments) })) future::FutureResult(value = ...future.value$value, visible = ...future.value$visible, rng = !identical(base::globalenv()$.Random.seed, ...future.rng), globalenv = if (FALSE) list(added = base::setdiff(base::names(base::.GlobalEnv), ...future.globalenv.names)) else NULL, started = ...future.startTime, version = "1.8")}, condition = base::local({ c <- base::c inherits <- base::inherits invokeRestart <- base::invokeRestart length <- base::length list <- base::list seq.int <- base::seq.int signalCondition <- base::signalCondition sys.calls <- base::sys.calls `[[` <- base::`[[` `+` <- base::`+` `<<-` <- base::`<<-` sysCalls <- function(calls = sys.calls(), from = 1L) { calls[seq.int(from = from + 12L, to = length(calls) - 3L)] } function(cond) { is_error <- inherits(cond, "error") ignore <- !is_error && !is.null(NULL) && inherits(cond, NULL) if (is_error) { sessionInformation <- function() { list(r = base::R.Version(), locale = base::Sys.getlocale(), rngkind = base::RNGkind(), namespaces = base::loadedNamespaces(), search = base::search(), system = base::Sys.info()) } ...future.conditions[[length(...future.conditions) + 1L]] <<- list(condition = cond, calls = c(sysCalls(from = ...future.frame), cond$call), session = sessionInformation(), timestamp = base::Sys.time(), signaled = 0L) signalCondition(cond) } else if (!ignore && TRUE && inherits(cond, c("condition", "immediateCondition"))) { signal <- TRUE && inherits(cond, "immediateCondition") ...future.conditions[[length(...future.conditions) + 1L]] <<- list(condition = cond, signaled = base::as.integer(signal)) if (TRUE && !signal) { muffleCondition <- function (cond, pattern = "^muffle") { inherits <- base::inherits invokeRestart <- base::invokeRestart is.null <- base::is.null muffled <- FALSE if (inherits(cond, "message")) { muffled <- grepl(pattern, "muffleMessage") if (muffled) invokeRestart("muffleMessage") } else if (inherits(cond, "warning")) { muffled <- grepl(pattern, "muffleWarning") if (muffled) invokeRestart("muffleWarning") } else if (inherits(cond, "condition")) { if (!is.null(pattern)) { computeRestarts <- base::computeRestarts grepl <- base::grepl restarts <- computeRestarts(cond) for (restart in restarts) { name <- restart$name if (is.null(name)) next if (!grepl(pattern, name)) next invokeRestart(restart) muffled <- TRUE break } } } invisible(muffled) } muffleCondition(cond, pattern = "^muffle") } } else { if (TRUE) { muffleCondition <- function (cond, pattern = "^muffle") { inherits <- base::inherits invokeRestart <- base::invokeRestart is.null <- base::is.null muffled <- FALSE if (inherits(cond, "message")) { muffled <- grepl(pattern, "muffleMessage") if (muffled) invokeRestart("muffleMessage") } else if (inherits(cond, "warning")) { muffled <- grepl(pattern, "muffleWarning") if (muffled) invokeRestart("muffleWarning") } else if (inherits(cond, "condition")) { if (!is.null(pattern)) { computeRestarts <- base::computeRestarts grepl <- base::grepl restarts <- computeRestarts(cond) for (restart in restarts) { name <- restart$name if (is.null(name)) next if (!grepl(pattern, name)) next invokeRestart(restart) muffled <- TRUE break } } } invisible(muffled) } muffleCondition(cond, pattern = "^muffle") } } }})) 34: doTryCatch(return(expr), name, parentenv, handler) 35: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 36: tryCatchList(expr, classes, parentenv, handlers) 37: base::tryCatch({ base::withCallingHandlers({ ...future.value <- base::withVisible(base::local({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments) })) future::FutureResult(value = ...future.value$value, visible = ...future.value$visible, rng = !identical(base::globalenv()$.Random.seed, ...future.rng), globalenv = if (FALSE) list(added = base::setdiff(base::names(base::.GlobalEnv), ...future.globalenv.names)) else NULL, started = ...future.startTime, version = "1.8") }, condition = base::local({ c <- base::c inherits <- base::inherits invokeRestart <- base::invokeRestart length <- base::length list <- base::list seq.int <- base::seq.int signalCondition <- base::signalCondition sys.calls <- base::sys.calls `[[` <- base::`[[` `+` <- base::`+` `<<-` <- base::`<<-` sysCalls <- function(calls = sys.calls(), from = 1L) { calls[seq.int(from = from + 12L, to = length(calls) - 3L)] } function(cond) { is_error <- inherits(cond, "error") ignore <- !is_error && !is.null(NULL) && inherits(cond, NULL) if (is_error) { sessionInformation <- function() { list(r = base::R.Version(), locale = base::Sys.getlocale(), rngkind = base::RNGkind(), namespaces = base::loadedNamespaces(), search = base::search(), system = base::Sys.info()) } ...future.conditions[[length(...future.conditions) + 1L]] <<- list(condition = cond, calls = c(sysCalls(from = ...future.frame), cond$call), session = sessionInformation(), timestamp = base::Sys.time(), signaled = 0L) signalCondition(cond) } else if (!ignore && TRUE && inherits(cond, c("condition", "immediateCondition"))) { signal <- TRUE && inherits(cond, "immediateCondition") ...future.conditions[[length(...future.conditions) + 1L]] <<- list(condition = cond, signaled = base::as.integer(signal)) if (TRUE && !signal) { muffleCondition <- function (cond, pattern = "^muffle") { inherits <- base::inherits invokeRestart <- base::invokeRestart is.null <- base::is.null muffled <- FALSE if (inherits(cond, "message")) { muffled <- grepl(pattern, "muffleMessage") if (muffled) invokeRestart("muffleMessage") } else if (inherits(cond, "warning")) { muffled <- grepl(pattern, "muffleWarning") if (muffled) invokeRestart("muffleWarning") } else if (inherits(cond, "condition")) { if (!is.null(pattern)) { computeRestarts <- base::computeRestarts grepl <- base::grepl restarts <- computeRestarts(cond) for (restart in restarts) { name <- restart$name if (is.null(name)) next if (!grepl(pattern, name)) next invokeRestart(restart) muffled <- TRUE break } } } invisible(muffled) } muffleCondition(cond, pattern = "^muffle") } } else { if (TRUE) { muffleCondition <- function (cond, pattern = "^muffle") { inherits <- base::inherits invokeRestart <- base::invokeRestart is.null <- base::is.null muffled <- FALSE if (inherits(cond, "message")) { muffled <- grepl(pattern, "muffleMessage") if (muffled) invokeRestart("muffleMessage") } else if (inherits(cond, "warning")) { muffled <- grepl(pattern, "muffleWarning") if (muffled) invokeRestart("muffleWarning") } else if (inherits(cond, "condition")) { if (!is.null(pattern)) { computeRestarts <- base::computeRestarts grepl <- base::grepl restarts <- computeRestarts(cond) for (restart in restarts) { name <- restart$name if (is.null(name)) next if (!grepl(pattern, name)) next invokeRestart(restart) muffled <- TRUE break } } } invisible(muffled) } muffleCondition(cond, pattern = "^muffle") } } } }))}, error = function(ex) { base::structure(base::list(value = NULL, visible = NULL, conditions = ...future.conditions, rng = !identical(base::globalenv()$.Random.seed, ...future.rng), started = ...future.startTime, finished = Sys.time(), session_uuid = NA_character_, version = "1.8"), class = "FutureResult")}, finally = { if (!identical(...future.workdir, getwd())) setwd(...future.workdir) { if (identical(getOption("nwarnings"), ...future.oldOptions$nwarnings)) { ...future.oldOptions$nwarnings <- NULL } base::options(...future.oldOptions) if (.Platform$OS.type == "windows") { old_names <- names(...future.oldEnvVars) envs <- base::Sys.getenv() names <- names(envs) common <- intersect(names, old_names) added <- setdiff(names, old_names) removed <- setdiff(old_names, names) changed <- common[...future.oldEnvVars[common] != envs[common]] NAMES <- toupper(changed) args <- list() for (kk in seq_along(NAMES)) { name <- changed[[kk]] NAME <- NAMES[[kk]] if (name != NAME && is.element(NAME, old_names)) next args[[name]] <- ...future.oldEnvVars[[name]] } NAMES <- toupper(added) for (kk in seq_along(NAMES)) { name <- added[[kk]] NAME <- NAMES[[kk]] if (name != NAME && is.element(NAME, old_names)) next args[[name]] <- "" } NAMES <- toupper(removed) for (kk in seq_along(NAMES)) { name <- removed[[kk]] NAME <- NAMES[[kk]] if (name != NAME && is.element(NAME, old_names)) next args[[name]] <- ...future.oldEnvVars[[name]] } if (length(args) > 0) base::do.call(base::Sys.setenv, args = args) args <- names <- old_names <- NAMES <- envs <- common <- added <- removed <- NULL } else { base::do.call(base::Sys.setenv, args = base::as.list(...future.oldEnvVars)) } { if (base::length(...future.futureOptionsAdded) > 0L) { opts <- base::vector("list", length = base::length(...future.futureOptionsAdded)) base::names(opts) <- ...future.futureOptionsAdded base::options(opts) } { { base::assign(".Random.seed", c(10403L, 84L, 515190382L, 2133433928L, 917665867L, 1283494313L, 1101294840L, 1366013990L, -351622847L, 676521683L, 1906871938L, 611071156L, 1955982391L, 889786157L, -2020897724L, 33313130L, -1561915947L, 293137263L, -125382026L, -1082686048L, 517280355L, 1329304321L, 257493616L, 1917969934L, -1708298631L, 1261124107L, -1796672710L, 394955324L, 1787087231L, 1253737173L, 1825149676L, 