Note: the module "R" cannot be unloaded because it was not loaded. WARNING: ignoring environment value of R_HOME R Under development (unstable) (2025-03-25 r88054) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > cargs <- commandArgs(trailingOnly=TRUE) > if(length(cargs)==0){ + ## before running interactively, make sure to start emacs/R with + ## environment defined in /scratch/...check_one.sh, particularly + ## R_LIBS_USER=/tmp/... otherwise we get error when installing + ## data.table. + base <- "/scratch/th798/data.table-revdeps/*" + cargs <- c( + Sys.glob(file.path(base,"deps.csv")), + "349", + Sys.glob(file.path(base, "data.table_release_*tar.gz")), + Sys.glob(file.path(base, "data.table_master_*tar.gz")) + ) + } > names(cargs) <- c("deps.csv", "task.str", "release", "master") > dput(cargs) c(deps.csv = "/scratch/th798/data.table-revdeps/2025-03-26/deps.csv", task.str = "891", release = "/scratch/th798/data.table-revdeps/2025-03-26/data.table_release_1.17.0.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-03-26/data.table_master_1.17.99.77b43940971091a63baeccf65ec3b2d729dc3a57.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/16120028/R-devel/891" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/16120028/R-devel/891/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "mxnorm" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/16120028/R-devel/891/library" [2] "/projects/genomic-ml/R/R-devel/library" > options(repos=c(#this should be in ~/.Rprofile too. + CRAN="http://cloud.r-project.org")) > print(Sys.time()) [1] "2025-03-26 01:23:53 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/16120028/R-devel/891/library' (as 'lib' is unspecified) also installing the dependencies 'shapefiles', 'fossil' trying URL 'http://cloud.r-project.org/src/contrib/shapefiles_0.7.2.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/fossil_0.4.0.tar.gz' trying URL 'http://cloud.r-project.org/src/contrib/mxnorm_1.0.3.tar.gz' * installing *source* package 'shapefiles' ... ** this is package 'shapefiles' version '0.7.2' ** package 'shapefiles' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (shapefiles) * installing *source* package 'fossil' ... ** this is package 'fossil' version '0.4.0' ** package 'fossil' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fossil) * installing *source* package 'mxnorm' ... ** this is package 'mxnorm' version '1.0.3' ** package 'mxnorm' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (mxnorm) The downloaded source packages are in '/tmp/th798/16120028/Rtmp09qkKe/downloaded_packages' > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 19.872 1.853 24.456 > print(Sys.time()) [1] "2025-03-26 01:24:18 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] "2025-03-26 01:24:18 MST" Installing package into '/tmp/th798/16120028/R-devel/891/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.17.0' ** 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/th798/16120028/R-devel/891/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] "2025-03-26 01:24:41 MST" * using log directory '/tmp/th798/16120028/R-devel/891/mxnorm.Rcheck' * using R Under development (unstable) (2025-03-25 r88054) * 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 'mxnorm/DESCRIPTION' ... OK * this is package 'mxnorm' version '1.0.3' * 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 'mxnorm' 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: 'e1071' 'glue' All declared Imports should be used. * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... 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 plot_mx_umap 8.275 0.072 8.612 run_reduce_umap 7.984 0.059 8.071 plot_mx_density 2.764 0.124 5.032 * 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: 1 NOTE See '/tmp/th798/16120028/R-devel/891/mxnorm.Rcheck/00check.log' for details. [1] "2025-03-26 01:29:05 MST" [1] "2025-03-26 01:29:05 MST" Installing package into '/tmp/th798/16120028/R-devel/891/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** this is package 'data.table' version '1.17.99' ** 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/th798/16120028/R-devel/891/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] "2025-03-26 01:29:32 MST" * using log directory '/tmp/th798/16120028/R-devel/891/mxnorm.Rcheck' * using R Under development (unstable) (2025-03-25 r88054) * 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 'mxnorm/DESCRIPTION' ... OK * this is package 'mxnorm' version '1.0.3' * 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 'mxnorm' 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: 'e1071' 'glue' All declared Imports should be used. * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... 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 plot_mx_umap 8.247 0.082 8.358 run_reduce_umap 7.919 0.078 8.022 * 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: 1 NOTE See '/tmp/th798/16120028/R-devel/891/mxnorm.Rcheck/00check.log' for details. [1] "2025-03-26 01:33:43 MST" > system(paste(c("diff -u", Rcheck.list), collapse=" ")) --- R_Under_development_unstable_2025-03-25_r88054/release_1.17.0.Rcheck/00check.log 2025-03-26 01:29:05.356731966 -0700 +++ R_Under_development_unstable_2025-03-25_r88054/master_1.17.99.77b43940971091a63baeccf65ec3b2d729dc3a57.Rcheck/00check.log 2025-03-26 01:33:43.057750479 -0700 @@ -60,9 +60,8 @@ * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed -plot_mx_umap 8.275 0.072 8.612 -run_reduce_umap 7.984 0.059 8.071 -plot_mx_density 2.764 0.124 5.032 +plot_mx_umap 8.247 0.082 8.358 +run_reduce_umap 7.919 0.078 8.022 * 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 4.4.3 (2025-02-28) -- "Trophy Case" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > cargs <- commandArgs(trailingOnly=TRUE) > if(length(cargs)==0){ + ## before running interactively, make sure to start emacs/R with + ## environment defined in /scratch/...check_one.sh, particularly + ## R_LIBS_USER=/tmp/... otherwise we get error when installing + ## data.table. + base <- "/scratch/th798/data.table-revdeps/*" + cargs <- c( + Sys.glob(file.path(base,"deps.csv")), + "349", + Sys.glob(file.path(base, "data.table_release_*tar.gz")), + Sys.glob(file.path(base, "data.table_master_*tar.gz")) + ) + } > names(cargs) <- c("deps.csv", "task.str", "release", "master") > dput(cargs) c(deps.csv = "/scratch/th798/data.table-revdeps/2025-03-26/deps.csv", task.str = "891", release = "/scratch/th798/data.table-revdeps/2025-03-26/data.table_release_1.17.0.tar.gz", master = "/scratch/th798/data.table-revdeps/2025-03-26/data.table_master_1.17.99.77b43940971091a63baeccf65ec3b2d729dc3a57.tar.gz" ) > (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers [1] "/tmp/th798/16120028/R-release/891" > if(requireNamespace("R.cache"))R.cache::getCachePath() Loading required namespace: R.cache [1] "/tmp/th798/16120028/R-release/891/R.cache" > task.id <- as.integer(cargs[["task.str"]]) > deps.df <- read.csv(cargs[["deps.csv"]]) > (rev.dep <- deps.df$Package[task.id]) [1] "mxnorm" > job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id) > setwd(task.dir) > .libPaths() [1] "/tmp/th798/16120028/R-release/891/library" [2] "/projects/genomic-ml/R/R-release/library" > options(repos=c(#this should be in ~/.Rprofile too. + CRAN="http://cloud.r-project.org")) > print(Sys.time()) [1] "2025-03-26 01:33:48 MST" > install.time <- system.time({ + install.packages(rev.dep, dep=TRUE) + }) Installing package into '/tmp/th798/16120028/R-release/891/library' (as 'lib' is unspecified) also installing the dependencies 'shapefiles', 'fossil' trying URL 'http://cloud.r-project.org/src/contrib/shapefiles_0.7.2.tar.gz' Content type 'application/x-gzip' length 10964 bytes (10 KB) ================================================== downloaded 10 KB trying URL 'http://cloud.r-project.org/src/contrib/fossil_0.4.0.tar.gz' Content type 'application/x-gzip' length 34655 bytes (33 KB) ================================================== downloaded 33 KB trying URL 'http://cloud.r-project.org/src/contrib/mxnorm_1.0.3.tar.gz' Content type 'application/x-gzip' length 1078608 bytes (1.0 MB) ================================================== downloaded 1.0 MB * installing *source* package 'shapefiles' ... ** package 'shapefiles' successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (shapefiles) * installing *source* package 'fossil' ... ** package 'fossil' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fossil) * installing *source* package 'mxnorm' ... ** package 'mxnorm' successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading 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 ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location 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 ** testing if installed package can be loaded from final location 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 ** testing if installed package keeps a record of temporary installation path * DONE (mxnorm) The downloaded source packages are in '/tmp/th798/16120028/Rtmp4Aiyhv/downloaded_packages' > cat("Time to install revdep:\n") Time to install revdep: > print(install.time) user system elapsed 18.837 1.625 21.362 > print(Sys.time()) [1] "2025-03-26 01:34:10 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] "2025-03-26 01:34:10 MST" Installing package into '/tmp/th798/16120028/R-release/891/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** 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/th798/16120028/R-release/891/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] "2025-03-26 01:34:31 MST" * using log directory '/tmp/th798/16120028/R-release/891/mxnorm.Rcheck' * using R version 4.4.3 (2025-02-28) * 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 'mxnorm/DESCRIPTION' ... OK * this is package 'mxnorm' version '1.0.3' * 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 'mxnorm' 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: 'e1071' 'glue' All declared Imports should be used. * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ...sh: line 1: 2486844 Segmentation fault (core dumped) LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/home/th798/R/R-release/bin/R' --vanilla > 'mxnorm-Ex.Rout' 2>&1 < 'mxnorm-Ex.R' ERROR Running examples in 