1067631682L, -1933739107L, -272199145L, -1473812610L, -1483012808L, -1945071077L, 304012153L, 1841692104L, 1692664310L, 1694274609L, 1439639139L, 1682577970L, 905136004L, 468383175L, -2022286179L, 1825119252L, -746800454L, 843324165L, -791084833L, 546609510L, 95571184L, 1230829587L, 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-554617705L, -1475068064L, 222000958L, 1930422283L, -512962419L, -2054862406L, -558536712L, 1084621729L, 2130378067L, 1030009972L, 970352130L, 1209858199L, -1328338335L, -1244519770L, 908634788L, -367452331L, 1983669247L, 142271128L, 1880377270L, 424193091L, -694008443L, -315810270L, 562644240L, -24410951L, -1914664597L, 101001308L, -955529846L, -1437884033L, 2093022409L, 55263582L, -579808756L, 1880167901L, -1054929689L, 1903898387L ), envir = base::globalenv(), inherits = FALSE) NULL } options(future.plan = NULL) if (is.na(NA_character_)) Sys.unsetenv("R_FUTURE_PLAN") else Sys.setenv(R_FUTURE_PLAN = NA_character_) future::plan(...future.strategy.old, .cleanup = FALSE, .init = FALSE) } } }}) 38: eval(expr, envir = envir, enclos = baseenv()) 39: eval(expr, envir = envir, enclos = baseenv()) 40: run.UniprocessFuture(future) 41: run(future) 42: run.Future(future) 43: run(future) 44: future(expr, substitute = FALSE, envir = future.envir, stdout = future.stdout, conditions = future.conditions, globals = globals_ii, packages = packages_ii, seed = future.seed, label = labels[ii]) 45: future_xapply(FUN = FUN, nX = nX, chunk_args = X, args = list(...), get_chunk = `chunkWith[[`, expr = expr, envir = envir, future.envir = future.envir, future.globals = future.globals, future.packages = future.packages, future.scheduling = future.scheduling, future.chunk.size = future.chunk.size, future.stdout = future.stdout, future.conditions = future.conditions, future.seed = future.seed, future.label = future.label, fcn_name = fcn_name, args_name = args_name, debug = debug) 46: future.apply::future_lapply(seq_len(feat_num), function(i) { if (report(i)) p(sprintf("Processed %d of %d", i, feat_num)) tryCatch({ data_temp <- cbind(sdata_matched, X_matched[, i, drop = FALSE]) y_temp <- colnames(X_matched)[i] formula_temp <- stats::update(formula_rhs, paste(y_temp, "~ .")) model_args_temp <- utils::modifyList(model_control, list(formula = formula_temp, data = data_temp)) model_temp <- do.call(fit_model, model_args_temp) coeff_temp <- summary(model_temp)$coefficients confint_temp <- if (inherits(model_temp, "lm")) { stats::confint(model_temp) } else { lme4::confint.merMod(model_temp, parm = "beta_") } fit_df <- data.frame(Coefficient = rownames(coeff_temp), coeff_temp, confint_temp, feat_id = y_temp, check.names = FALSE, row.names = NULL) ranef_varcor <- if (inherits(model_temp, "lm")) { NULL } else { df <- as.data.frame(lme4::VarCorr(model_temp)) df$feat_id <- y_temp df } lrt_result <- if (is.null(term_LRT)) { NULL } else { lrt_temp <- lapply(term_LRT, function(z) { if (grepl("\\|", z)) { term_temp <- paste0("(", z, ")") } else { term_temp <- z } formula_null <- stats::update(formula_temp, paste(". ~ . -", term_temp)) model_args_null <- utils::modifyList(model_args_temp, list(formula = formula_null)) rand_eff_null <- lme4::findbars(formula_null) has_ranef_null <- length(rand_eff_null) > 0 fit_model_null <- if (has_ranef_null) lmerTest::lmer else stats::lm model_null <- do.call(fit_model_null, model_args_null) lrt_stats <- if (inherits(model_null, "lm") && inherits(model_temp, "lmerModLmerTest")) { stats::anova(model_temp, model_null) } else { stats::anova(model_null, model_temp) } lrt_stats$term <- z lrt_stats }) df <- do.call(rbind, lrt_temp) df$feat_id <- y_temp df } list(fit = fit_df, ranef = ranef_varcor, lrt = lrt_result, error = NULL) }, error = function(e) { warning(paste("Model failed for feature", i, ":", e$message)) list(fit = NULL, ranef = NULL, lrt = NULL, error = data.frame(feat_id = colnames(X_matched)[i], error = e$message)) })}, future.seed = TRUE) 47: dana(X = mock_X, sample_data = sample_data, formula_rhs = ~group + (1 | subject), term_LRT = "group", platform = "nmr", verbose = FALSE) 48: eval(code, test_env) 49: eval(code, test_env) 50: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error) 51: doTryCatch(return(expr), name, parentenv, handler) 52: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 53: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 54: doTryCatch(return(expr), name, parentenv, handler) 55: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 56: tryCatchList(expr, classes, parentenv, handlers) 57: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) 58: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter()) 59: test_that("dana handles LRT terms correctly", { skip_if_not_installed("lmerTest") skip_if_not_installed("future") mock_X <- matrix(rnorm(20), nrow = 5) rownames(mock_X) <- paste0("id", 1:5) colnames(mock_X) <- paste0("feat", 1:4) sample_data <- data.frame(sample_id = rownames(mock_X), group = factor(c("A", "A", "B", "B", "B")), subject = factor(c(1, 1, 2, 2, 3)), row.names = rownames(mock_X)) res <- dana(X = mock_X, sample_data = sample_data, formula_rhs = ~group + (1 | subject), term_LRT = "group", platform = "nmr", verbose = FALSE) expect_s3_class(res, "dana") expect_true(nrow(res$fit) > 0) expect_true(nrow(res$lrt) > 0) expect_true("term" %in% colnames(res$lrt))}) 60: eval(code, test_env) 61: eval(code, test_env) 62: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error) 63: doTryCatch(return(expr), name, parentenv, handler) 64: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 65: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 66: doTryCatch(return(expr), name, parentenv, handler) 67: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 68: tryCatchList(expr, classes, parentenv, handlers) 69: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) 70: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new()) 71: source_file(path, env = env(env), desc = desc, error_call = error_call) 72: FUN(X[[i]], ...) 73: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call) 74: doTryCatch(return(expr), name, parentenv, handler) 75: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 76: tryCatchList(expr, classes, parentenv, handlers) 77: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) 78: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)) 79: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call) 80: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel) 81: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") 82: test_check("readyomics") An irrecoverable exception occurred. R is aborting now ... * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building 'readyomics.Rmd' using rmarkdown Quitting from lines at lines 210-220 [unnamed-chunk-14] (readyomics.Rmd) Error: processing vignette 'readyomics.Rmd' failed with diagnostics: object 'X_dist' not found --- failed re-building 'readyomics.Rmd' SUMMARY: processing the following file failed: 'readyomics.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 3 ERRORs See '/tmp/th798/21128216/R-release/1180/readyomics.Rcheck/00check.log' for details. [1] "2025-08-24 00:46:17 MST" [1] "2025-08-24 00:46:17 MST" Installing package into '/tmp/th798/21128216/R-release/1180/library' (as 'lib' is unspecified) Warning: invalid package '/scratch/th798/data.table-revdeps/2025-08-24/data.table_master_1.17.99.55bbc3d1646a80ba1d5b2c073c17b9575e7c186a.tar.gz' Error: ERROR: no packages specified [1] "2025-08-24 00:46:17 MST" * using log directory '/tmp/th798/21128216/R-release/1180/readyomics.Rcheck' * using R version 4.5.1 (2025-06-13) * 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 'readyomics/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'readyomics' version '0.1.0' * 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 'readyomics' 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 ...sh: line 1: 1128595 Segmentation fault (core dumped) LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/home/th798/R/R-release/bin/R' --vanilla > 'readyomics-Ex.Rout' 2>&1 < 'readyomics-Ex.R' ERROR Running examples in 'readyomics-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: dana > ### Title: Differential analysis (dana) > ### Aliases: dana > > ### ** Examples > > mock_X <- matrix( + rnorm(50 * 10) + + rep(c(rep(0, 25), rep(2, 25)), each = 10) * rep(1:10 %in% 1:3, each = 50), + nrow = 50 + ) > > rownames(mock_X) <- paste0("sample", 1:50) > colnames(mock_X) <- paste0("feat", 1:10) > > sample_data <- data.frame( + sample_id = rownames(mock_X), + group = factor(rep(c("A", "B"), each = 25)), + subject = factor(rep(1:25, each = 2)), + row.names = rownames(mock_X) + ) > > # Example with parallel computation setup (not run) > # future::plan(multisession) > # progressr::handlers(global = TRUE) > # progressr::with_progress({ > result <- dana(X = mock_X, + sample_data = sample_data, + formula_rhs = ~ group + (1 | subject), + term_LRT = c("group", "1 | subject"), # Multiple terms allowed + platform = "ms", + assay = "lipidomics", + verbose = FALSE + ) Warning in check_dep_version() : ABI version mismatch: lme4 was built with Matrix ABI version 1 Current Matrix ABI version is 2 Please re-install lme4 from source or restore original 'Matrix' package *** caught segfault *** address (nil), cause 'unknown' Traceback: 1: .Call(merPredDCreate, as(X, "matrix"), Lambdat, LamtUt, Lind, RZX, Ut, Utr, V, VtV, Vtr, Xwts, Zt, beta0, delb, delu, theta, u0) 2: initializePtr() 3: .Object$initialize(...) 4: initialize(value, ...) 5: initialize(value, ...) 6: methods::new(def, ...) 7: (new("refMethodDef", .Data = function (...) { methods::new(def, ...)}, mayCall = c("methods", "new"), name = "new", refClassName = "refGeneratorSlot", superClassMethod = ""))(Zt = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L), p = 0:50, Dim = c(25L, 50L), Dimnames = list( c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25"), c("sample1", "sample2", "sample3", "sample4", "sample5", "sample6", "sample7", "sample8", "sample9", "sample10", "sample11", "sample12", "sample13", "sample14", "sample15", "sample16", "sample17", "sample18", "sample19", "sample20", "sample21", "sample22", "sample23", "sample24", "sample25", "sample26", "sample27", "sample28", "sample29", "sample30", "sample31", "sample32", "sample33", "sample34", "sample35", "sample36", "sample37", "sample38", "sample39", "sample40", "sample41", "sample42", "sample43", "sample44", "sample45", "sample46", "sample47", "sample48", "sample49", "sample50")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), theta = 1, Lambdat = new("dgCMatrix", i = 0:24, p = 0:25, Dim = c(25L, 25L), Dimnames = list(NULL, NULL), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), Lind = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), n = 50L, X = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)) 8: do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")], n = nrow(X), list(X = X))) 9: (function (fr, X, reTrms, REML = TRUE, start = NULL, verbose = 0, control = lmerControl(), ...) { p <- ncol(X) rho <- new.env(parent = parent.env(environment())) rho$pp <- do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")], n = nrow(X), list(X = X))) REMLpass <- if (REML) p else 0L rho$resp <- if (missing(fr)) mkRespMod(REML = REMLpass, ...) else mkRespMod(fr, REML = REMLpass) pp <- resp <- NULL rho$lmer_Deviance <- lmer_Deviance devfun <- function(theta) .Call(lmer_Deviance, pp$ptr(), resp$ptr(), as.double(theta)) environment(devfun) <- rho if (is.null(start) && all(reTrms$cnms == "(Intercept)") && length(reTrms$flist) == length(reTrms$lower) && !is.null(y <- model.response(fr))) { v <- sapply(reTrms$flist, function(f) var(ave(y, f))) v.e <- var(y) - sum(v) if (!is.na(v.e) && v.e > 0) { v.rel <- v/v.e if (all(v.rel >= reTrms$lower^2)) rho$pp$setTheta(sqrt(v.rel)) } } if (length(rho$resp$y) > 0) devfun(rho$pp$theta) rho$lower <- reTrms$lower devfun})(fr = list(feat1 = c(-0.626453810742332, 0.183643324222082, -0.835628612410047, 1.59528080213779, 0.329507771815361, -0.820468384118015, 0.487429052428485, 0.738324705129217, 0.575781351653492, -0.305388387156356, 1.51178116845085, 0.389843236411431, -0.621240580541804, -2.2146998871775, 1.12493091814311, -0.0449336090152309, -0.0161902630989461, 0.943836210685299, 0.821221195098089, 0.593901321217509, 0.918977371608218, 0.782136300731067, 0.0745649833651906, -1.98935169586337, 0.61982574789471, -0.0561287395290008, -0.155795506705329, -1.47075238389927, -0.47815005510862, 0.417941560199702, 1.35867955152904, -0.102787727342996, 0.387671611559369, -0.0538050405829051, -1.37705955682861, -0.41499456329968, -0.394289953710349, -0.0593133967111857, 1.10002537198388, 0.763175748457544, -0.164523596253587, -0.253361680136508, 0.696963375404737, 0.556663198673657, -0.68875569454952, -0.70749515696212, 0.36458196213683, 0.768532924515416, -0.112346212150228, 0.881107726454215), group = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), subject = c(1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L, 25L, 25L)), X = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), reTrms = list(Zt = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L), p = 0:50, Dim = c(25L, 50L), Dimnames = list( c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25"), c("sample1", "sample2", "sample3", "sample4", "sample5", "sample6", "sample7", "sample8", "sample9", "sample10", "sample11", "sample12", "sample13", "sample14", "sample15", "sample16", "sample17", "sample18", "sample19", "sample20", "sample21", "sample22", "sample23", "sample24", "sample25", "sample26", "sample27", "sample28", "sample29", "sample30", "sample31", "sample32", "sample33", "sample34", "sample35", "sample36", "sample37", "sample38", "sample39", "sample40", "sample41", "sample42", "sample43", "sample44", "sample45", "sample46", "sample47", "sample48", "sample49", "sample50")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), theta = 1, Lind = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L ), Gp = c(0L, 25L), lower = 0, Lambdat = new("dgCMatrix", i = 0:24, p = 0:25, Dim = c(25L, 25L), Dimnames = list( NULL, NULL), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list()), flist = list(subject = c(1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L, 25L, 25L)), cnms = list(subject = "(Intercept)"), Ztlist = list(`1 | subject` = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L), p = 0:50, Dim = c(25L, 50L), Dimnames = list(c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25"), c("sample1", "sample2", "sample3", "sample4", "sample5", "sample6", "sample7", "sample8", "sample9", "sample10", "sample11", "sample12", "sample13", "sample14", "sample15", "sample16", "sample17", "sample18", "sample19", "sample20", "sample21", "sample22", "sample23", "sample24", "sample25", "sample26", "sample27", "sample28", "sample29", "sample30", "sample31", "sample32", "sample33", "sample34", "sample35", "sample36", "sample37", "sample38", "sample39", "sample40", "sample41", "sample42", "sample43", "sample44", "sample45", "sample46", "sample47", "sample48", "sample49", "sample50")), x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list())), nl = c(subject = 25L)), REML = TRUE, wmsgs = character(0), start = NULL, verbose = 0L, control = list(optimizer = "nloptwrap", restart_edge = TRUE, boundary.tol = 1e-05, calc.derivs = TRUE, use.last.params = FALSE, checkControl = list(check.nobs.vs.rankZ = "ignore", check.nobs.vs.nlev = "stop", check.nlev.gtreq.5 = "ignore", check.nlev.gtr.1 = "stop", check.nobs.vs.nRE = "stop", check.rankX = "message+drop.cols", check.scaleX = "warning", check.formula.LHS = "stop"), checkConv = list(check.conv.grad = list(action = "warning", tol = 0.002, relTol = NULL), check.conv.singular = list( action = "message", tol = 1e-04), check.conv.hess = list( action = "warning", tol = 1e-06)), optCtrl = list())) 10: do.call(mkLmerDevfun, c(lmod, list(start = start, verbose = verbose, control = control))) 11: lme4::lmer(formula = feat1 ~ group + (1 | subject), data = list( sample_id = c("sample1", "sample2", "sample3", "sample4", "sample5", "sample6", "sample7", "sample8", "sample9", "sample10", "sample11", "sample12", "sample13", "sample14", "sample15", "sample16", "sample17", "sample18", "sample19", "sample20", "sample21", "sample22", "sample23", "sample24", "sample25", "sample26", "sample27", "sample28", "sample29", "sample30", "sample31", "sample32", "sample33", "sample34", "sample35", "sample36", "sample37", "sample38", "sample39", "sample40", "sample41", "sample42", "sample43", "sample44", "sample45", "sample46", "sample47", "sample48", "sample49", "sample50" ), group = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), subject = c(1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L, 25L, 25L), feat1 = c(-0.626453810742332, 0.183643324222082, -0.835628612410047, 1.59528080213779, 0.329507771815361, -0.820468384118015, 0.487429052428485, 0.738324705129217, 0.575781351653492, -0.305388387156356, 1.51178116845085, 0.389843236411431, -0.621240580541804, -2.2146998871775, 1.12493091814311, -0.0449336090152309, -0.0161902630989461, 0.943836210685299, 0.821221195098089, 0.593901321217509, 0.918977371608218, 0.782136300731067, 0.0745649833651906, -1.98935169586337, 0.61982574789471, -0.0561287395290008, -0.155795506705329, -1.47075238389927, -0.47815005510862, 0.417941560199702, 1.35867955152904, -0.102787727342996, 0.387671611559369, -0.0538050405829051, -1.37705955682861, -0.41499456329968, -0.394289953710349, -0.0593133967111857, 1.10002537198388, 0.763175748457544, -0.164523596253587, -0.253361680136508, 0.696963375404737, 0.556663198673657, -0.68875569454952, -0.70749515696212, 0.36458196213683, 0.768532924515416, -0.112346212150228, 0.881107726454215))) 12: eval(expr, p) 13: eval(expr, p) 14: eval.parent(mc) 15: (function (formula, data = NULL, REML = TRUE, control = lmerControl(), start = NULL, verbose = 0L, subset, weights, na.action, offset, contrasts = NULL, devFunOnly = FALSE) { orig_call <- mc <- match.call() mc[[1L]] <- quote(lme4::lmer) model <- eval.parent(mc) if (devFunOnly) return(model) args <- as.list(mc) args$devFunOnly <- TRUE if (!"control" %in% names(as.list(mc))) args$control <- lme4::lmerControl(check.rankX = "silent.drop.cols") Call <- as.call(c(list(quote(lme4::lmer)), args[-1])) devfun <- eval.parent(Call) res <- as_lmerModLT(model, devfun) res@call <- orig_call return(res)})(formula = feat1 ~ group + (1 | subject), data = list(sample_id = c("sample1", "sample2", "sample3", "sample4", "sample5", "sample6", "sample7", "sample8", "sample9", "sample10", "sample11", "sample12", "sample13", "sample14", "sample15", "sample16", "sample17", "sample18", "sample19", "sample20", "sample21", "sample22", "sample23", "sample24", "sample25", "sample26", "sample27", "sample28", "sample29", "sample30", "sample31", "sample32", "sample33", "sample34", "sample35", "sample36", "sample37", "sample38", "sample39", "sample40", "sample41", "sample42", "sample43", "sample44", "sample45", "sample46", "sample47", "sample48", "sample49", "sample50"), group = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), subject = c(1L, 1L, 2L, 2L, 3L, 3L, 4L, 4L, 5L, 5L, 6L, 6L, 7L, 7L, 8L, 8L, 9L, 9L, 10L, 10L, 11L, 11L, 12L, 12L, 13L, 13L, 14L, 14L, 15L, 15L, 16L, 16L, 17L, 17L, 18L, 18L, 19L, 19L, 20L, 20L, 21L, 21L, 22L, 22L, 23L, 23L, 24L, 24L, 25L, 25L), feat1 = c(-0.626453810742332, 0.183643324222082, -0.835628612410047, 1.59528080213779, 0.329507771815361, -0.820468384118015, 0.487429052428485, 0.738324705129217, 0.575781351653492, -0.305388387156356, 1.51178116845085, 0.389843236411431, -0.621240580541804, -2.2146998871775, 1.12493091814311, -0.0449336090152309, -0.0161902630989461, 0.943836210685299, 0.821221195098089, 0.593901321217509, 0.918977371608218, 0.782136300731067, 0.0745649833651906, -1.98935169586337, 0.61982574789471, -0.0561287395290008, -0.155795506705329, -1.47075238389927, -0.47815005510862, 0.417941560199702, 1.35867955152904, -0.102787727342996, 0.387671611559369, -0.0538050405829051, -1.37705955682861, -0.41499456329968, -0.394289953710349, -0.0593133967111857, 1.10002537198388, 0.763175748457544, -0.164523596253587, -0.253361680136508, 0.696963375404737, 0.556663198673657, -0.68875569454952, -0.70749515696212, 0.36458196213683, 0.768532924515416, -0.112346212150228, 0.881107726454215))) 16: do.call(fit_model, model_args_temp) 17: doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, classes, parentenv, handlers) 20: tryCatch({ data_temp <- cbind(sdata_matched, X_matched[, i, drop = FALSE]) y_temp <- colnames(X_matched)[i] formula_temp <- stats::update(formula_rhs, paste(y_temp, "~ .")) model_args_temp <- utils::modifyList(model_control, list(formula = formula_temp, data = data_temp)) model_temp <- do.call(fit_model, model_args_temp) coeff_temp <- summary(model_temp)$coefficients confint_temp <- if (inherits(model_temp, "lm")) { stats::confint(model_temp) } else { lme4::confint.merMod(model_temp, parm = "beta_") } fit_df <- data.frame(Coefficient = rownames(coeff_temp), coeff_temp, confint_temp, feat_id = y_temp, check.names = FALSE, row.names = NULL) ranef_varcor <- if (inherits(model_temp, "lm")) { NULL } else { df <- as.data.frame(lme4::VarCorr(model_temp)) df$feat_id <- y_temp df } lrt_result <- if (is.null(term_LRT)) { NULL } else { lrt_temp <- lapply(term_LRT, function(z) { if (grepl("\\|", z)) { term_temp <- paste0("(", z, ")") } else { term_temp <- z } formula_null <- stats::update(formula_temp, paste(". ~ . -", term_temp)) model_args_null <- utils::modifyList(model_args_temp, list(formula = formula_null)) rand_eff_null <- lme4::findbars(formula_null) has_ranef_null <- length(rand_eff_null) > 0 fit_model_null <- if (has_ranef_null) lmerTest::lmer else stats::lm model_null <- do.call(fit_model_null, model_args_null) lrt_stats <- if (inherits(model_null, "lm") && inherits(model_temp, "lmerModLmerTest")) { stats::anova(model_temp, model_null) } else { stats::anova(model_null, model_temp) } lrt_stats$term <- z lrt_stats }) df <- do.call(rbind, lrt_temp) df$feat_id <- y_temp df } list(fit = fit_df, ranef = ranef_varcor, lrt = lrt_result, error = NULL)}, error = function(e) { warning(paste("Model failed for feature", i, ":", e$message)) list(fit = NULL, ranef = NULL, lrt = NULL, error = data.frame(feat_id = colnames(X_matched)[i], error = e$message))}) 21: ...future.FUN(...future.X_jj, ...) 22: FUN(X[[i]], ...) 23: lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...)}) 24: (function (...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) }})() 25: do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) }}, args = future.call.arguments) 26: eval(quote({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments)}), new.env()) 27: eval(quote({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments)}), new.env()) 28: eval(expr, p) 29: eval(expr, p) 30: eval.parent(substitute(eval(quote(expr), envir))) 31: base::local({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments)}) 32: base::withVisible(base::local({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments)})) 33: base::withCallingHandlers({ ...future.value <- base::withVisible(base::local({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments) })) future::FutureResult(value = ...future.value$value, visible = ...future.value$visible, rng = !identical(base::globalenv()$.Random.seed, ...future.rng), globalenv = if (FALSE) list(added = base::setdiff(base::names(base::.GlobalEnv), ...future.globalenv.names)) else NULL, started = ...future.startTime, version = "1.8")}, condition = base::local({ c <- base::c inherits <- base::inherits invokeRestart <- base::invokeRestart length <- base::length list <- base::list seq.int <- base::seq.int signalCondition <- base::signalCondition sys.calls <- base::sys.calls `[[` <- base::`[[` `+` <- base::`+` `<<-` <- base::`<<-` sysCalls <- function(calls = sys.calls(), from = 1L) { calls[seq.int(from = from + 12L, to = length(calls) - 3L)] } function(cond) { is_error <- inherits(cond, "error") ignore <- !is_error && !is.null(NULL) && inherits(cond, NULL) if (is_error) { sessionInformation <- function() { list(r = base::R.Version(), locale = base::Sys.getlocale(), rngkind = base::RNGkind(), namespaces = base::loadedNamespaces(), search = base::search(), system = base::Sys.info()) } ...future.conditions[[length(...future.conditions) + 1L]] <<- list(condition = cond, calls = c(sysCalls(from = ...future.frame), cond$call), session = sessionInformation(), timestamp = base::Sys.time(), signaled = 0L) signalCondition(cond) } else if (!ignore && TRUE && inherits(cond, c("condition", "immediateCondition"))) { signal <- TRUE && inherits(cond, "immediateCondition") ...future.conditions[[length(...future.conditions) + 1L]] <<- list(condition = cond, signaled = base::as.integer(signal)) if (TRUE && !signal) { muffleCondition <- function (cond, pattern = "^muffle") { inherits <- base::inherits invokeRestart <- base::invokeRestart is.null <- base::is.null muffled <- FALSE if (inherits(cond, "message")) { muffled <- grepl(pattern, "muffleMessage") if (muffled) invokeRestart("muffleMessage") } else if (inherits(cond, "warning")) { muffled <- grepl(pattern, "muffleWarning") if (muffled) invokeRestart("muffleWarning") } else if (inherits(cond, "condition")) { if (!is.null(pattern)) { computeRestarts <- base::computeRestarts grepl <- base::grepl restarts <- computeRestarts(cond) for (restart in restarts) { name <- restart$name if (is.null(name)) next if (!grepl(pattern, name)) next invokeRestart(restart) muffled <- TRUE break } } } invisible(muffled) } muffleCondition(cond, pattern = "^muffle") } } else { if (TRUE) { muffleCondition <- function (cond, pattern = "^muffle") { inherits <- base::inherits invokeRestart <- base::invokeRestart is.null <- base::is.null muffled <- FALSE if (inherits(cond, "message")) { muffled <- grepl(pattern, "muffleMessage") if (muffled) invokeRestart("muffleMessage") } else if (inherits(cond, "warning")) { muffled <- grepl(pattern, "muffleWarning") if (muffled) invokeRestart("muffleWarning") } else if (inherits(cond, "condition")) { if (!is.null(pattern)) { computeRestarts <- base::computeRestarts grepl <- base::grepl restarts <- computeRestarts(cond) for (restart in restarts) { name <- restart$name if (is.null(name)) next if (!grepl(pattern, name)) next invokeRestart(restart) muffled <- TRUE break } } } invisible(muffled) } muffleCondition(cond, pattern = "^muffle") } } }})) 34: doTryCatch(return(expr), name, parentenv, handler) 35: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 36: tryCatchList(expr, classes, parentenv, handlers) 37: base::tryCatch({ base::withCallingHandlers({ ...future.value <- base::withVisible(base::local({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments) })) future::FutureResult(value = ...future.value$value, visible = ...future.value$visible, rng = !identical(base::globalenv()$.Random.seed, ...future.rng), globalenv = if (FALSE) list(added = base::setdiff(base::names(base::.GlobalEnv), ...future.globalenv.names)) else NULL, started = ...future.startTime, version = "1.8") }, condition = base::local({ c <- base::c inherits <- base::inherits invokeRestart <- base::invokeRestart length <- base::length list <- base::list