'mxnorm-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plot_mx_proportions > ### Title: Visualize variance proportions by marker and table > ### Aliases: plot_mx_proportions > > ### ** Examples > > mx_data = mx_dataset(mxnorm::mx_sample, "slide_id", "image_id", + c("marker1_vals","marker2_vals","marker3_vals"), + c("metadata1_vals")) > mx_data = mx_normalize(mx_data, transform="log10",method="None") > mx_data = run_var_proportions(mx_data, table="both") *** 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: 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3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), p = 0:3000, Dim = c(4L, 3000L), Dimnames = list( c("slide1", "slide2", "slide3", "slide4"), 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", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", 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"248", "249", "250", "251", "252", "253", "254", "255", "256", "257", "258", "259", "260", "261", "262", "263", "264", "265", "266", "267", "268", "269", "270", "271", "272", "273", "274", "275", "276", "277", "278", "279", "280", "281", "282", "283", "284", "285", "286", "287", "288", "289", "290", "291", "292", "293", "294", "295", "296", "297", "298", "299", "300", "301", "302", "303", "304", "305", "306", "307", "308", "309", "310", "311", "312", "313", "314", "315", "316", "317", "318", "319", "320", "321", "322", "323", "324", "325", "326", "327", "328", "329", "330", "331", "332", "333", "334", "335", "336", "337", "338", "339", "340", "341", "342", "343", "344", "345", "346", "347", "348", "349", "350", "351", "352", "353", "354", "355", "356", "357", "358", "359", "360", "361", "362", "363", "364", "365", "366", "367", "368", "369", "370", "371", "372", "373", "374", "375", "376", "377", "378", "379", "380", "381", "382", "383", "384", "385", "386", "387", "388", "389", "390", "391", "392", "393", "394", "395", "396", "397", "398", "399", "400", "401", "402", "403", "404", "405", "406", "407", "408", "409", "410", "411", "412", "413", "414", "415", "416", "417", "418", "419", "420", "421", "422", "423", "424", "425", "426", "427", "428", "429", "430", "431", "432", "433", "434", "435", "436", "437", "438", "439", "440", "441", "442", "443", "444", "445", "446", "447", "448", "449", "450", "451", "452", "453", "454", "455", "456", "457", "458", "459", "460", "461", "462", "463", "464", "465", "466", "467", "468", "469", "470", "471", "472", "473", "474", "475", "476", "477", "478", "479", "480", "481", "482", "483", "484", "485", "486", "487", "488", "489", "490", "491", "492", "493", "494", "495", "496", "497", "498", "499", "500", "501", "502", "503", "504", "505", "506", "507", "508", "509", "510", "511", "512", "513", "514", "515", "516", "517", "518", "519", "520", "521", "522", "523", "524", "525", "526", "527", "528", "529", "530", "531", "532", "533", "534", "535", "536", "537", "538", "539", "540", "541", "542", "543", "544", "545", "546", "547", "548", "549", "550", "551", "552", "553", "554", "555", "556", "557", "558", "559", "560", "561", "562", "563", "564", "565", "566", "567", "568", "569", "570", "571", "572", "573", "574", "575", "576", "577", "578", "579", "580", "581", "582", "583", "584", "585", "586", "587", "588", "589", "590", "591", "592", "593", "594", "595", "596", "597", "598", "599", "600", "601", "602", "603", "604", "605", "606", "607", "608", "609", "610", "611", "612", "613", "614", "615", "616", "617", "618", "619", "620", "621", "622", "623", "624", "625", "626", "627", "628", "629", "630", "631", "632", "633", "634", "635", "636", "637", "638", "639", "640", "641", "642", "643", "644", "645", "646", "647", "648", "649", "650", "651", "652", "653", "654", "655", "656", "657", "658", "659", "660", "661", "662", "663", "664", "665", "666", "667", "668", "669", "670", "671", "672", "673", "674", "675", "676", "677", "678", "679", "680", "681", "682", "683", "684", "685", "686", "687", "688", "689", "690", "691", "692", "693", "694", "695", "696", "697", "698", "699", "700", "701", "702", "703", "704", "705", "706", "707", "708", "709", "710", "711", "712", "713", "714", "715", "716", "717", "718", "719", "720", "721", "722", "723", "724", "725", "726", "727", "728", "729", "730", "731", "732", "733", "734", "735", "736", "737", "738", "739", "740", "741", "742", "743", "744", "745", "746", "747", "748", "749", "750", "751", "752", "753", "754", "755", "756", "757", "758", "759", "760", "761", "762", "763", "764", "765", "766", "767", "768", "769", "770", "771", "772", "773", "774", "775", "776", "777", "778", "779", "780", "781", "782", "783", "784", "785", "786", "787", "788", "789", "790", "791", "792", "793", "794", "795", "796", "797", "798", "799", "800", "801", "802", "803", "804", "805", "806", "807", "808", "809", "810", "811", "812", "813", "814", "815", "816", "817", "818", "819", "820", "821", "822", "823", "824", "825", "826", "827", "828", "829", "830", "831", "832", "833", "834", "835", "836", "837", "838", "839", "840", "841", "842", "843", "844", "845", "846", "847", "848", "849", "850", "851", "852", "853", "854", "855", "856", "857", "858", "859", "860", "861", "862", "863", "864", "865", "866", "867", "868", "869", "870", "871", "872", "873", "874", "875", "876", "877", "878", "879", "880", "881", "882", "883", "884", "885", "886", "887", "888", "889", "890", "891", "892", "893", "894", "895", "896", "897", "898", "899", "900", "901", "902", "903", "904", "905", "906", "907", "908", "909", "910", "911", "912", "913", "914", "915", "916", "917", "918", "919", "920", "921", "922", "923", "924", "925", "926", "927", "928", "929", "930", "931", "932", "933", "934", "935", "936", "937", "938", "939", "940", "941", "942", "943", "944", "945", "946", "947", "948", "949", "950", "951", "952", "953", "954", "955", "956", "957", "958", "959", "960", "961", "962", "963", "964", "965", "966", "967", "968", "969", "970", "971", "972", "973", "974", "975", "976", "977", "978", "979", "980", "981", "982", "983", "984", "985", "986", "987", "988", "989", "990", "991", "992", "993", "994", "995", "996", "997", "998", "999", "1000", "1001", "1002", "1003", "1004", "1005", "1006", "1007", "1008", "1009", "1010", "1011", "1012", "1013", "1014", "1015", "1016", "1017", "1018", "1019", "1020", "1021", "1022", "1023", "1024", "1025", "1026", "1027", "1028", "1029", "1030", "1031", "1032", "1033", "1034", "1035", "1036", "1037", "1038", "1039", "1040", "1041", "1042", "1043", "1044", "1045", "1046", "1047", "1048", "1049", "1050", "1051", "1052", "1053", "1054", "1055", "1056", "1057", "1058", "1059", "1060", "1061", "1062", "1063", "1064", "1065", "1066", "1067", "1068", "1069", "1070", "1071", "1072", "1073", "1074", "1075", "1076", "1077", "1078", "1079", "1080", "1081", "1082", "1083", "1084", "1085", "1086", "1087", "1088", "1089", "1090", "1091", 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"1217", "1218", "1219", "1220", "1221", "1222", "1223", "1224", "1225", "1226", "1227", "1228", "1229", "1230", "1231", "1232", "1233", "1234", "1235", "1236", "1237", "1238", "1239", "1240", "1241", "1242", "1243", "1244", "1245", "1246", "1247", "1248", "1249", "1250", "1251", "1252", "1253", "1254", "1255", "1256", "1257", "1258", "1259", "1260", "1261", "1262", "1263", "1264", "1265", "1266", "1267", "1268", "1269", "1270", "1271", "1272", "1273", "1274", "1275", "1276", "1277", "1278", "1279", "1280", "1281", "1282", "1283", "1284", "1285", "1286", "1287", "1288", "1289", "1290", "1291", "1292", "1293", "1294", "1295", "1296", "1297", "1298", "1299", "1300", "1301", "1302", "1303", "1304", "1305", "1306", "1307", "1308", "1309", "1310", "1311", "1312", "1313", "1314", "1315", "1316", "1317", "1318", "1319", "1320", "1321", "1322", "1323", "1324", "1325", "1326", "1327", "1328", "1329", "1330", "1331", "1332", "1333", "1334", "1335", "1336", "1337", "1338", "1339", "1340", "1341", 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1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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(marker1_vals = c(15, 11, 12, 11, 12, 11, 16, 12, 11, 10, 15, 14, 14, 13, 14, 11, 12, 16, 16, 13, 13, 12, 9, 11, 13, 14, 14, 11, 11, 11, 13, 12, 13, 12, 13, 10, 13, 11, 13, 12, 13, 11, 15, 14, 13, 13, 14, 13, 8, 14, 12, 13, 15, 11, 13, 15, 13, 10, 11, 14, 14, 15, 11, 14, 13, 11, 13, 13, 11, 12, 11, 12, 11, 14, 15, 12, 14, 14, 11, 10, 10, 14, 15, 14, 11, 12, 13, 12, 14, 12, 12, 16, 14, 11, 12, 9, 10, 12, 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40, 43, 46, 40, 58, 49, 44, 38, 43, 43, 33, 30, 54, 34, 51, 41, 53, 30, 47, 52, 48, 41, 32, 50, 55, 30, 33, 39, 41, 44, 50, 32, 51, 34, 30, 53, 56, 37, 39, 36, 50, 39, 43, 50, 46, 30, 39, 55, 31, 53, 45, 42, 42, 42, 48, 39, 30, 57, 46, 59, 60, 52, 40, 46, 55, 54, 58, 37, 45, 45, 60, 30, 32, 49, 30, 38, 45, 30, 31, 52, 53, 33, 51, 39, 46, 47, 51, 43, 45, 44, 41, 40, 47, 39, 40, 35, 30, 35, 48, 50, 60, 34, 30, 39, 45, 59, 49, 60, 38, 35, 35, 42, 34, 40, 57, 47, 44, 55, 57, 49, 44, 36, 46, 60, 55, 31, 54, 54, 30, 60, 37, 30, 41, 45, 46, 36, 35, 51, 33, 48, 30, 53, 34, 34, 42, 42, 59, 58, 60, 54, 56, 38, 54, 60, 55, 55, 58, 37, 37, 43, 52, 38, 59, 31, 45, 46, 50, 44, 30, 51, 37, 31, 60, 52, 40, 55, 34, 53, 60, 39, 37, 34, 54, 37, 53, 47, 50, 35, 48, 53, 41, 46, 33, 36, 45, 51, 37, 46, 30, 51, 48, 34, 34, 31, 56, 33, 39, 40, 42, 50, 56, 52, 49, 40, 39, 50, 48, 42, 58, 34, 37, 44, 32, 48, 50, 34, 55, 34, 34, 49, 56, 48, 45, 31, 43, 49, 43, 38, 54, 41, 52, 43, 60, 39, 41, 38, 38, 40, 58, 35, 35, 40, 55, 59, 38, 43, 49, 48, 48, 31, 45, 59, 57, 40, 39, 35, 35, 49, 35, 60, 33, 39, 32, 37, 44, 32, 30, 32, 46, 33, 49, 40, 45, 45, 47, 51, 40, 55, 60, 30, 49, 33, 53, 57, 51, 34, 56, 56, 43, 43, 51, 31, 39, 31, 51, 58, 37, 60, 53, 54, 50, 30, 34, 57, 56, 49, 47, 44, 50, 40, 35, 40, 58, 60, 40, 33, 39, 40, 60, 53, 58, 54, 32, 40, 33, 42, 33, 54, 47, 41, 44, 46, 49, 50, 39, 54, 47, 44, 58, 54, 55, 49, 42, 50, 55, 58, 31, 49, 31, 40, 43, 32, 47, 49, 49, 45, 36, 59, 34, 58, 50, 58, 45, 50, 55, 40, 49, 41, 45, 35, 43, 48, 59, 32, 59, 40, 54, 51, 55, 59, 50, 33, 51, 55, 60, 36, 34, 44, 34, 37, 35, 55, 46, 59, 38, 44, 46, 52, 50, 34, 44, 40, 43, 57, 39, 47, 57, 37, 56, 31, 49, 56, 34, 48, 