seq.int <- base::seq.int signalCondition <- base::signalCondition sys.calls <- base::sys.calls `[[` <- base::`[[` `+` <- base::`+` `<<-` <- base::`<<-` sysCalls <- function(calls = sys.calls(), from = 1L) { calls[seq.int(from = from + 12L, to = length(calls) - 3L)] } function(cond) { is_error <- inherits(cond, "error") ignore <- !is_error && !is.null(NULL) && inherits(cond, NULL) if (is_error) { sessionInformation <- function() { list(r = base::R.Version(), locale = base::Sys.getlocale(), rngkind = base::RNGkind(), namespaces = base::loadedNamespaces(), search = base::search(), system = base::Sys.info()) } ...future.conditions[[length(...future.conditions) + 1L]] <<- list(condition = cond, calls = c(sysCalls(from = ...future.frame), cond$call), session = sessionInformation(), timestamp = base::Sys.time(), signaled = 0L) signalCondition(cond) } else if (!ignore && TRUE && inherits(cond, c("condition", "immediateCondition"))) { signal <- TRUE && inherits(cond, "immediateCondition") ...future.conditions[[length(...future.conditions) + 1L]] <<- list(condition = cond, signaled = base::as.integer(signal)) if (TRUE && !signal) { muffleCondition <- function (cond, pattern = "^muffle") { inherits <- base::inherits invokeRestart <- base::invokeRestart is.null <- base::is.null muffled <- FALSE if (inherits(cond, "message")) { muffled <- grepl(pattern, "muffleMessage") if (muffled) invokeRestart("muffleMessage") } else if (inherits(cond, "warning")) { muffled <- grepl(pattern, "muffleWarning") if (muffled) invokeRestart("muffleWarning") } else if (inherits(cond, "condition")) { if (!is.null(pattern)) { computeRestarts <- base::computeRestarts grepl <- base::grepl restarts <- computeRestarts(cond) for (restart in restarts) { name <- restart$name if (is.null(name)) next if (!grepl(pattern, name)) next invokeRestart(restart) muffled <- TRUE break } } } invisible(muffled) } muffleCondition(cond, pattern = "^muffle") } } else { if (TRUE) { muffleCondition <- function (cond, pattern = "^muffle") { inherits <- base::inherits invokeRestart <- base::invokeRestart is.null <- base::is.null muffled <- FALSE if (inherits(cond, "message")) { muffled <- grepl(pattern, "muffleMessage") if (muffled) invokeRestart("muffleMessage") } else if (inherits(cond, "warning")) { muffled <- grepl(pattern, "muffleWarning") if (muffled) invokeRestart("muffleWarning") } else if (inherits(cond, "condition")) { if (!is.null(pattern)) { computeRestarts <- base::computeRestarts grepl <- base::grepl restarts <- computeRestarts(cond) for (restart in restarts) { name <- restart$name if (is.null(name)) next if (!grepl(pattern, name)) next invokeRestart(restart) muffled <- TRUE break } } } invisible(muffled) } muffleCondition(cond, pattern = "^muffle") } } } }))}, error = function(ex) { base::structure(base::list(value = NULL, visible = NULL, conditions = ...future.conditions, rng = !identical(base::globalenv()$.Random.seed, ...future.rng), started = ...future.startTime, finished = Sys.time(), session_uuid = NA_character_, version = "1.8"), class = "FutureResult")}, finally = { if (!identical(...future.workdir, getwd())) setwd(...future.workdir) { if (identical(getOption("nwarnings"), ...future.oldOptions$nwarnings)) { ...future.oldOptions$nwarnings <- NULL } base::options(...future.oldOptions) if (.Platform$OS.type == "windows") { old_names <- names(...future.oldEnvVars) envs <- base::Sys.getenv() names <- names(envs) common <- intersect(names, old_names) added <- setdiff(names, old_names) removed <- setdiff(old_names, names) changed <- common[...future.oldEnvVars[common] != envs[common]] NAMES <- toupper(changed) args <- list() for (kk in seq_along(NAMES)) { name <- changed[[kk]] NAME <- NAMES[[kk]] if (name != NAME && is.element(NAME, old_names)) next args[[name]] <- ...future.oldEnvVars[[name]] } NAMES <- toupper(added) for (kk in seq_along(NAMES)) { name <- added[[kk]] NAME <- NAMES[[kk]] if (name != NAME && is.element(NAME, old_names)) next args[[name]] <- "" } NAMES <- toupper(removed) for (kk in seq_along(NAMES)) { name <- removed[[kk]] NAME <- NAMES[[kk]] if (name != NAME && is.element(NAME, old_names)) next args[[name]] <- ...future.oldEnvVars[[name]] } if (length(args) > 0) base::do.call(base::Sys.setenv, args = args) args <- names <- old_names <- NAMES <- envs <- common <- added <- removed <- NULL } else { base::do.call(base::Sys.setenv, args = base::as.list(...future.oldEnvVars)) } { if (base::length(...future.futureOptionsAdded) > 0L) { opts <- base::vector("list", length = base::length(...future.futureOptionsAdded)) base::names(opts) <- ...future.futureOptionsAdded base::options(opts) } { { base::assign(".Random.seed", c(10403L, 378L, 1980538363L, -125047968L, -820381145L, -1073960099L, -33499050L, 1164085917L, 1218464490L, -1045685882L, -1933699935L, 795942478L, 495210185L, 1943097543L, -229514104L, -1232480817L, 352489432L, 351006324L, -867325393L, -1442019852L, 629147155L, 966152721L, 1616591578L, 200016369L, 1339052126L, -225299422L, -1512315715L, 103118938L, 1508496509L, 226325507L, 1531586180L, 1851232347L, -180012444L, 1939719752L, 1161394291L, 1375986488L, -1867206193L, -269449371L, 1080036398L, 1121658053L, 1200423730L, -1114719938L, 1019413465L, 699098406L, -2049351935L, -216610673L, 1752238736L, -1881625753L, 1183034576L, 289280140L, -1743926729L, -243822724L, -1713104501L, 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1981426537L, 176783780L, 523648218L, -589977567L, 1914642721L, -1871760254L, -1586947104L, -346442695L, 703798945L, 732710968L, -165412766L, 1888428821L, 1893337521L, -743130742L, -1050505356L, 471691885L, -1581648751L, 1125688788L, 2098523018L, 358039561L, -1567651463L, 597627866L, 1346302752L, -160376471L, 1063411465L, -623243680L, 897524434L, 995310533L, -1124453319L, -1103252830L, -1708500724L, -983918331L, 324701481L, -1224973676L, -1261295304L, -2057610510L ), envir = base::globalenv(), inherits = FALSE) NULL } options(future.plan = NULL) if (is.na(NA_character_)) Sys.unsetenv("R_FUTURE_PLAN") else Sys.setenv(R_FUTURE_PLAN = NA_character_) future::plan(...future.strategy.old, .cleanup = FALSE, .init = FALSE) } } }}) 38: eval(expr, envir = envir, enclos = baseenv()) 39: eval(expr, envir = envir, enclos = baseenv()) 40: run.UniprocessFuture(future) 41: run(future) 42: run.Future(future) 43: run(future) 44: future(expr, substitute = FALSE, envir = future.envir, stdout = future.stdout, conditions = future.conditions, globals = globals_ii, packages = packages_ii, seed = future.seed, label = labels[ii]) 45: future_xapply(FUN = FUN, nX = nX, chunk_args = X, args = list(...), get_chunk = `chunkWith[[`, expr = expr, envir = envir, future.envir = future.envir, future.globals = future.globals, future.packages = future.packages, future.scheduling = future.scheduling, future.chunk.size = future.chunk.size, future.stdout = future.stdout, future.conditions = future.conditions, future.seed = future.seed, future.label = future.label, fcn_name = fcn_name, args_name = args_name, debug = debug) 46: future.apply::future_lapply(seq_len(feat_num), function(i) { if (report(i)) p(sprintf("Processed %d of %d", i, feat_num)) tryCatch({ data_temp <- cbind(sdata_matched, X_matched[, i, drop = FALSE]) y_temp <- colnames(X_matched)[i] formula_temp <- stats::update(formula_rhs, paste(y_temp, "~ .")) model_args_temp <- utils::modifyList(model_control, list(formula = formula_temp, data = data_temp)) model_temp <- do.call(fit_model, model_args_temp) coeff_temp <- summary(model_temp)$coefficients confint_temp <- if (inherits(model_temp, "lm")) { stats::confint(model_temp) } else { lme4::confint.merMod(model_temp, parm = "beta_") } fit_df <- data.frame(Coefficient = rownames(coeff_temp), coeff_temp, confint_temp, feat_id = y_temp, check.names = FALSE, row.names = NULL) ranef_varcor <- if (inherits(model_temp, "lm")) { NULL } else { df <- as.data.frame(lme4::VarCorr(model_temp)) df$feat_id <- y_temp df } lrt_result <- if (is.null(term_LRT)) { NULL } else { lrt_temp <- lapply(term_LRT, function(z) { if (grepl("\\|", z)) { term_temp <- paste0("(", z, ")") } else { term_temp <- z } formula_null <- stats::update(formula_temp, paste(". ~ . -", term_temp)) model_args_null <- utils::modifyList(model_args_temp, list(formula = formula_null)) rand_eff_null <- lme4::findbars(formula_null) has_ranef_null <- length(rand_eff_null) > 0 fit_model_null <- if (has_ranef_null) lmerTest::lmer else stats::lm model_null <- do.call(fit_model_null, model_args_null) lrt_stats <- if (inherits(model_null, "lm") && inherits(model_temp, "lmerModLmerTest")) { stats::anova(model_temp, model_null) } else { stats::anova(model_null, model_temp) } lrt_stats$term <- z lrt_stats }) df <- do.call(rbind, lrt_temp) df$feat_id <- y_temp df } list(fit = fit_df, ranef = ranef_varcor, lrt = lrt_result, error = NULL) }, error = function(e) { warning(paste("Model failed for feature", i, ":", e$message)) list(fit = NULL, ranef = NULL, lrt = NULL, error = data.frame(feat_id = colnames(X_matched)[i], error = e$message)) })}, future.seed = TRUE) 47: dana(X = mock_X, sample_data = sample_data, formula_rhs = ~group + (1 | subject), term_LRT = c("group", "1 | subject"), platform = "ms", assay = "lipidomics", verbose = FALSE) An irrecoverable exception occurred. R is aborting now ... Examples with CPU (user + system) or elapsed time > 5s user system elapsed build_phyloseq 8.074 0.393 8.65 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R'/home/th798/R/R-release/bin/BATCH: line 60: 1130916 Segmentation fault (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 ERROR Running the tests in 'tests/testthat.R' failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(readyomics) > > test_check("readyomics") Error in smooth.spline(lambda, pi0, df = smooth.df) : missing or infinite values in inputs are not allowed 2 samples found in common between 2 rows in 'X' and 2 rows in 'sample_data'. *** caught segfault *** address (nil), cause 'unknown' Traceback: 1: .Call(merPredDCreate, as(X, "matrix"), Lambdat, LamtUt, Lind, RZX, Ut, Utr, V, VtV, Vtr, Xwts, Zt, beta0, delb, delu, theta, u0) 2: initializePtr() 3: .Object$initialize(...) 