39, 55, 52, 55, 53, 53, 39, 30, 45, 42, 56, 56, 38, 41, 30, 33, 60, 51, 47, 35, 52, 55, 31, 44, 44, 34, 56, 46, 37, 45, 37, 38, 56, 51, 35, 52, 32, 44, 45, 54, 31, 53, 50, 45, 40, 31, 49, 36, 44, 59, 36, 34, 34, 42, 30, 56, 40, 36, 35, 37, 56, 42, 45, 37, 37, 51, 34, 39, 40, 53, 41, 45, 34, 48, 49, 45, 34, 54, 41, 46, 52, 49, 59, 49, 53, 43, 55, 54, 42, 50, 36, 54, 34, 42, 51, 45, 33, 48, 53, 48, 49, 36, 40, 56, 54, 47, 53, 46, 55, 39, 38, 53, 39, 51, 48, 32, 54, 56, 45, 55, 50, 55, 56, 49, 57, 34, 50, 35, 33, 36, 44, 33, 52, 59, 49, 31, 38, 50, 39, 42, 31, 32, 59, 54, 56, 59, 50, 35, 46, 52, 52, 37, 56, 55, 58, 31, 47, 32, 52, 43, 46, 39, 36, 52, 57, 43, 42, 52, 43, 52, 47, 57, 40, 35, 55, 58, 38, 60, 52, 44, 59, 54, 50, 42, 60, 46, 46, 39, 40, 30, 30, 48, 56, 35, 60, 42, 34, 42, 44, 38, 55, 31, 35, 56, 60, 43, 57, 41, 48, 31, 50, 39, 50, 42, 46, 39, 58, 42, 50, 31, 35, 49, 49, 48, 52, 53, 52, 32, 47, 46, 60, 60), slide_id = 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, 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, 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, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 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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, 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, 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, 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, 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, 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, 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, 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, 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, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 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3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), p = 0:3000, Dim = c(4L, 3000L), Dimnames = list( c("slide1", "slide2", "slide3", "slide4"), 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", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", 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"188", "189", "190", "191", "192", "193", "194", "195", "196", "197", "198", "199", "200", "201", "202", "203", "204", "205", "206", "207", "208", "209", "210", "211", "212", "213", "214", "215", "216", "217", "218", "219", "220", "221", "222", "223", "224", "225", "226", "227", "228", "229", "230", "231", "232", "233", "234", "235", "236", "237", "238", "239", "240", "241", "242", "243", "244", "245", "246", "247", "248", "249", "250", "251", "252", "253", "254", "255", "256", "257", "258", "259", "260", "261", "262", "263", "264", "265", "266", "267", "268", "269", "270", "271", "272", "273", "274", "275", "276", "277", "278", "279", "280", "281", "282", "283", "284", "285", "286", "287", "288", "289", "290", "291", "292", "293", "294", "295", "296", "297", "298", "299", "300", "301", "302", "303", "304", "305", "306", "307", "308", "309", "310", "311", "312", "313", "314", "315", "316", "317", "318", "319", "320", "321", "322", "323", "324", "325", "326", "327", "328", "329", "330", "331", "332", "333", "334", "335", "336", "337", "338", "339", "340", "341", "342", "343", "344", "345", "346", "347", "348", "349", "350", "351", "352", "353", "354", "355", "356", "357", "358", "359", "360", "361", "362", "363", "364", "365", "366", "367", "368", "369", "370", "371", "372", "373", "374", "375", "376", "377", "378", "379", "380", "381", "382", "383", "384", "385", "386", "387", "388", "389", "390", "391", "392", "393", "394", "395", "396", "397", "398", "399", "400", "401", "402", "403", "404", "405", "406", "407", "408", "409", "410", "411", "412", "413", "414", "415", "416", "417", "418", "419", "420", "421", "422", "423", "424", "425", "426", "427", "428", "429", "430", "431", "432", "433", "434", "435", "436", "437", "438", "439", "440", "441", "442", "443", "444", "445", "446", "447", "448", "449", "450", "451", "452", "453", "454", "455", "456", "457", "458", "459", "460", "461", "462", "463", "464", "465", "466", "467", "468", "469", "470", "471", "472", "473", "474", "475", "476", "477", "478", "479", "480", "481", "482", "483", "484", "485", "486", "487", "488", "489", "490", "491", "492", "493", "494", "495", "496", "497", "498", "499", "500", "501", "502", "503", "504", "505", "506", "507", "508", "509", "510", "511", "512", "513", "514", "515", "516", "517", "518", "519", "520", "521", "522", "523", "524", "525", "526", "527", "528", "529", "530", "531", "532", "533", "534", "535", "536", "537", "538", "539", "540", "541", "542", "543", "544", "545", "546", "547", "548", "549", "550", "551", "552", "553", "554", "555", "556", "557", "558", "559", "560", "561", "562", "563", "564", "565", "566", "567", "568", "569", "570", "571", "572", "573", "574", "575", "576", "577", "578", "579", "580", "581", "582", "583", "584", "585", "586", "587", "588", "589", "590", "591", "592", "593", "594", "595", "596", "597", "598", "599", "600", "601", "602", "603", "604", "605", "606", "607", "608", "609", "610", "611", "612", "613", "614", "615", "616", "617", "618", "619", "620", "621", "622", "623", "624", "625", "626", "627", "628", "629", "630", "631", "632", "633", "634", "635", "636", "637", "638", "639", "640", "641", "642", "643", "644", "645", "646", "647", "648", "649", "650", "651", "652", "653", "654", "655", "656", "657", "658", "659", "660", "661", "662", "663", "664", "665", "666", "667", "668", "669", "670", "671", "672", "673", "674", "675", "676", "677", "678", "679", "680", "681", "682", "683", "684", "685", "686", "687", "688", "689", "690", "691", "692", "693", "694", "695", "696", "697", "698", "699", "700", "701", "702", "703", "704", "705", "706", "707", "708", "709", "710", "711", "712", "713", "714", "715", "716", "717", "718", "719", "720", "721", "722", "723", "724", "725", "726", "727", "728", "729", "730", "731", "732", "733", "734", "735", "736", "737", "738", "739", "740", "741", "742", "743", "744", "745", "746", "747", "748", "749", "750", "751", "752", "753", "754", "755", "756", "757", "758", "759", "760", "761", "762", "763", "764", "765", "766", "767", "768", "769", "770", "771", "772", "773", "774", "775", "776", "777", "778", "779", "780", "781", "782", "783", "784", "785", "786", "787", "788", "789", "790", "791", "792", "793", "794", "795", "796", "797", "798", "799", "800", "801", "802", "803", "804", "805", "806", "807", "808", "809", "810", "811", "812", "813", "814", "815", "816", "817", "818", "819", "820", "821", "822", "823", "824", "825", "826", "827", "828", "829", "830", "831", "832", "833", "834", "835", "836", "837", "838", "839", "840", "841", "842", "843", "844", "845", "846", "847", "848", "849", "850", "851", "852", "853", "854", "855", "856", "857", "858", "859", "860", "861", "862", "863", "864", "865", "866", "867", "868", "869", "870", "871", "872", "873", "874", "875", "876", "877", "878", "879", "880", "881", "882", "883", "884", "885", "886", "887", "888", "889", "890", "891", "892", "893", "894", "895", "896", "897", "898", "899", "900", "901", "902", "903", "904", "905", "906", "907", "908", "909", "910", "911", "912", "913", "914", "915", "916", "917", "918", "919", "920", "921", "922", "923", "924", "925", "926", "927", "928", "929", "930", "931", "932", "933", "934", "935", "936", "937", "938", "939", "940", "941", "942", "943", "944", "945", "946", "947", "948", "949", "950", "951", "952", "953", "954", "955", "956", "957", "958", "959", "960", "961", "962", "963", "964", "965", "966", "967", "968", "969", "970", "971", "972", "973", "974", "975", "976", "977", "978", "979", "980", "981", "982", "983", "984", "985", "986", "987", "988", "989", "990", "991", "992", "993", "994", "995", "996", "997", "998", "999", "1000", "1001", "1002", "1003", "1004", "1005", "1006", "1007", "1008", "1009", "1010", "1011", "1012", "1013", "1014", "1015", "1016", "1017", "1018", "1019", "1020", "1021", "1022", "1023", "1024", "1025", "1026", "1027", "1028", "1029", "1030", "1031", "1032", "1033", "1034", "1035", "1036", "1037", "1038", "1039", "1040", "1041", "1042", "1043", "1044", "1045", "1046", "1047", "1048", "1049", "1050", "1051", "1052", "1053", "1054", "1055", "1056", "1057", "1058", "1059", "1060", "1061", "1062", "1063", "1064", "1065", "1066", "1067", "1068", "1069", "1070", "1071", "1072", "1073", "1074", "1075", "1076", "1077", "1078", "1079", "1080", "1081", "1082", "1083", "1084", "1085", "1086", "1087", "1088", "1089", "1090", "1091", "1092", "1093", "1094", "1095", "1096", "1097", "1098", "1099", "1100", "1101", "1102", "1103", "1104", "1105", "1106", "1107", "1108", "1109", "1110", "1111", "1112", "1113", "1114", "1115", "1116", "1117", "1118", "1119", "1120", "1121", "1122", "1123", "1124", "1125", "1126", "1127", "1128", "1129", "1130", "1131", "1132", "1133", "1134", "1135", "1136", "1137", "1138", "1139", "1140", "1141", "1142", "1143", "1144", "1145", "1146", "1147", "1148", "1149", "1150", "1151", "1152", "1153", "1154", "1155", "1156", "1157", "1158", "1159", "1160", "1161", "1162", "1163", "1164", 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"1290", "1291", "1292", "1293", "1294", "1295", "1296", "1297", "1298", "1299", "1300", "1301", "1302", "1303", "1304", "1305", "1306", "1307", "1308", "1309", "1310", "1311", "1312", "1313", "1314", "1315", "1316", "1317", "1318", "1319", "1320", "1321", "1322", "1323", "1324", "1325", "1326", "1327", "1328", "1329", "1330", "1331", "1332", "1333", "1334", "1335", "1336", "1337", "1338", "1339", "1340", "1341", "1342", "1343", "1344", "1345", "1346", "1347", "1348", "1349", "1350", "1351", "1352", "1353", "1354", "1355", "1356", "1357", "1358", "1359", "1360", "1361", "1362", "1363", "1364", "1365", "1366", "1367", "1368", "1369", "1370", "1371", "1372", "1373", "1374", "1375", "1376", "1377", "1378", "1379", "1380", "1381", "1382", "1383", "1384", "1385", "1386", "1387", "1388", "1389", "1390", "1391", "1392", "1393", "1394", "1395", "1396", "1397", "1398", "1399", "1400", "1401", "1402", "1403", "1404", "1405", "1406", "1407", "1408", "1409", "1410", "1411", "1412", "1413", "1414", 