4: initialize(value, ...) 5: initialize(value, ...) 6: methods::new(def, ...) 7: (new("refMethodDef", .Data = function (...) { methods::new(def, ...)}, mayCall = c("methods", "new"), name = "new", refClassName = "refGeneratorSlot", superClassMethod = ""))(Zt = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L), p = 0:5, Dim = c(3L, 5L), Dimnames = list(c("1", "2", "3"), c("id1", "id2", "id3", "id4", "id5")), x = c(1, 1, 1, 1, 1), factors = list()), theta = 1, Lambdat = new("dgCMatrix", i = 0:2, p = 0:3, Dim = c(3L, 3L), Dimnames = list(NULL, NULL), x = c(1, 1, 1), factors = list()), Lind = c(1L, 1L, 1L), n = 5L, X = c(1, 1, 1, 1, 1, 0, 0, 1, 1, 1)) 8: do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")], n = nrow(X), list(X = X))) 9: (function (fr, X, reTrms, REML = TRUE, start = NULL, verbose = 0, control = lmerControl(), ...) { p <- ncol(X) rho <- new.env(parent = parent.env(environment())) rho$pp <- do.call(merPredD$new, c(reTrms[c("Zt", "theta", "Lambdat", "Lind")], n = nrow(X), list(X = X))) REMLpass <- if (REML) p else 0L rho$resp <- if (missing(fr)) mkRespMod(REML = REMLpass, ...) else mkRespMod(fr, REML = REMLpass) pp <- resp <- NULL rho$lmer_Deviance <- lmer_Deviance devfun <- function(theta) .Call(lmer_Deviance, pp$ptr(), resp$ptr(), as.double(theta)) environment(devfun) <- rho if (is.null(start) && all(reTrms$cnms == "(Intercept)") && length(reTrms$flist) == length(reTrms$lower) && !is.null(y <- model.response(fr))) { v <- sapply(reTrms$flist, function(f) var(ave(y, f))) v.e <- var(y) - sum(v) if (!is.na(v.e) && v.e > 0) { v.rel <- v/v.e if (all(v.rel >= reTrms$lower^2)) rho$pp$setTheta(sqrt(v.rel)) } } if (length(rho$resp$y) > 0) devfun(rho$pp$theta) rho$lower <- reTrms$lower devfun})(fr = list(feat1 = c(-0.217974914658295, -1.02600444830724, -0.72889122929114, -0.625039267849257, -1.68669331074241), group = c(1L, 1L, 2L, 2L, 2L), subject = c(1L, 1L, 2L, 2L, 3L)), X = c(1, 1, 1, 1, 1, 0, 0, 1, 1, 1), reTrms = list(Zt = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L), p = 0:5, Dim = c(3L, 5L), Dimnames = list( c("1", "2", "3"), c("id1", "id2", "id3", "id4", "id5" )), x = c(1, 1, 1, 1, 1), factors = list()), theta = 1, Lind = c(1L, 1L, 1L), Gp = c(0L, 3L), lower = 0, Lambdat = new("dgCMatrix", i = 0:2, p = 0:3, Dim = c(3L, 3L), Dimnames = list(NULL, NULL), x = c(1, 1, 1), factors = list()), flist = list( subject = c(1L, 1L, 2L, 2L, 3L)), cnms = list(subject = "(Intercept)"), Ztlist = list(`1 | subject` = new("dgCMatrix", i = c(0L, 0L, 1L, 1L, 2L), p = 0:5, Dim = c(3L, 5L), Dimnames = list( c("1", "2", "3"), c("id1", "id2", "id3", "id4", "id5" )), x = c(1, 1, 1, 1, 1), factors = list())), nl = c(subject = 3L)), REML = TRUE, wmsgs = character(0), start = NULL, verbose = 0L, control = list(optimizer = "nloptwrap", restart_edge = TRUE, boundary.tol = 1e-05, calc.derivs = TRUE, use.last.params = FALSE, checkControl = list(check.nobs.vs.rankZ = "ignore", check.nobs.vs.nlev = "stop", check.nlev.gtreq.5 = "ignore", check.nlev.gtr.1 = "stop", check.nobs.vs.nRE = "stop", check.rankX = "message+drop.cols", check.scaleX = "warning", check.formula.LHS = "stop"), checkConv = list(check.conv.grad = list(action = "warning", tol = 0.002, relTol = NULL), check.conv.singular = list( action = "message", tol = 1e-04), check.conv.hess = list( action = "warning", tol = 1e-06)), optCtrl = list())) 10: do.call(mkLmerDevfun, c(lmod, list(start = start, verbose = verbose, control = control))) 11: lme4::lmer(formula = feat1 ~ group + (1 | subject), data = list( sample_id = c("id1", "id2", "id3", "id4", "id5"), group = c(1L, 1L, 2L, 2L, 2L), subject = c(1L, 1L, 2L, 2L, 3L), feat1 = c(-0.217974914658295, -1.02600444830724, -0.72889122929114, -0.625039267849257, -1.68669331074241))) 12: eval(expr, p) 13: eval(expr, p) 14: eval.parent(mc) 15: (function (formula, data = NULL, REML = TRUE, control = lmerControl(), start = NULL, verbose = 0L, subset, weights, na.action, offset, contrasts = NULL, devFunOnly = FALSE) { orig_call <- mc <- match.call() mc[[1L]] <- quote(lme4::lmer) model <- eval.parent(mc) if (devFunOnly) return(model) args <- as.list(mc) args$devFunOnly <- TRUE if (!"control" %in% names(as.list(mc))) args$control <- lme4::lmerControl(check.rankX = "silent.drop.cols") Call <- as.call(c(list(quote(lme4::lmer)), args[-1])) devfun <- eval.parent(Call) res <- as_lmerModLT(model, devfun) res@call <- orig_call return(res)})(formula = feat1 ~ group + (1 | subject), data = list(sample_id = c("id1", "id2", "id3", "id4", "id5"), group = c(1L, 1L, 2L, 2L, 2L), subject = c(1L, 1L, 2L, 2L, 3L), feat1 = c(-0.217974914658295, -1.02600444830724, -0.72889122929114, -0.625039267849257, -1.68669331074241))) 16: do.call(fit_model, model_args_temp) 17: doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, classes, parentenv, handlers) 20: tryCatch({ data_temp <- cbind(sdata_matched, X_matched[, i, drop = FALSE]) y_temp <- colnames(X_matched)[i] formula_temp <- stats::update(formula_rhs, paste(y_temp, "~ .")) model_args_temp <- utils::modifyList(model_control, list(formula = formula_temp, data = data_temp)) model_temp <- do.call(fit_model, model_args_temp) coeff_temp <- summary(model_temp)$coefficients confint_temp <- if (inherits(model_temp, "lm")) { stats::confint(model_temp) } else { lme4::confint.merMod(model_temp, parm = "beta_") } fit_df <- data.frame(Coefficient = rownames(coeff_temp), coeff_temp, confint_temp, feat_id = y_temp, check.names = FALSE, row.names = NULL) ranef_varcor <- if (inherits(model_temp, "lm")) { NULL } else { df <- as.data.frame(lme4::VarCorr(model_temp)) df$feat_id <- y_temp df } lrt_result <- if (is.null(term_LRT)) { NULL } else { lrt_temp <- lapply(term_LRT, function(z) { if (grepl("\\|", z)) { term_temp <- paste0("(", z, ")") } else { term_temp <- z } formula_null <- stats::update(formula_temp, paste(". ~ . -", term_temp)) model_args_null <- utils::modifyList(model_args_temp, list(formula = formula_null)) rand_eff_null <- lme4::findbars(formula_null) has_ranef_null <- length(rand_eff_null) > 0 fit_model_null <- if (has_ranef_null) lmerTest::lmer else stats::lm model_null <- do.call(fit_model_null, model_args_null) lrt_stats <- if (inherits(model_null, "lm") && inherits(model_temp, "lmerModLmerTest")) { stats::anova(model_temp, model_null) } else { stats::anova(model_null, model_temp) } lrt_stats$term <- z lrt_stats }) df <- do.call(rbind, lrt_temp) df$feat_id <- y_temp df } list(fit = fit_df, ranef = ranef_varcor, lrt = lrt_result, error = NULL)}, error = function(e) { warning(paste("Model failed for feature", i, ":", e$message)) list(fit = NULL, ranef = NULL, lrt = NULL, error = data.frame(feat_id = colnames(X_matched)[i], error = e$message))}) 21: ...future.FUN(...future.X_jj, ...) 22: FUN(X[[i]], ...) 23: lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...)}) 24: (function (...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) }})() 25: do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) }}, args = future.call.arguments) 26: eval(quote({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments)}), new.env()) 27: eval(quote({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments)}), new.env()) 28: eval(expr, p) 29: eval(expr, p) 30: eval.parent(substitute(eval(quote(expr), envir))) 31: base::local({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments)}) 32: base::withVisible(base::local({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments)})) 33: base::withCallingHandlers({ ...future.value <- base::withVisible(base::local({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments) })) future::FutureResult(value = ...future.value$value, visible = ...future.value$visible, rng = !identical(base::globalenv()$.Random.seed, ...future.rng), globalenv = if (FALSE) list(added = base::setdiff(base::names(base::.GlobalEnv), ...future.globalenv.names)) else NULL, started = ...future.startTime, version = "1.8")}, condition = base::local({ c <- base::c inherits <- base::inherits invokeRestart <- base::invokeRestart length <- base::length list <- base::list seq.int <- base::seq.int signalCondition <- base::signalCondition sys.calls <- base::sys.calls `[[` <- base::`[[` `+` <- base::`+` `<<-` <- base::`<<-` sysCalls <- function(calls = sys.calls(), from = 1L) { calls[seq.int(from = from + 12L, to = length(calls) - 3L)] } function(cond) { is_error <- inherits(cond, "error") ignore <- !is_error && !is.null(NULL) && inherits(cond, NULL) if (is_error) { sessionInformation <- function() { list(r = base::R.Version(), locale = base::Sys.getlocale(), rngkind = base::RNGkind(), namespaces = base::loadedNamespaces(), search = base::search(), system = base::Sys.info()) } ...future.conditions[[length(...future.conditions) + 1L]] <<- list(condition = cond, calls = c(sysCalls(from = ...future.frame), cond$call), session = sessionInformation(), timestamp = base::Sys.time(), signaled = 0L) signalCondition(cond) } else if (!ignore && TRUE && inherits(cond, c("condition", "immediateCondition"))) { signal <- TRUE && inherits(cond, "immediateCondition") ...future.conditions[[length(...future.conditions) + 1L]] <<- list(condition = cond, signaled = base::as.integer(signal)) if (TRUE && !signal) { muffleCondition <- function (cond, pattern = "^muffle") { inherits <- base::inherits invokeRestart <- base::invokeRestart is.null <- base::is.null muffled <- FALSE if (inherits(cond, "message")) { muffled <- grepl(pattern, "muffleMessage") if (muffled) invokeRestart("muffleMessage") } else if (inherits(cond, "warning")) { muffled <- grepl(pattern, "muffleWarning") if (muffled) invokeRestart("muffleWarning") } else if (inherits(cond, "condition")) { if (!is.null(pattern)) { computeRestarts <- base::computeRestarts grepl <- base::grepl restarts <- computeRestarts(cond) for (restart in restarts) { name <- restart$name if (is.null(name)) next if (!grepl(pattern, name)) next invokeRestart(restart) muffled <- TRUE break } } } invisible(muffled) } muffleCondition(cond, pattern = "^muffle") } } else { if (TRUE) { muffleCondition <- function (cond, pattern = "^muffle") { inherits <- base::inherits invokeRestart <- base::invokeRestart is.null <- base::is.null muffled <- FALSE if (inherits(cond, "message")) { muffled <- grepl(pattern, "muffleMessage") if (muffled) invokeRestart("muffleMessage") } else if (inherits(cond, "warning")) { muffled <- grepl(pattern, "muffleWarning") if (muffled) invokeRestart("muffleWarning") } else if (inherits(cond, "condition")) { if (!is.null(pattern)) { computeRestarts <- base::computeRestarts grepl <- base::grepl restarts <- computeRestarts(cond) for (restart in restarts) { name <- restart$name if (is.null(name)) next if (!grepl(pattern, name)) next invokeRestart(restart) muffled <- TRUE break } } } invisible(muffled) } muffleCondition(cond, pattern = "^muffle") } } }})) 34: doTryCatch(return(expr), name, parentenv, handler) 35: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 36: tryCatchList(expr, classes, parentenv, handlers) 37: base::tryCatch({ base::withCallingHandlers({ ...future.value <- base::withVisible(base::local({ do.call(function(...) { ...future.globals.maxSize.org <- getOption("future.globals.maxSize") if (!identical(...future.globals.maxSize.org, ...future.globals.maxSize)) { oopts <- options(future.globals.maxSize = ...future.globals.maxSize) on.exit(options(oopts), add = TRUE) } { lapply(seq_along(...future.elements_ii), FUN = function(jj) { ...future.X_jj <- ...future.elements_ii[[jj]] assign(".Random.seed", ...future.seeds_ii[[jj]], envir = globalenv(), inherits = FALSE) ...future.FUN(...future.X_jj, ...) }) } }, args = future.call.arguments) })) future::FutureResult(value = ...future.value$value, visible = ...future.value$visible, rng = !identical(base::globalenv()$.Random.seed, ...future.rng), globalenv = if (FALSE) list(added = base::setdiff(base::names(base::.GlobalEnv), ...future.globalenv.names)) else NULL, started = ...future.startTime, version = "1.8") }, condition = base::local({ c <- base::c inherits <- base::inherits invokeRestart <- base::invokeRestart length <- base::length list <- base::list seq.int <- base::seq.int signalCondition <- base::signalCondition sys.calls <- base::sys.calls `[[` <- base::`[[` `+` <- base::`+` `<<-` <- base::`<<-` sysCalls <- function(calls = sys.calls(), from = 1L) { calls[seq.int(from = from + 12L, to = length(calls) - 3L)] } function(cond) { is_error <- inherits(cond, "error") ignore <- !is_error && !is.null(NULL) && inherits(cond, NULL) if (is_error) { sessionInformation <- function() { list(r = base::R.Version(), locale = base::Sys.getlocale(), rngkind = base::RNGkind(), namespaces = base::loadedNamespaces(), search = base::search(), system = base::Sys.info()) } ...future.conditions[[length(...future.conditions) + 1L]] <<- list(condition = cond, calls = c(sysCalls(from = ...future.frame), cond$call), session = sessionInformation(), timestamp = base::Sys.time(), signaled = 0L) signalCondition(cond) } else if (!ignore && TRUE && inherits(cond, c("condition", "immediateCondition"))) { signal <- TRUE && inherits(cond, "immediateCondition") ...future.conditions[[length(...future.conditions) + 1L]] <<- list(condition = cond, signaled = base::as.integer(signal)) if (TRUE && !signal) { muffleCondition <- function (cond, pattern = "^muffle") { inherits <- base::inherits invokeRestart <- base::invokeRestart is.null <- base::is.null muffled <- FALSE if (inherits(cond, "message")) { muffled <- grepl(pattern, "muffleMessage") if (muffled) invokeRestart("muffleMessage") } else if (inherits(cond, "warning")) { muffled <- grepl(pattern, "muffleWarning") if (muffled) invokeRestart("muffleWarning") } else if (inherits(cond, "condition")) { if (!is.null(pattern)) { computeRestarts <- base::computeRestarts grepl <- base::grepl restarts <- computeRestarts(cond) for (restart in restarts) { name <- restart$name if (is.null(name)) next if (!grepl(pattern, name)) next invokeRestart(restart) muffled <- TRUE break } } } invisible(muffled) } muffleCondition(cond, pattern = "^muffle") } } else { if (TRUE) { muffleCondition <- function (cond, pattern = "^muffle") { inherits <- base::inherits invokeRestart <- base::invokeRestart is.null <- base::is.null muffled <- FALSE if (inherits(cond, "message")) { muffled <- grepl(pattern, "muffleMessage") if (muffled) invokeRestart("muffleMessage") } else if (inherits(cond, "warning")) { muffled <- grepl(pattern, "muffleWarning") if (muffled) invokeRestart("muffleWarning") } else if (inherits(cond, "condition")) { if (!is.null(pattern)) { computeRestarts <- base::computeRestarts grepl <- base::grepl restarts <- computeRestarts(cond) for (restart in restarts) { name <- restart$name if (is.null(name)) next if (!grepl(pattern, name)) next invokeRestart(restart) muffled <- TRUE break } } } invisible(muffled) } muffleCondition(cond, pattern = "^muffle") } } } }))}, error = function(ex) { base::structure(base::list(value = NULL, visible = NULL, conditions = ...future.conditions, rng = !identical(base::globalenv()$.Random.seed, ...future.rng), started = ...future.startTime, finished = Sys.time(), session_uuid = NA_character_, version = "1.8"), class = "FutureResult")}, finally = { if (!identical(...future.workdir, getwd())) setwd(...future.workdir) { if (identical(getOption("nwarnings"), ...future.oldOptions$nwarnings)) { ...future.oldOptions$nwarnings <- NULL } base::options(...future.oldOptions) if (.Platform$OS.type == "windows") { old_names <- names(...future.oldEnvVars) envs <- base::Sys.getenv() names <- names(envs) common <- intersect(names, old_names) added <- setdiff(names, old_names) removed <- setdiff(old_names, names) changed <- common[...future.oldEnvVars[common] != envs[common]] NAMES <- toupper(changed) args <- list() for (kk in seq_along(NAMES)) { name <- changed[[kk]] NAME <- NAMES[[kk]] if (name != NAME && is.element(NAME, old_names)) next args[[name]] <- ...future.oldEnvVars[[name]] } NAMES <- toupper(added) for (kk in seq_along(NAMES)) { name <- added[[kk]] NAME <- NAMES[[kk]] if (name != NAME && is.element(NAME, old_names)) next args[[name]] <- "" } NAMES <- toupper(removed) for (kk in seq_along(NAMES)) { name <- removed[[kk]] NAME <- NAMES[[kk]] if (name != NAME && is.element(NAME, old_names)) next args[[name]] <- ...future.oldEnvVars[[name]] } if (length(args) > 0) base::do.call(base::Sys.setenv, args = args) args <- names <- old_names <- NAMES <- envs <- common <- added <- removed <- NULL } else { base::do.call(base::Sys.setenv, args = base::as.list(...future.oldEnvVars)) } { if (base::length(...future.futureOptionsAdded) > 0L) { opts <- base::vector("list", length = base::length(...future.futureOptionsAdded)) base::names(opts) <- ...future.futureOptionsAdded base::options(opts) } { { base::assign(".Random.seed", c(10403L, 84L, 515190382L, 2133433928L, 917665867L, 1283494313L, 1101294840L, 1366013990L, -351622847L, 676521683L, 1906871938L, 611071156L, 1955982391L, 889786157L, -2020897724L, 33313130L, -1561915947L, 293137263L, -125382026L, -1082686048L, 517280355L, 1329304321L, 257493616L, 1917969934L, -1708298631L, 1261124107L, -1796672710L, 394955324L, 1787087231L, 1253737173L, 1825149676L, 