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"1540", "1541", "1542", "1543", "1544", "1545", "1546", "1547", "1548", "1549", "1550", "1551", "1552", "1553", "1554", "1555", "1556", "1557", "1558", "1559", "1560", "1561", "1562", "1563", "1564", "1565", "1566", "1567", "1568", "1569", "1570", "1571", "1572", "1573", "1574", "1575", "1576", "1577", "1578", "1579", "1580", "1581", "1582", "1583", "1584", "1585", "1586", "1587", "1588", "1589", "1590", "1591", "1592", "1593", "1594", "1595", "1596", "1597", "1598", "1599", "1600", "1601", "1602", "1603", "1604", "1605", "1606", "1607", "1608", "1609", "1610", "1611", "1612", "1613", "1614", "1615", "1616", "1617", "1618", "1619", "1620", "1621", "1622", "1623", "1624", "1625", "1626", "1627", "1628", "1629", "1630", "1631", "1632", "1633", "1634", "1635", "1636", "1637", "1638", "1639", "1640", "1641", "1642", "1643", "1644", "1645", "1646", "1647", "1648", "1649", "1650", "1651", "1652", "1653", "1654", "1655", "1656", "1657", "1658", "1659", "1660", "1661", "1662", "1663", "1664", 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3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), p = 0:3000, Dim = c(4L, 3000L), Dimnames = list(c("slide1", "slide2", "slide3", "slide4"), 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", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", "111", "112", "113", "114", "115", "116", "117", "118", "119", "120", "121", "122", "123", "124", "125", "126", "127", "128", "129", "130", "131", "132", "133", "134", "135", "136", "137", "138", "139", "140", "141", "142", "143", "144", "145", "146", "147", "148", "149", "150", "151", "152", "153", "154", "155", "156", "157", "158", "159", "160", "161", "162", "163", "164", "165", "166", "167", "168", "169", "170", "171", "172", "173", "174", "175", "176", "177", "178", "179", "180", "181", "182", "183", "184", "185", "186", "187", "188", "189", "190", "191", "192", "193", "194", "195", "196", "197", "198", "199", "200", "201", "202", "203", "204", "205", "206", "207", "208", "209", "210", "211", "212", "213", "214", "215", "216", "217", "218", "219", "220", "221", "222", "223", "224", "225", "226", "227", "228", "229", "230", "231", "232", "233", "234", "235", "236", "237", "238", "239", "240", "241", "242", "243", "244", "245", "246", "247", "248", "249", "250", "251", "252", "253", "254", "255", "256", "257", "258", "259", "260", "261", "262", "263", "264", "265", "266", "267", "268", "269", "270", "271", "272", "273", "274", "275", "276", "277", "278", "279", "280", "281", 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"425", "426", "427", "428", "429", "430", "431", "432", "433", "434", "435", "436", "437", "438", "439", "440", "441", "442", "443", "444", "445", "446", "447", "448", "449", "450", "451", "452", "453", "454", "455", "456", "457", "458", "459", "460", "461", "462", "463", "464", "465", "466", "467", "468", "469", "470", "471", "472", "473", "474", "475", "476", "477", "478", "479", "480", "481", "482", "483", "484", "485", "486", "487", "488", "489", "490", "491", "492", "493", "494", "495", "496", "497", "498", "499", "500", "501", "502", "503", "504", "505", "506", "507", "508", "509", "510", "511", "512", "513", "514", "515", "516", "517", "518", "519", "520", "521", "522", "523", "524", "525", "526", "527", "528", "529", "530", "531", "532", "533", "534", "535", "536", "537", "538", "539", "540", "541", "542", "543", "544", "545", "546", "547", "548", "549", "550", "551", "552", "553", "554", "555", "556", "557", "558", "559", "560", "561", "562", "563", "564", "565", "566", "567", "568", "569", "570", "571", "572", "573", "574", "575", "576", "577", "578", "579", "580", "581", "582", "583", "584", "585", "586", "587", "588", "589", "590", "591", "592", "593", "594", "595", "596", "597", "598", "599", "600", "601", "602", "603", "604", "605", "606", "607", "608", "609", "610", "611", "612", "613", "614", "615", "616", "617", "618", "619", "620", "621", "622", "623", "624", "625", "626", "627", "628", "629", "630", "631", "632", "633", "634", "635", "636", "637", "638", "639", "640", "641", "642", "643", "644", "645", "646", "647", "648", "649", "650", "651", "652", "653", "654", "655", "656", "657", "658", "659", "660", "661", "662", "663", "664", "665", "666", "667", "668", "669", "670", "671", "672", "673", "674", "675", "676", "677", "678", "679", "680", "681", "682", "683", "684", "685", "686", "687", "688", "689", "690", "691", "692", "693", "694", "695", "696", "697", "698", "699", "700", "701", "702", "703", "704", "705", "706", "707", "708", "709", "710", 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1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list())), nl = c(slide_id = 4L)), 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(f, data = dat, ...) 12: get_var_proportions(mx_data, metadata_cols, table = "raw", m = marker, formula_override) 13: run_var_proportions(mx_data, table = "both") An irrecoverable exception occurred. R is aborting now ... * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R'/home/th798/R/R-release/bin/BATCH: line 60: 2488580 Segmentation fault (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 ERROR Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(mxnorm) Warning message: In check_dep_version() : ABI version mismatch: lme4 was built with Matrix ABI version 1 Current Matrix ABI version is 2 Please re-install lme4 from source or restore original 'Matrix' package > > test_check("mxnorm") *** caught segfault *** address (nil), cause 'unknown' Traceback: 1: .Call(merPredDCreate, as(X, "matrix"), Lambdat, LamtUt, Lind, RZX, Ut, Utr, V, VtV, Vtr, Xwts, Zt, beta0, delb, delu, theta, u0) 2: initializePtr() 3: .Object$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, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 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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(marker1_vals = c(15, 11, 12, 11, 12, 11, 16, 12, 11, 10, 15, 14, 14, 13, 14, 11, 12, 16, 16, 13, 13, 12, 9, 11, 13, 14, 14, 11, 11, 11, 13, 12, 13, 12, 13, 10, 13, 11, 13, 12, 13, 11, 15, 14, 13, 13, 14, 13, 8, 14, 12, 13, 15, 11, 13, 15, 13, 10, 11, 14, 14, 15, 11, 14, 13, 11, 13, 13, 11, 12, 11, 12, 11, 14, 15, 12, 14, 14, 11, 10, 10, 14, 15, 14, 11, 12, 13, 12, 14, 12, 12, 16, 14, 11, 12, 9, 10, 12, 10, 12, 12, 11, 9, 13, 13, 10, 12, 14, 15, 11, 11, 12, 12, 11, 11, 12, 13, 12, 14, 11, 12, 15, 12, 12, 12, 15, 13, 17, 12, 13, 12, 14, 8, 13, 13, 14, 12, 12, 16, 14, 12, 11, 13, 12, 13, 16, 13, 15, 11, 14, 13, 11, 14, 12, 13, 10, 10, 13, 13, 16, 13, 9, 12, 16, 10, 13, 13, 11, 12, 12, 13, 12, 12, 13, 14, 10, 15, 14, 12, 13, 12, 13, 12, 15, 12, 10, 12, 14, 8, 12, 15, 14, 13, 10, 15, 10, 12, 12, 11, 11, 14, 15, 11, 11, 11, 11, 13, 15, 10, 9, 11, 14, 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3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), p = 0:3000, Dim = c(4L, 3000L), Dimnames = list( c("slide1", "slide2", "slide3", "slide4"), 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", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", 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3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), p = 0:3000, Dim = c(4L, 3000L), Dimnames = list(c("slide1", "slide2", "slide3", "slide4"), 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", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", "111", "112", "113", "114", "115", "116", "117", "118", "119", "120", "121", "122", "123", "124", "125", "126", "127", "128", "129", "130", "131", "132", "133", "134", "135", "136", "137", "138", "139", "140", "141", "142", "143", "144", "145", "146", "147", "148", "149", "150", "151", "152", "153", "154", "155", "156", "157", "158", "159", "160", "161", "162", "163", "164", "165", "166", "167", "168", "169", "170", "171", "172", "173", "174", "175", "176", "177", "178", "179", "180", "181", "182", "183", "184", "185", "186", "187", "188", "189", "190", "191", "192", "193", "194", "195", "196", "197", "198", "199", "200", "201", "202", "203", "204", "205", "206", "207", "208", "209", "210", "211", "212", "213", "214", "215", "216", "217", "218", "219", "220", "221", "222", "223", "224", "225", "226", "227", "228", "229", "230", "231", "232", "233", "234", "235", "236", "237", "238", "239", "240", "241", "242", "243", "244", "245", "246", "247", "248", "249", "250", "251", "252", "253", "254", "255", "256", "257", "258", "259", "260", "261", "262", "263", "264", "265", "266", "267", "268", "269", "270", "271", "272", "273", "274", "275", "276", "277", "278", "279", "280", "281", "282", "283", "284", "285", "286", "287", "288", "289", "290", "291", "292", "293", "294", "295", "296", "297", "298", "299", "300", "301", "302", "303", "304", "305", "306", "307", "308", "309", "310", "311", "312", "313", "314", "315", "316", "317", "318", "319", "320", "321", "322", "323", "324", "325", "326", "327", "328", "329", "330", "331", "332", "333", "334", "335", "336", "337", "338", "339", "340", "341", "342", "343", "344", "345", "346", "347", "348", "349", "350", "351", "352", "353", "354", "355", "356", "357", "358", "359", "360", "361", "362", "363", "364", "365", "366", "367", "368", "369", "370", "371", "372", "373", "374", "375", "376", "377", "378", "379", "380", "381", "382", "383", "384", "385", "386", "387", "388", "389", "390", "391", "392", "393", "394", "395", "396", "397", "398", "399", "400", "401", "402", "403", "404", "405", "406", "407", "408", "409", "410", "411", "412", "413", "414", "415", "416", "417", "418", "419", "420", "421", "422", "423", "424", "425", "426", "427", "428", "429", "430", "431", "432", "433", "434", "435", "436", "437", "438", "439", "440", "441", "442", "443", "444", "445", "446", "447", "448", "449", "450", "451", "452", "453", "454", "455", "456", "457", "458", "459", "460", "461", "462", "463", "464", "465", "466", "467", "468", "469", "470", "471", "472", "473", "474", "475", "476", "477", "478", "479", "480", "481", "482", "483", "484", "485", "486", "487", "488", "489", "490", "491", "492", "493", "494", "495", "496", "497", "498", "499", "500", "501", "502", "503", "504", "505", "506", "507", "508", "509", "510", "511", "512", "513", "514", "515", "516", "517", "518", "519", "520", "521", "522", "523", "524", "525", "526", "527", "528", "529", "530", "531", "532", "533", "534", "535", "536", "537", "538", "539", "540", "541", "542", "543", "544", "545", "546", "547", "548", "549", "550", "551", "552", "553", "554", "555", "556", "557", "558", "559", "560", "561", "562", "563", "564", "565", "566", "567", "568", "569", "570", "571", "572", "573", "574", "575", "576", "577", "578", "579", "580", "581", "582", "583", "584", "585", "586", "587", "588", "589", "590", "591", "592", "593", "594", "595", "596", "597", "598", "599", "600", "601", "602", "603", "604", "605", "606", "607", "608", "609", "610", "611", "612", "613", "614", "615", "616", "617", "618", "619", "620", "621", "622", "623", "624", "625", "626", "627", "628", "629", "630", "631", "632", "633", "634", "635", "636", "637", "638", "639", "640", "641", "642", "643", "644", "645", "646", "647", "648", "649", "650", "651", "652", "653", "654", "655", "656", "657", "658", "659", "660", "661", "662", "663", "664", "665", "666", "667", "668", "669", "670", "671", "672", "673", "674", "675", "676", "677", "678", "679", "680", "681", "682", "683", "684", "685", "686", "687", "688", "689", "690", "691", "692", "693", "694", "695", "696", "697", "698", "699", "700", "701", "702", "703", "704", "705", "706", "707", "708", "709", "710", "711", "712", "713", "714", "715", "716", "717", "718", "719", "720", "721", "722", "723", "724", "725", "726", "727", "728", "729", "730", "731", "732", "733", "734", "735", "736", "737", "738", "739", "740", "741", "742", "743", "744", "745", "746", "747", "748", "749", "750", "751", "752", "753", "754", "755", "756", "757", "758", "759", "760", "761", "762", "763", "764", "765", "766", "767", "768", "769", "770", "771", "772", "773", "774", "775", "776", "777", "778", "779", "780", "781", "782", "783", "784", "785", "786", "787", "788", "789", "790", "791", "792", "793", "794", "795", "796", "797", "798", "799", "800", "801", "802", "803", "804", "805", "806", "807", "808", "809", "810", "811", "812", "813", "814", "815", "816", "817", "818", "819", "820", "821", "822", "823", "824", "825", "826", "827", "828", "829", "830", "831", "832", "833", "834", "835", "836", "837", "838", "839", "840", "841", "842", "843", "844", "845", "846", "847", "848", "849", "850", "851", "852", "853", "854", "855", "856", "857", "858", "859", "860", "861", "862", "863", "864", "865", "866", "867", "868", "869", "870", "871", "872", "873", "874", "875", "876", "877", "878", "879", "880", "881", "882", "883", "884", "885", "886", "887", "888", "889", "890", "891", "892", "893", "894", "895", "896", "897", "898", "899", "900", "901", "902", "903", "904", "905", "906", "907", "908", "909", "910", "911", "912", "913", "914", "915", "916", "917", "918", "919", "920", "921", "922", "923", "924", "925", "926", "927", "928", "929", "930", "931", "932", "933", "934", "935", "936", "937", "938", "939", "940", "941", "942", "943", "944", "945", "946", "947", "948", "949", "950", "951", "952", "953", "954", "955", "956", "957", "958", "959", "960", "961", "962", "963", "964", "965", "966", "967", "968", "969", "970", "971", "972", "973", "974", "975", "976", "977", "978", "979", "980", "981", "982", "983", "984", "985", "986", "987", "988", "989", "990", "991", "992", "993", "994", "995", "996", "997", "998", "999", "1000", "1001", "1002", "1003", "1004", "1005", "1006", "1007", "1008", "1009", "1010", "1011", "1012", "1013", "1014", "1015", "1016", "1017", "1018", "1019", "1020", "1021", "1022", "1023", "1024", "1025", "1026", "1027", "1028", "1029", "1030", "1031", "1032", "1033", "1034", "1035", "1036", "1037", "1038", "1039", "1040", "1041", "1042", "1043", "1044", "1045", "1046", "1047", "1048", "1049", "1050", "1051", "1052", "1053", "1054", "1055", "1056", "1057", "1058", "1059", "1060", "1061", "1062", "1063", "1064", "1065", "1066", "1067", "1068", "1069", "1070", "1071", "1072", "1073", "1074", "1075", "1076", "1077", "1078", "1079", "1080", "1081", "1082", "1083", "1084", "1085", "1086", "1087", "1088", "1089", "1090", "1091", "1092", "1093", "1094", "1095", "1096", "1097", "1098", "1099", "1100", "1101", "1102", "1103", "1104", "1105", "1106", "1107", "1108", "1109", "1110", "1111", "1112", "1113", "1114", "1115", "1116", "1117", "1118", "1119", "1120", "1121", "1122", "1123", "1124", "1125", "1126", "1127", "1128", "1129", "1130", "1131", "1132", "1133", "1134", "1135", "1136", "1137", "1138", "1139", "1140", "1141", "1142", "1143", "1144", "1145", "1146", "1147", "1148", "1149", "1150", "1151", "1152", "1153", "1154", "1155", "1156", "1157", "1158", "1159", "1160", "1161", "1162", "1163", "1164", "1165", "1166", "1167", "1168", "1169", "1170", "1171", "1172", "1173", "1174", "1175", "1176", "1177", "1178", "1179", "1180", "1181", "1182", "1183", "1184", "1185", "1186", "1187", "1188", "1189", "1190", "1191", "1192", "1193", "1194", "1195", "1196", "1197", "1198", "1199", "1200", "1201", "1202", "1203", "1204", "1205", "1206", "1207", "1208", "1209", "1210", "1211", "1212", "1213", "1214", "1215", "1216", "1217", "1218", "1219", "1220", "1221", "1222", "1223", "1224", "1225", "1226", "1227", "1228", "1229", "1230", "1231", "1232", "1233", "1234", "1235", "1236", "1237", "1238", "1239", "1240", "1241", "1242", "1243", "1244", "1245", "1246", "1247", "1248", "1249", "1250", "1251", "1252", "1253", "1254", "1255", "1256", "1257", "1258", "1259", "1260", "1261", "1262", "1263", "1264", "1265", "1266", "1267", "1268", "1269", "1270", "1271", "1272", "1273", "1274", "1275", "1276", "1277", "1278", "1279", "1280", "1281", "1282", "1283", "1284", "1285", "1286", "1287", "1288", "1289", "1290", "1291", "1292", "1293", "1294", "1295", "1296", "1297", "1298", "1299", "1300", "1301", "1302", "1303", "1304", "1305", 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"2806", "2807", "2808", "2809", "2810", "2811", "2812", "2813", "2814", "2815", "2816", "2817", "2818", "2819", "2820", "2821", "2822", "2823", "2824", "2825", "2826", "2827", "2828", "2829", "2830", "2831", "2832", "2833", "2834", "2835", "2836", "2837", "2838", "2839", "2840", "2841", "2842", "2843", "2844", "2845", "2846", "2847", "2848", "2849", "2850", "2851", "2852", "2853", "2854", "2855", "2856", "2857", "2858", "2859", "2860", "2861", "2862", "2863", "2864", "2865", "2866", "2867", "2868", "2869", "2870", "2871", "2872", "2873", "2874", "2875", "2876", "2877", "2878", "2879", "2880", "2881", "2882", "2883", "2884", "2885", "2886", "2887", "2888", "2889", "2890", "2891", "2892", "2893", "2894", "2895", "2896", "2897", "2898", "2899", "2900", "2901", "2902", "2903", "2904", "2905", "2906", "2907", "2908", "2909", "2910", "2911", "2912", "2913", "2914", "2915", "2916", "2917", "2918", "2919", "2920", "2921", "2922", "2923", "2924", "2925", "2926", "2927", "2928", "2929", "2930", "2931", "2932", "2933", "2934", "2935", "2936", "2937", "2938", "2939", "2940", "2941", "2942", "2943", "2944", "2945", "2946", "2947", "2948", "2949", "2950", "2951", "2952", "2953", "2954", "2955", "2956", "2957", "2958", "2959", "2960", "2961", "2962", "2963", "2964", "2965", "2966", "2967", "2968", "2969", "2970", "2971", "2972", "2973", "2974", "2975", "2976", "2977", "2978", "2979", "2980", "2981", "2982", "2983", "2984", "2985", "2986", "2987", "2988", "2989", "2990", "2991", "2992", "2993", "2994", "2995", "2996", "2997", "2998", "2999", "3000")), 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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(slide_id = 4L)), 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(f, data = dat, ...) 12: get_var_proportions(mx_data, metadata_cols, table = "raw", m = marker, formula_override) 13: run_var_proportions(mx_data, table = "both") 14: eval(code, test_env) 15: eval(code, test_env) 16: 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) 17: doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 20: doTryCatch(return(expr), name, parentenv, handler) 21: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 22: tryCatchList(expr, classes, parentenv, handlers) 23: 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) { }) 24: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter()) 25: test_that("plotting works", { mx_data = mx_dataset(mxnorm::mx_sample, "slide_id", "image_id", c("marker1_vals", "marker2_vals", "marker3_vals"), c("metadata1_vals")) mx_data = mx_normalize(mx_data, transform = "log10", method = "None") expect_error(plot_mx_proportions(mx_data)) expect_error(plot_mx_proportions(rnorm(100))) mx_data = run_var_proportions(mx_data, table = "both") expect_equal(class(plot_mx_proportions(mx_data)), c("gg", "ggplot"))}) 26: eval(code, test_env) 27: eval(code, test_env) 28: 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) 29: doTryCatch(return(expr), name, parentenv, handler) 30: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 31: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 32: doTryCatch(return(expr), name, parentenv, handler) 33: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 34: tryCatchList(expr, classes, parentenv, handlers) 35: 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) { }) 36: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new()) 37: source_file(path, env = env(env), desc = desc, error_call = error_call) 38: FUN(X[[i]], ...) 39: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call) 40: doTryCatch(return(expr), name, parentenv, handler) 41: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 42: tryCatchList(expr, classes, parentenv, handlers) 43: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) 44: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)) 45: 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) 46: 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) 47: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") 48: test_check("mxnorm") 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 ...sh: line 1: 2489963 Segmentation fault (core dumped) '/home/th798/R/R-release/bin/R' --vanilla --no-echo > '/tmp/th798/16120028/R-release/891/mxnorm.Rcheck/build_vignettes.log' 2>&1 < '/tmp/th798/16120028/Rtmph0lkK7/file25b6ea3fb095b0' ERROR Error(s) in re-building vignettes: --- re-building 'mxnorm-vignette.Rmd' using rmarkdown *** 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, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 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3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), p = 0:3000, Dim = c(4L, 3000L), Dimnames = list( c("slide1", "slide2", "slide3", "slide4"), 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", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", "111", "112", "113", "114", "115", "116", "117", "118", "119", "120", "121", "122", "123", "124", "125", "126", "127", "128", "129", "130", "131", "132", "133", "134", "135", "136", "137", "138", "139", "140", "141", "142", "143", "144", "145", "146", "147", "148", "149", "150", "151", "152", "153", "154", "155", "156", "157", "158", "159", "160", "161", "162", "163", "164", "165", "166", "167", "168", "169", "170", "171", "172", "173", "174", "175", "176", "177", "178", "179", "180", "181", "182", "183", "184", "185", "186", "187", "188", "189", "190", "191", "192", "193", "194", "195", "196", "197", "198", "199", "200", "201", "202", "203", "204", "205", "206", "207", "208", "209", "210", "211", "212", "213", "214", "215", "216", "217", "218", "219", "220", "221", "222", "223", "224", "225", "226", "227", "228", "229", "230", "231", "232", "233", "234", "235", "236", "237", "238", "239", "240", "241", "242", "243", "244", "245", "246", "247", "248", "249", "250", "251", "252", "253", "254", "255", "256", "257", "258", "259", "260", "261", "262", "263", "264", "265", "266", "267", "268", "269", "270", "271", "272", "273", "274", "275", "276", "277", "278", "279", "280", "281", "282", "283", "284", "285", "286", "287", "288", "289", "290", "291", "292", "293", "294", "295", "296", "297", "298", "299", "300", "301", "302", "303", "304", "305", "306", "307", "308", "309", "310", "311", "312", "313", "314", "315", "316", "317", "318", "319", "320", "321", "322", "323", "324", "325", "326", "327", "328", "329", "330", "331", "332", "333", "334", "335", "336", "337", "338", "339", "340", "341", "342", "343", "344", "345", "346", "347", "348", "349", "350", "351", "352", "353", "354", "355", "356", "357", "358", "359", "360", "361", "362", "363", "364", "365", "366", "367", "368", "369", "370", "371", "372", "373", "374", "375", "376", "377", "378", "379", "380", "381", "382", "383", "384", "385", "386", "387", "388", "389", "390", "391", "392", "393", "394", "395", "396", "397", "398", "399", "400", "401", "402", "403", "404", "405", "406", "407", "408", "409", "410", "411", "412", "413", "414", "415", "416", "417", "418", "419", "420", "421", "422", "423", "424", "425", "426", "427", "428", "429", "430", "431", "432", "433", "434", "435", "436", "437", "438", "439", "440", "441", "442", "443", "444", "445", "446", "447", "448", "449", "450", "451", "452", "453", "454", "455", "456", "457", "458", "459", "460", "461", "462", "463", "464", "465", "466", "467", "468", "469", "470", "471", "472", "473", "474", "475", "476", "477", "478", "479", "480", "481", "482", "483", "484", "485", "486", "487", "488", "489", "490", "491", "492", "493", "494", "495", "496", "497", "498", "499", "500", "501", "502", "503", "504", "505", "506", "507", "508", "509", "510", "511", "512", "513", "514", "515", "516", "517", "518", "519", "520", "521", "522", "523", "524", "525", "526", "527", "528", "529", "530", "531", "532", "533", "534", "535", "536", "537", "538", "539", "540", "541", "542", "543", "544", "545", "546", "547", "548", "549", "550", "551", "552", "553", "554", "555", "556", "557", "558", "559", "560", "561", "562", "563", "564", "565", "566", "567", "568", "569", "570", "571", "572", "573", "574", "575", "576", "577", "578", "579", "580", "581", "582", "583", "584", "585", "586", "587", "588", "589", "590", "591", "592", "593", "594", "595", "596", "597", "598", "599", "600", "601", "602", "603", "604", "605", "606", "607", "608", "609", "610", "611", "612", "613", "614", "615", "616", "617", "618", "619", "620", "621", "622", "623", "624", "625", "626", "627", "628", "629", "630", "631", "632", "633", "634", "635", "636", "637", "638", "639", "640", "641", "642", "643", "644", "645", "646", "647", "648", "649", "650", "651", "652", "653", "654", "655", "656", "657", "658", "659", "660", "661", "662", "663", "664", "665", "666", "667", "668", "669", "670", "671", "672", "673", "674", "675", "676", "677", "678", "679", "680", "681", "682", "683", "684", "685", "686", "687", "688", "689", "690", "691", "692", "693", "694", "695", "696", "697", "698", "699", "700", "701", "702", "703", "704", "705", "706", "707", "708", "709", "710", "711", "712", "713", "714", "715", "716", "717", "718", "719", "720", "721", "722", "723", "724", "725", "726", "727", "728", "729", "730", "731", "732", "733", "734", "735", "736", "737", "738", "739", "740", "741", "742", "743", "744", "745", "746", "747", "748", "749", "750", "751", "752", "753", "754", "755", "756", "757", "758", "759", "760", "761", "762", "763", "764", "765", "766", "767", "768", "769", "770", "771", "772", "773", "774", "775", "776", "777", "778", "779", "780", "781", "782", "783", "784", "785", "786", "787", "788", "789", "790", "791", "792", "793", "794", "795", "796", "797", "798", "799", "800", "801", "802", "803", "804", "805", "806", "807", "808", "809", "810", "811", "812", "813", "814", "815", "816", "817", "818", "819", "820", "821", "822", "823", "824", "825", "826", "827", "828", "829", "830", "831", "832", "833", "834", "835", "836", "837", "838", "839", "840", "841", "842", "843", "844", "845", "846", "847", "848", "849", "850", "851", "852", "853", "854", "855", "856", "857", "858", "859", "860", "861", "862", "863", "864", "865", "866", "867", "868", "869", "870", "871", "872", "873", "874", "875", "876", "877", "878", "879", "880", "881", "882", "883", "884", "885", "886", "887", "888", "889", "890", "891", "892", "893", "894", "895", "896", "897", "898", "899", "900", "901", "902", "903", "904", "905", "906", "907", "908", "909", "910", "911", "912", "913", "914", "915", "916", "917", "918", "919", "920", "921", "922", "923", "924", "925", "926", "927", "928", "929", "930", "931", "932", "933", "934", "935", "936", "937", "938", "939", "940", "941", "942", "943", "944", "945", "946", "947", "948", "949", "950", "951", "952", "953", "954", "955", "956", "957", "958", "959", "960", "961", "962", "963", "964", "965", "966", "967", "968", "969", "970", "971", "972", "973", "974", "975", "976", "977", "978", "979", "980", "981", "982", "983", "984", "985", "986", "987", "988", "989", "990", "991", "992", "993", "994", "995", "996", "997", "998", "999", "1000", "1001", "1002", "1003", "1004", "1005", "1006", "1007", "1008", "1009", "1010", "1011", "1012", "1013", "1014", "1015", "1016", "1017", "1018", "1019", "1020", "1021", "1022", "1023", "1024", "1025", "1026", "1027", "1028", "1029", "1030", "1031", "1032", "1033", "1034", "1035", "1036", "1037", "1038", "1039", "1040", "1041", "1042", "1043", "1044", "1045", "1046", "1047", "1048", "1049", "1050", "1051", "1052", "1053", "1054", "1055", "1056", "1057", "1058", "1059", "1060", "1061", "1062", "1063", "1064", "1065", "1066", "1067", "1068", "1069", "1070", "1071", "1072", "1073", "1074", "1075", "1076", "1077", "1078", "1079", "1080", "1081", "1082", "1083", "1084", "1085", "1086", "1087", "1088", "1089", "1090", "1091", "1092", "1093", "1094", "1095", "1096", "1097", "1098", "1099", "1100", "1101", "1102", "1103", "1104", "1105", "1106", "1107", "1108", "1109", "1110", "1111", "1112", "1113", "1114", "1115", "1116", "1117", "1118", "1119", "1120", "1121", "1122", "1123", "1124", "1125", "1126", "1127", "1128", "1129", "1130", "1131", "1132", "1133", "1134", "1135", "1136", "1137", "1138", "1139", "1140", "1141", "1142", "1143", "1144", "1145", "1146", "1147", "1148", "1149", "1150", "1151", "1152", "1153", "1154", "1155", "1156", "1157", "1158", "1159", "1160", "1161", "1162", "1163", "1164", "1165", "1166", "1167", "1168", "1169", "1170", "1171", "1172", "1173", "1174", "1175", "1176", "1177", "1178", "1179", "1180", "1181", "1182", "1183", "1184", "1185", "1186", "1187", "1188", "1189", "1190", "1191", "1192", "1193", "1194", "1195", "1196", "1197", "1198", "1199", "1200", "1201", "1202", "1203", "1204", "1205", "1206", "1207", "1208", "1209", "1210", "1211", "1212", "1213", "1214", "1215", "1216", "1217", "1218", "1219", "1220", "1221", "1222", "1223", "1224", "1225", "1226", "1227", "1228", "1229", "1230", "1231", "1232", "1233", "1234", "1235", "1236", "1237", "1238", "1239", "1240", "1241", "1242", "1243", "1244", "1245", "1246", "1247", "1248", "1249", "1250", "1251", "1252", "1253", "1254", "1255", "1256", "1257", "1258", "1259", "1260", "1261", "1262", "1263", 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"2514", "2515", "2516", "2517", "2518", "2519", "2520", "2521", "2522", "2523", "2524", "2525", "2526", "2527", "2528", "2529", "2530", "2531", "2532", "2533", "2534", "2535", "2536", "2537", "2538", "2539", "2540", "2541", "2542", "2543", "2544", "2545", "2546", "2547", "2548", "2549", "2550", "2551", "2552", "2553", "2554", "2555", "2556", "2557", "2558", "2559", "2560", "2561", "2562", "2563", "2564", "2565", "2566", "2567", "2568", "2569", "2570", "2571", "2572", "2573", "2574", "2575", "2576", "2577", "2578", "2579", "2580", "2581", "2582", "2583", "2584", "2585", "2586", "2587", "2588", "2589", "2590", "2591", "2592", "2593", "2594", "2595", "2596", "2597", "2598", "2599", "2600", "2601", "2602", "2603", "2604", "2605", "2606", "2607", "2608", "2609", "2610", "2611", "2612", "2613", "2614", "2615", "2616", "2617", "2618", "2619", "2620", "2621", "2622", "2623", "2624", "2625", "2626", "2627", "2628", "2629", "2630", "2631", "2632", "2633", "2634", "2635", "2636", "2637", "2638", 