1067631682L, -1933739107L, -272199145L, -1473812610L, -1483012808L, -1945071077L, 304012153L, 1841692104L, 1692664310L, 1694274609L, 1439639139L, 1682577970L, 905136004L, 468383175L, -2022286179L, 1825119252L, -746800454L, 843324165L, -791084833L, 546609510L, 95571184L, 1230829587L, -449925711L, -25450400L, -438295042L, 939299209L, 898991803L, 1166361226L, 834198892L, -1321751825L, 945132837L, 1166025692L, 594481586L, -2133225299L, -1023008665L, -1066252402L, -1972719512L, -422011797L, 723093001L, -597432168L, 3593158L, 1816848161L, -330497101L, -224728286L, -304915180L, 1256803735L, -328698483L, 825726116L, -725207414L, -423645963L, 763278159L, 1574841430L, -146985216L, 346434115L, 1275498977L, 1058862416L, -368284754L, -458061479L, 194901867L, 1055147738L, 276055964L, -1633625185L, 1995784693L, 404485260L, -1890017950L, 635523389L, -182568521L, 1833287262L, -425109608L, 251352827L, 494771865L, -492271832L, -1599881770L, -1599085999L, 1360804099L, -1037224814L, 342690340L, 825283815L, 62654781L, -1615635020L, -896490982L, 79915365L, -494708737L, 997068422L, -133622256L, -657470285L, 333924177L, -510678272L, -807349794L, 487586345L, -2074920485L, -2146818326L, -1240775540L, -1648669745L, -470776955L, 540594236L, 213786898L, 1225844237L, 1155953991L, 680730414L, 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-554617705L, -1475068064L, 222000958L, 1930422283L, -512962419L, -2054862406L, -558536712L, 1084621729L, 2130378067L, 1030009972L, 970352130L, 1209858199L, -1328338335L, -1244519770L, 908634788L, -367452331L, 1983669247L, 142271128L, 1880377270L, 424193091L, -694008443L, -315810270L, 562644240L, -24410951L, -1914664597L, 101001308L, -955529846L, -1437884033L, 2093022409L, 55263582L, -579808756L, 1880167901L, -1054929689L, 1903898387L ), envir = base::globalenv(), inherits = FALSE) NULL } options(future.plan = NULL) if (is.na(NA_character_)) Sys.unsetenv("R_FUTURE_PLAN") else Sys.setenv(R_FUTURE_PLAN = NA_character_) future::plan(...future.strategy.old, .cleanup = FALSE, .init = FALSE) } } }}) 38: eval(expr, envir = envir, enclos = baseenv()) 39: eval(expr, envir = envir, enclos = baseenv()) 40: run.UniprocessFuture(future) 41: run(future) 42: run.Future(future) 43: run(future) 44: future(expr, substitute = FALSE, envir = future.envir, stdout = future.stdout, conditions = future.conditions, globals = globals_ii, packages = packages_ii, seed = future.seed, label = labels[ii]) 45: future_xapply(FUN = FUN, nX = nX, chunk_args = X, args = list(...), get_chunk = `chunkWith[[`, expr = expr, envir = envir, future.envir = future.envir, future.globals = future.globals, future.packages = future.packages, future.scheduling = future.scheduling, future.chunk.size = future.chunk.size, future.stdout = future.stdout, future.conditions = future.conditions, future.seed = future.seed, future.label = future.label, fcn_name = fcn_name, args_name = args_name, debug = debug) 46: future.apply::future_lapply(seq_len(feat_num), function(i) { if (report(i)) p(sprintf("Processed %d of %d", i, feat_num)) tryCatch({ data_temp <- cbind(sdata_matched, X_matched[, i, drop = FALSE]) y_temp <- colnames(X_matched)[i] formula_temp <- stats::update(formula_rhs, paste(y_temp, "~ .")) model_args_temp <- utils::modifyList(model_control, list(formula = formula_temp, data = data_temp)) model_temp <- do.call(fit_model, model_args_temp) coeff_temp <- summary(model_temp)$coefficients confint_temp <- if (inherits(model_temp, "lm")) { stats::confint(model_temp) } else { lme4::confint.merMod(model_temp, parm = "beta_") } fit_df <- data.frame(Coefficient = rownames(coeff_temp), coeff_temp, confint_temp, feat_id = y_temp, check.names = FALSE, row.names = NULL) ranef_varcor <- if (inherits(model_temp, "lm")) { NULL } else { df <- as.data.frame(lme4::VarCorr(model_temp)) df$feat_id <- y_temp df } lrt_result <- if (is.null(term_LRT)) { NULL } else { lrt_temp <- lapply(term_LRT, function(z) { if (grepl("\\|", z)) { term_temp <- paste0("(", z, ")") } else { term_temp <- z } formula_null <- stats::update(formula_temp, paste(". ~ . -", term_temp)) model_args_null <- utils::modifyList(model_args_temp, list(formula = formula_null)) rand_eff_null <- lme4::findbars(formula_null) has_ranef_null <- length(rand_eff_null) > 0 fit_model_null <- if (has_ranef_null) lmerTest::lmer else stats::lm model_null <- do.call(fit_model_null, model_args_null) lrt_stats <- if (inherits(model_null, "lm") && inherits(model_temp, "lmerModLmerTest")) { stats::anova(model_temp, model_null) } else { stats::anova(model_null, model_temp) } lrt_stats$term <- z lrt_stats }) df <- do.call(rbind, lrt_temp) df$feat_id <- y_temp df } list(fit = fit_df, ranef = ranef_varcor, lrt = lrt_result, error = NULL) }, error = function(e) { warning(paste("Model failed for feature", i, ":", e$message)) list(fit = NULL, ranef = NULL, lrt = NULL, error = data.frame(feat_id = colnames(X_matched)[i], error = e$message)) })}, future.seed = TRUE) 47: dana(X = mock_X, sample_data = sample_data, formula_rhs = ~group + (1 | subject), term_LRT = "group", platform = "nmr", verbose = FALSE) 48: eval(code, test_env) 49: eval(code, test_env) 50: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error) 51: doTryCatch(return(expr), name, parentenv, handler) 52: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 53: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 54: doTryCatch(return(expr), name, parentenv, handler) 55: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 56: tryCatchList(expr, classes, parentenv, handlers) 57: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) 58: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter()) 59: test_that("dana handles LRT terms correctly", { skip_if_not_installed("lmerTest") skip_if_not_installed("future") mock_X <- matrix(rnorm(20), nrow = 5) rownames(mock_X) <- paste0("id", 1:5) colnames(mock_X) <- paste0("feat", 1:4) sample_data <- data.frame(sample_id = rownames(mock_X), group = factor(c("A", "A", "B", "B", "B")), subject = factor(c(1, 1, 2, 2, 3)), row.names = rownames(mock_X)) res <- dana(X = mock_X, sample_data = sample_data, formula_rhs = ~group + (1 | subject), term_LRT = "group", platform = "nmr", verbose = FALSE) expect_s3_class(res, "dana") expect_true(nrow(res$fit) > 0) expect_true(nrow(res$lrt) > 0) expect_true("term" %in% colnames(res$lrt))}) 60: eval(code, test_env) 61: eval(code, test_env) 62: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error) 63: doTryCatch(return(expr), name, parentenv, handler) 64: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 65: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 66: doTryCatch(return(expr), name, parentenv, handler) 67: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 68: tryCatchList(expr, classes, parentenv, handlers) 69: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) 70: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new()) 71: source_file(path, env = env(env), desc = desc, error_call = error_call) 72: FUN(X[[i]], ...) 73: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call) 74: doTryCatch(return(expr), name, parentenv, handler) 75: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 76: tryCatchList(expr, classes, parentenv, handlers) 77: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) 78: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)) 79: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call) 80: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel) 81: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") 82: test_check("readyomics") An irrecoverable exception occurred. R is aborting now ... * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building 'readyomics.Rmd' using rmarkdown Quitting from lines at lines 210-220 [unnamed-chunk-14] (readyomics.Rmd) Error: processing vignette 'readyomics.Rmd' failed with diagnostics: object 'X_dist' not found --- failed re-building 'readyomics.Rmd' SUMMARY: processing the following file failed: 'readyomics.Rmd' Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 3 ERRORs See '/tmp/th798/21128216/R-release/1180/readyomics.Rcheck/00check.log' for details. [1] "2025-08-24 00:48:20 MST" Warning message: In install.packages(dt.tar.gz, repos = NULL) : installation of package '/scratch/th798/data.table-revdeps/2025-08-24/data.table_master_1.17.99.55bbc3d1646a80ba1d5b2c073c17b9575e7c186a.tar.gz' had non-zero exit status > system(paste(c("diff -u", Rcheck.list), collapse=" ")) --- R_version_4.5.1_2025-06-13/release_1.17.8.Rcheck/00check.log 2025-08-24 00:46:17.006849108 -0700 +++ R_version_4.5.1_2025-06-13/master_1.17.99.55bbc3d1646a80ba1d5b2c073c17b9575e7c186a.Rcheck/00check.log 2025-08-24 00:48:20.097936838 -0700 @@ -148,7 +148,7 @@ An irrecoverable exception occurred. R is aborting now ... Examples with CPU (user + system) or elapsed time > 5s user system elapsed -build_phyloseq 8.585 0.392 9.156 +build_phyloseq 8.074 0.393 8.65 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ERROR Running 'testthat.R' > 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") + 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) + } >