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"2764", "2765", "2766", "2767", "2768", "2769", "2770", "2771", "2772", "2773", "2774", "2775", "2776", "2777", "2778", "2779", "2780", "2781", "2782", "2783", "2784", "2785", "2786", "2787", "2788", "2789", "2790", "2791", "2792", "2793", "2794", "2795", "2796", "2797", "2798", "2799", "2800", "2801", "2802", "2803", "2804", "2805", "2806", "2807", "2808", "2809", "2810", "2811", "2812", "2813", "2814", "2815", "2816", "2817", "2818", "2819", "2820", "2821", "2822", "2823", "2824", "2825", "2826", "2827", "2828", "2829", "2830", "2831", "2832", "2833", "2834", "2835", "2836", "2837", "2838", "2839", "2840", "2841", "2842", "2843", "2844", "2845", "2846", "2847", "2848", "2849", "2850", "2851", "2852", "2853", "2854", "2855", "2856", "2857", "2858", "2859", "2860", "2861", "2862", "2863", "2864", "2865", "2866", "2867", "2868", "2869", "2870", "2871", "2872", "2873", "2874", "2875", "2876", "2877", "2878", "2879", "2880", "2881", "2882", "2883", "2884", "2885", "2886", "2887", "2888", 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4L), Dimnames = list(NULL, NULL), x = c(1, 1, 1, 1), factors = list()), Lind = c(1L, 1L, 1L, 1L), n = 3000L, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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(marker1_vals = c(15, 11, 12, 11, 12, 11, 16, 12, 11, 10, 15, 14, 14, 13, 14, 11, 12, 16, 16, 13, 13, 12, 9, 11, 13, 14, 14, 11, 11, 11, 13, 12, 13, 12, 13, 10, 13, 11, 13, 12, 13, 11, 15, 14, 13, 13, 14, 13, 8, 14, 12, 13, 15, 11, 13, 15, 13, 10, 11, 14, 14, 15, 11, 14, 13, 11, 13, 13, 11, 12, 11, 12, 11, 14, 15, 12, 14, 14, 11, 10, 10, 14, 15, 14, 11, 12, 13, 12, 14, 12, 12, 16, 14, 11, 12, 9, 10, 12, 10, 12, 12, 11, 9, 13, 13, 10, 12, 14, 15, 11, 11, 12, 12, 11, 11, 12, 13, 12, 14, 11, 12, 15, 12, 12, 12, 15, 13, 17, 12, 13, 12, 14, 8, 13, 13, 14, 12, 12, 16, 14, 12, 11, 13, 12, 13, 16, 13, 15, 11, 14, 13, 11, 14, 12, 13, 10, 10, 13, 13, 16, 13, 9, 12, 16, 10, 13, 13, 11, 12, 12, 13, 12, 12, 13, 14, 10, 15, 14, 12, 13, 12, 13, 12, 15, 12, 10, 12, 14, 8, 12, 15, 14, 13, 10, 15, 10, 12, 12, 11, 11, 14, 15, 11, 11, 11, 11, 13, 15, 10, 9, 11, 14, 12, 13, 11, 12, 13, 13, 12, 11, 10, 11, 14, 10, 12, 12, 13, 17, 11, 9, 11, 13, 12, 12, 14, 17, 12, 10, 11, 12, 14, 12, 12, 12, 10, 12, 11, 13, 12, 12, 11, 10, 13, 10, 12, 12, 15, 16, 13, 12, 12, 15, 14, 14, 12, 12, 12, 11, 12, 14, 12, 10, 13, 14, 10, 15, 12, 11, 13, 11, 15, 12, 13, 11, 11, 12, 12, 13, 16, 15, 12, 13, 15, 13, 15, 10, 12, 12, 11, 16, 17, 11, 13, 12, 12, 11, 15, 14, 13, 12, 10, 12, 12, 13, 12, 11, 11, 11, 11, 15, 13, 13, 10, 11, 10, 11, 10, 9, 13, 13, 8, 10, 11, 14, 12, 11, 9, 12, 13, 11, 10, 12, 9, 13, 12, 15, 13, 15, 11, 14, 12, 12, 10, 10, 9, 12, 10, 15, 14, 18, 11, 16, 10, 11, 12, 15, 14, 9, 14, 12, 12, 8, 10, 12, 13, 14, 13, 13, 14, 15, 11, 12, 13, 11, 13, 12, 14, 11, 11, 10, 10, 16, 12, 13, 14, 13, 11, 10, 11, 12, 12, 17, 16, 10, 13, 13, 10, 12, 11, 19, 14, 10, 14, 12, 11, 10, 13, 11, 13, 12, 13, 10, 12, 13, 9, 13, 15, 14, 11, 10, 10, 10, 14, 14, 13, 15, 10, 14, 15, 15, 12, 13, 16, 8, 11, 13, 15, 13, 11, 12, 9, 12, 12, 11, 12, 11, 13, 10, 14, 9, 12, 10, 13, 12, 15, 13, 10, 9, 12, 13, 14, 14, 11, 16, 12, 11, 14, 13, 12, 13, 14, 14, 11, 12, 12, 14, 14, 11, 14, 14, 14, 15, 12, 13, 11, 15, 15, 11, 12, 11, 12, 11, 13, 13, 12, 11, 14, 13, 13, 14, 12, 15, 14, 12, 11, 12, 14, 11, 15, 14, 14, 12, 14, 13, 10, 12, 11, 12, 12, 11, 11, 10, 11, 10, 12, 15, 12, 12, 12, 16, 14, 11, 11, 12, 11, 12, 8, 13, 13, 11, 13, 12, 10, 12, 12, 12, 12, 11, 12, 14, 13, 16, 12, 15, 12, 15, 14, 13, 12, 11, 11, 12, 13, 11, 14, 12, 12, 12, 11, 12, 13, 16, 13, 11, 12, 13, 11, 9, 13, 11, 13, 13, 15, 13, 13, 13, 12, 11, 14, 12, 13, 16, 11, 15, 11, 14, 13, 13, 15, 12, 11, 13, 18, 11, 10, 12, 11, 13, 11, 13, 13, 14, 12, 12, 16, 9, 14, 14, 13, 12, 13, 12, 14, 15, 13, 10, 10, 13, 9, 11, 14, 10, 15, 13, 9, 11, 11, 11, 13, 12, 12, 13, 10, 9, 11, 12, 8, 14, 11, 12, 12, 10, 15, 14, 9, 11, 12, 10, 14, 14, 14, 10, 11, 13, 11, 13, 12, 13, 10, 11, 10, 11, 10, 13, 11, 13, 11, 11, 11, 16, 11, 14, 13, 13, 11, 15, 12, 12, 13, 11, 14, 14, 9, 18, 14, 12, 13, 10, 8, 13, 13, 10, 13, 13, 15, 13, 14, 11, 11, 13, 11, 13, 16, 13, 14, 14, 12, 12, 15, 13, 15, 12, 11, 15, 13, 13, 11, 15, 10, 12, 10, 14, 11, 14, 12, 14, 13, 15, 13, 17, 18, 24, 24, 23, 23, 20, 17, 25, 17, 25, 14, 21, 20, 19, 22, 26, 26, 21, 22, 22, 20, 16, 19, 15, 15, 17, 32, 23, 23, 22, 18, 18, 23, 22, 17, 18, 18, 19, 23, 21, 17, 16, 27, 25, 20, 16, 18, 23, 18, 15, 16, 25, 20, 22, 17, 21, 17, 21, 21, 20, 17, 21, 20, 18, 21, 20, 20, 17, 18, 30, 21, 18, 17, 20, 21, 20, 22, 21, 22, 21, 25, 17, 20, 20, 24, 18, 19, 23, 22, 24, 16, 21, 17, 24, 17, 19, 22, 16, 21, 19, 20, 20, 17, 21, 24, 16, 23, 22, 17, 21, 24, 21, 19, 20, 17, 21, 14, 21, 19, 18, 23, 18, 16, 23, 20, 16, 21, 25, 20, 24, 15, 24, 18, 21, 14, 22, 17, 20, 25, 21, 21, 14, 17, 14, 20, 22, 16, 22, 26, 25, 20, 19, 17, 17, 19, 19, 22, 29, 20, 26, 21, 26, 20, 26, 21, 19, 19, 18, 19, 20, 20, 19, 15, 21, 26, 16, 21, 19, 19, 17, 15, 19, 19, 14, 22, 22, 22, 20, 25, 17, 21, 23, 23, 16, 21, 21, 23, 23, 13, 22, 23, 18, 23, 21, 23, 20, 26, 20, 18, 21, 21, 22, 19, 19, 17, 19, 21, 22, 15, 19, 24, 19, 22, 23, 17, 18, 23, 18, 18, 16, 23, 25, 19, 22, 25, 19, 18, 24, 23, 19, 19, 17, 18, 21, 20, 19, 19, 21, 27, 23, 27, 18, 21, 22, 20, 17, 21, 22, 19, 27, 16, 17, 25, 17, 21, 24, 24, 22, 14, 20, 22, 16, 13, 21, 19, 18, 19, 16, 26, 22, 22, 14, 18, 16, 26, 28, 22, 19, 15, 23, 15, 18, 31, 20, 26, 17, 16, 15, 18, 16, 22, 18, 23, 21, 22, 16, 19, 19, 22, 18, 21, 19, 18, 22, 19, 20, 19, 15, 25, 17, 18, 25, 23, 24, 21, 19, 20, 15, 17, 19, 21, 20, 19, 24, 20, 17, 23, 18, 18, 16, 21, 20, 22, 20, 16, 17, 18, 15, 23, 23, 17, 19, 20, 24, 16, 15, 21, 20, 23, 18, 23, 19, 20, 23, 20, 15, 18, 13, 20, 19, 18, 19, 20, 23, 22, 20, 21, 20, 23, 24, 16, 16, 23, 17, 17, 20, 20, 19, 22, 18, 24, 19, 20, 17, 25, 24, 18, 17, 18, 18, 21, 22, 16, 18, 19, 18, 14, 25, 18, 20, 26, 22, 15, 20, 16, 22, 17, 17, 17, 19, 23, 23, 23, 24, 21, 20, 17, 22, 25, 20, 21, 22, 17, 23, 16, 16, 20, 25, 22, 23, 18, 21, 21, 23, 20, 18, 19, 19, 15, 22, 19, 22, 14, 18, 18, 21, 22, 22, 20, 22, 19, 22, 20, 28, 18, 23, 16, 22, 20, 19, 22, 18, 21, 20, 16, 16, 19, 16, 21, 24, 20, 18, 23, 19, 18, 28, 19, 20, 17, 17, 16, 16, 24, 18, 17, 21, 19, 22, 21, 22, 18, 18, 19, 21, 17, 15, 15, 22, 19, 22, 15, 18, 24, 22, 18, 20, 22, 21, 20, 14, 16, 19, 19, 19, 20, 18, 22, 20, 21, 19, 23, 22, 18, 28, 17, 20, 25, 24, 18, 23, 19, 20, 25, 20, 19, 20, 15, 16, 21, 18, 20, 19, 22, 20, 25, 20, 17, 22, 18, 14, 20, 19, 19, 23, 28, 17, 24, 16, 26, 17, 15, 20, 19, 20, 18, 24, 22, 21, 21, 24, 23, 20, 18, 25, 17, 27, 18, 24, 20, 23, 26, 23, 19, 23, 17, 21, 19, 24, 17, 19, 23, 18, 22, 22, 21, 17, 23, 22, 23, 18, 14, 15, 14, 26, 25, 23, 21, 20, 24, 15, 17, 25, 19, 19, 18, 17, 20, 25, 15, 17, 26, 22, 18, 18, 19, 22, 23, 27, 17, 16, 18, 24, 29, 14, 21, 19, 16, 18, 14, 21, 24, 27, 20, 17, 25, 18, 16, 25, 16, 17, 21, 20, 18, 19, 31, 24, 21, 23, 18, 13, 21, 20, 18, 21, 17, 18, 26, 22, 24, 21, 16, 15, 22, 18, 17, 20, 19, 28, 16, 22, 19, 20, 18, 23, 14, 22, 22, 24, 25, 17, 19, 21, 21, 20, 18, 17, 29, 23, 23, 19, 26, 24, 16, 20, 19, 23, 18, 20, 22, 18, 17, 23, 18, 24, 18, 19, 23, 18, 19, 22, 22, 20, 22, 21, 18, 19, 22, 21, 20, 18, 16, 19, 19, 18, 15, 24, 20, 25, 23, 24, 96, 85, 90, 93, 92, 98, 93, 76, 93, 93, 96, 97, 70, 96, 88, 95, 89, 88, 96, 92, 76, 84, 89, 81, 83, 99, 95, 84, 92, 77, 97, 93, 91, 98, 87, 96, 95, 78, 90, 89, 99, 94, 94, 95, 95, 96, 99, 98, 95, 95, 93, 99, 96, 96, 92, 87, 98, 89, 96, 96, 84, 94, 94, 93, 94, 87, 95, 89, 96, 97, 95, 90, 99, 95, 88, 95, 87, 98, 97, 99, 100, 99, 97, 90, 90, 84, 74, 84, 96, 95, 99, 99, 84, 84, 83, 80, 80, 67, 80, 93, 96, 98, 73, 91, 100, 83, 97, 76, 98, 96, 69, 98, 99, 93, 88, 77, 89, 90, 98, 93, 97, 99, 99, 96, 88, 98, 70, 93, 91, 95, 97, 98, 96, 98, 92, 89, 79, 79, 98, 90, 93, 96, 84, 85, 96, 70, 89, 89, 77, 86, 70, 90, 53, 95, 82, 97, 95, 81, 85, 96, 97, 96, 94, 92, 92, 89, 88, 99, 100, 100, 98, 89, 98, 100, 97, 100, 98, 98, 82, 98, 99, 96, 91, 92, 88, 94, 99, 99, 96, 75, 80, 79, 96, 87, 100, 87, 93, 88, 98, 81, 91, 86, 97, 93, 77, 97, 92, 85, 91, 93, 93, 90, 91, 98, 100, 99, 96, 95, 87, 97, 98, 91, 87, 94, 85, 100, 99, 96, 85, 100, 90, 100, 91, 80, 97, 61, 58, 83, 93, 99, 94, 90, 95, 85, 98, 94, 81, 99, 95, 64, 94, 86, 90, 88, 97, 94, 81, 89, 96, 97, 90, 98, 93, 98, 95, 95, 100, 95, 94, 96, 100, 99, 100, 81, 98, 99, 86, 81, 99, 90, 77, 99, 97, 99, 79, 94, 92, 95, 90, 99, 94, 84, 83, 95, 94, 93, 86, 99, 99, 98, 75, 93, 96, 91, 92, 100, 91, 86, 100, 92, 95, 99, 79, 83, 84, 93, 84, 97, 94, 95, 93, 89, 91, 98, 99, 87, 79, 87, 97, 89, 84, 90, 99, 86, 100, 82, 98, 91, 88, 85, 97, 91, 82, 98, 66, 80, 97, 95, 79, 99, 94, 91, 93, 94, 90, 96, 99, 79, 92, 81, 90, 93, 89, 85, 82, 91, 88, 81, 95, 95, 93, 95, 95, 86, 96, 94, 99, 99, 82, 84, 86, 96, 98, 94, 86, 100, 91, 96, 97, 99, 97, 91, 97, 95, 78, 98, 93, 90, 99, 90, 91, 90, 96, 98, 96, 85, 88, 89, 77, 96, 91, 87, 97, 97, 95, 61, 91, 93, 81, 99, 98, 95, 96, 96, 85, 64, 97, 96, 96, 91, 90, 96, 91, 95, 97, 97, 99, 93, 74, 96, 85, 96, 99, 97, 100, 99, 94, 94, 100, 65, 92, 93, 85, 95, 95, 86, 95, 97, 99, 91, 78, 91, 89, 94, 99, 92, 82, 100, 91, 99, 97, 97, 96, 94, 85, 96, 84, 92, 96, 98, 96, 96, 94, 91, 73, 100, 100, 97, 86, 98, 92, 90, 92, 83, 97, 92, 94, 94, 93, 87, 96, 93, 96, 93, 96, 89, 89, 96, 94, 100, 89, 92, 98, 86, 93, 98, 99, 87, 85, 93, 92, 93, 97, 97, 98, 57, 95, 87, 95, 100, 87, 91, 94, 79, 76, 94, 98, 83, 98, 87, 97, 100, 83, 92, 98, 94, 95, 91, 97, 83, 99, 95, 99, 96, 90, 75, 95, 100, 94, 84, 94, 96, 97, 94, 66, 95, 83, 89, 100, 72, 96, 94, 96, 83, 97, 84, 88, 97, 92, 89, 81, 99, 93, 92, 95, 84, 74, 88, 81, 95, 97, 89, 82, 86, 92, 83, 83, 92, 93, 99, 78, 93, 85, 98, 99, 99, 97, 82, 89, 94, 99, 83, 95, 96, 75, 73, 97, 91, 84, 95, 78, 96, 61, 100, 77, 93, 81, 96, 96, 93, 99, 97, 91, 96, 89, 71, 92, 100, 100, 96, 80, 94, 90, 100, 100, 97, 86, 93, 74, 86, 99, 82, 94, 99, 95, 96, 78, 92, 74, 83, 94, 89, 66, 95, 94, 90, 83, 98, 90, 91, 96, 95, 86, 99, 99, 100, 88, 80, 91, 99, 86, 94, 92, 86, 100, 98, 93, 97, 77, 75, 100, 97, 98, 93, 86, 97, 100, 88, 97, 95, 98, 95, 90, 80, 95, 88, 78, 98, 94, 94, 80, 92, 100, 93, 96, 98, 93, 93, 93, 91, 68, 95, 100, 96, 87, 81, 97, 92, 85, 59, 73, 98, 94, 72, 88, 77, 86, 99, 98, 93, 88, 82, 96, 85, 91, 100, 81, 87, 94, 96, 57, 30, 37, 46, 47, 50, 32, 60, 38, 48, 49, 42, 45, 50, 58, 37, 58, 54, 57, 32, 32, 44, 38, 41, 46, 53, 34, 40, 43, 41, 55, 49, 44, 42, 54, 50, 39, 44, 55, 56, 56, 49, 58, 39, 54, 58, 59, 49, 51, 38, 40, 48, 54, 40, 54, 32, 36, 60, 43, 36, 52, 42, 34, 54, 38, 40, 42, 34, 41, 41, 53, 58, 45, 44, 35, 43, 53, 46, 52, 49, 34, 33, 45, 33, 50, 58, 40, 32, 57, 42, 45, 60, 57, 60, 40, 43, 46, 40, 58, 49, 44, 38, 43, 43, 33, 30, 54, 34, 51, 41, 53, 30, 47, 52, 48, 41, 32, 50, 55, 30, 33, 39, 41, 44, 50, 32, 51, 34, 30, 53, 56, 37, 39, 36, 50, 39, 43, 50, 46, 30, 39, 55, 31, 53, 45, 42, 42, 42, 48, 39, 30, 57, 46, 59, 60, 52, 40, 46, 55, 54, 58, 37, 45, 45, 60, 30, 32, 49, 30, 38, 45, 30, 31, 52, 53, 33, 51, 39, 46, 47, 51, 43, 45, 44, 41, 40, 47, 39, 40, 35, 30, 35, 48, 50, 60, 34, 30, 39, 45, 59, 49, 60, 38, 35, 35, 42, 34, 40, 57, 47, 44, 55, 57, 49, 44, 36, 46, 60, 55, 31, 54, 54, 30, 60, 37, 30, 41, 45, 46, 36, 35, 51, 33, 48, 30, 53, 34, 34, 42, 42, 59, 58, 60, 54, 56, 38, 54, 60, 55, 55, 58, 37, 37, 43, 52, 38, 59, 31, 45, 46, 50, 44, 30, 51, 37, 31, 60, 52, 40, 55, 34, 53, 60, 39, 37, 34, 54, 37, 53, 47, 50, 35, 48, 53, 41, 46, 33, 36, 45, 51, 37, 46, 30, 51, 48, 34, 34, 31, 56, 33, 39, 40, 42, 50, 56, 52, 49, 40, 39, 50, 48, 42, 58, 34, 37, 44, 32, 48, 50, 34, 55, 34, 34, 49, 56, 48, 45, 31, 43, 49, 43, 38, 54, 41, 52, 43, 60, 39, 41, 38, 38, 40, 58, 35, 35, 40, 55, 59, 38, 43, 49, 48, 48, 31, 45, 59, 57, 40, 39, 35, 35, 49, 35, 60, 33, 39, 32, 37, 44, 32, 30, 32, 46, 33, 49, 40, 45, 45, 47, 51, 40, 55, 60, 30, 49, 33, 53, 57, 51, 34, 56, 56, 43, 43, 51, 31, 39, 31, 51, 58, 37, 60, 53, 54, 50, 30, 34, 57, 56, 49, 47, 44, 50, 40, 35, 40, 58, 60, 40, 33, 39, 40, 60, 53, 58, 54, 32, 40, 33, 42, 33, 54, 47, 41, 44, 46, 49, 50, 39, 54, 47, 44, 58, 54, 55, 49, 42, 50, 55, 58, 31, 49, 31, 40, 43, 32, 47, 49, 49, 45, 36, 59, 34, 58, 50, 58, 45, 50, 55, 40, 49, 41, 45, 35, 43, 48, 59, 32, 59, 40, 54, 51, 55, 59, 50, 33, 51, 55, 60, 36, 34, 44, 34, 37, 35, 55, 46, 59, 38, 44, 46, 52, 50, 34, 44, 40, 43, 57, 39, 47, 57, 37, 56, 31, 49, 56, 34, 48, 39, 55, 52, 55, 53, 53, 39, 30, 45, 42, 56, 56, 38, 41, 30, 33, 60, 51, 47, 35, 52, 55, 31, 44, 44, 34, 56, 46, 37, 45, 37, 38, 56, 51, 35, 52, 32, 44, 45, 54, 31, 53, 50, 45, 40, 31, 49, 36, 44, 59, 36, 34, 34, 42, 30, 56, 40, 36, 35, 37, 56, 42, 45, 37, 37, 51, 34, 39, 40, 53, 41, 45, 34, 48, 49, 45, 34, 54, 41, 46, 52, 49, 59, 49, 53, 43, 55, 54, 42, 50, 36, 54, 34, 42, 51, 45, 33, 48, 53, 48, 49, 36, 40, 56, 54, 47, 53, 46, 55, 39, 38, 53, 39, 51, 48, 32, 54, 56, 45, 55, 50, 55, 56, 49, 57, 34, 50, 35, 33, 36, 44, 33, 52, 59, 49, 31, 38, 50, 39, 42, 31, 32, 59, 54, 56, 59, 50, 35, 46, 52, 52, 37, 56, 55, 58, 31, 47, 32, 52, 43, 46, 39, 36, 52, 57, 43, 42, 52, 43, 52, 47, 57, 40, 35, 55, 58, 38, 60, 52, 44, 59, 54, 50, 42, 60, 46, 46, 39, 40, 30, 30, 48, 56, 35, 60, 42, 34, 42, 44, 38, 55, 31, 35, 56, 60, 43, 57, 41, 48, 31, 50, 39, 50, 42, 46, 39, 58, 42, 50, 31, 35, 49, 49, 48, 52, 53, 52, 32, 47, 46, 60, 60), slide_id = 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, 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, 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, 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, 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, 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, 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, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 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3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), p = 0:3000, Dim = c(4L, 3000L), Dimnames = list( c("slide1", "slide2", "slide3", "slide4"), 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", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", 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3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), p = 0:3000, Dim = c(4L, 3000L), Dimnames = list(c("slide1", "slide2", "slide3", "slide4"), 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", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", 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"337", "338", "339", "340", "341", "342", "343", "344", "345", "346", "347", "348", "349", "350", "351", "352", "353", "354", "355", "356", "357", "358", "359", "360", "361", "362", "363", "364", "365", "366", "367", "368", "369", "370", "371", "372", "373", "374", "375", "376", "377", "378", "379", "380", "381", "382", "383", "384", "385", "386", "387", "388", "389", "390", "391", "392", "393", "394", "395", "396", "397", "398", "399", "400", "401", "402", "403", "404", "405", "406", "407", "408", "409", "410", "411", "412", "413", "414", "415", "416", "417", "418", "419", "420", "421", "422", "423", "424", "425", "426", "427", "428", "429", "430", "431", "432", "433", "434", "435", "436", "437", "438", "439", "440", "441", "442", "443", "444", "445", "446", "447", "448", "449", "450", "451", "452", "453", "454", "455", "456", "457", "458", "459", "460", "461", "462", "463", "464", "465", "466", "467", "468", "469", "470", "471", "472", "473", "474", "475", "476", "477", "478", "479", "480", "481", "482", "483", "484", "485", "486", "487", "488", "489", "490", "491", "492", "493", "494", "495", "496", "497", "498", "499", "500", "501", "502", "503", "504", "505", "506", "507", "508", "509", "510", "511", "512", "513", "514", "515", "516", "517", "518", "519", "520", "521", "522", "523", "524", "525", "526", "527", "528", "529", "530", "531", "532", "533", "534", "535", "536", "537", "538", "539", "540", "541", "542", "543", "544", "545", "546", "547", "548", "549", "550", "551", "552", "553", "554", "555", "556", "557", "558", "559", "560", "561", "562", "563", "564", "565", "566", "567", "568", "569", "570", "571", "572", "573", "574", "575", "576", "577", "578", "579", "580", "581", "582", "583", "584", "585", "586", "587", "588", "589", "590", "591", "592", "593", "594", "595", "596", "597", "598", "599", "600", "601", "602", "603", "604", "605", "606", "607", "608", "609", "610", "611", "612", "613", "614", "615", "616", "617", "618", "619", "620", "621", "622", "623", "624", "625", "626", "627", "628", "629", "630", "631", "632", "633", "634", "635", "636", "637", "638", "639", "640", "641", "642", "643", "644", "645", "646", "647", "648", "649", "650", "651", "652", "653", "654", "655", "656", "657", "658", "659", "660", "661", "662", "663", "664", "665", "666", "667", "668", "669", "670", "671", "672", "673", "674", "675", "676", "677", "678", "679", "680", "681", "682", "683", "684", "685", "686", "687", "688", "689", "690", "691", "692", "693", "694", "695", "696", "697", "698", "699", "700", "701", "702", "703", "704", "705", "706", "707", "708", "709", "710", "711", "712", "713", "714", "715", "716", "717", "718", "719", "720", "721", "722", "723", "724", "725", "726", "727", "728", "729", "730", "731", "732", "733", "734", "735", "736", "737", "738", "739", "740", "741", "742", "743", "744", "745", "746", "747", "748", "749", "750", "751", "752", "753", "754", "755", "756", "757", "758", "759", "760", "761", "762", "763", "764", "765", "766", "767", "768", "769", "770", "771", "772", "773", "774", "775", "776", "777", "778", "779", "780", "781", "782", "783", "784", "785", "786", "787", "788", "789", "790", "791", "792", "793", "794", "795", "796", "797", "798", "799", "800", "801", "802", "803", "804", "805", "806", "807", "808", "809", "810", "811", "812", "813", "814", "815", "816", "817", "818", "819", "820", "821", "822", "823", "824", "825", "826", "827", "828", "829", "830", "831", "832", "833", "834", "835", "836", "837", "838", "839", "840", "841", "842", "843", "844", "845", "846", "847", "848", "849", "850", "851", "852", "853", "854", "855", "856", "857", "858", "859", "860", "861", "862", "863", "864", "865", "866", "867", "868", "869", "870", "871", "872", "873", "874", "875", "876", "877", "878", "879", "880", "881", "882", "883", "884", "885", "886", "887", "888", "889", "890", "891", "892", "893", "894", "895", "896", "897", "898", "899", "900", "901", "902", "903", "904", "905", "906", "907", "908", "909", "910", "911", "912", "913", "914", "915", "916", "917", "918", "919", "920", "921", "922", "923", "924", "925", "926", "927", "928", "929", "930", "931", "932", "933", "934", "935", "936", "937", "938", "939", "940", "941", "942", "943", "944", "945", "946", "947", "948", "949", "950", "951", "952", "953", "954", "955", "956", "957", "958", "959", "960", "961", "962", "963", "964", "965", "966", "967", "968", "969", "970", "971", "972", "973", "974", "975", "976", "977", "978", "979", "980", "981", "982", "983", "984", "985", "986", "987", "988", "989", "990", "991", "992", "993", "994", "995", "996", "997", "998", "999", "1000", "1001", "1002", "1003", "1004", "1005", "1006", "1007", "1008", "1009", "1010", "1011", "1012", "1013", "1014", "1015", "1016", "1017", "1018", "1019", "1020", "1021", "1022", "1023", "1024", "1025", "1026", "1027", "1028", "1029", "1030", "1031", "1032", "1033", "1034", "1035", "1036", "1037", "1038", "1039", "1040", "1041", "1042", "1043", "1044", 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"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(f, data = dat, ...) 12: get_var_proportions(mx_data, metadata_cols, table = "raw", m = marker, formula_override) 13: run_var_proportions(mx_data, table = "both", metadata_cols = NULL, formula_override = NULL, save_models = FALSE) 14: eval(expr, envir, enclos) 15: eval(expr, envir, enclos) 16: eval_with_user_handlers(expr, envir, enclos, user_handlers) 17: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)) 18: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler) 19: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)) 20: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))) 21: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing) 22: evaluate::evaluate(...) 23: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) 24: in_dir(input_dir(), expr) 25: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 26: eng_r(options) 27: block_exec(params) 28: call_block(x) 29: process_group(group) 30: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)) 31: withCallingHandlers(expr, error = function(e) { loc = if (is.function(fun)) trimws(fun(label)) else "" if (loc != "") loc = sprintf(" at lines %s", loc) message(one_string(handler(e, loc)))}) 32: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 33: process_file(text, output) 34: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 35: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 36: vweave_rmarkdown(...) 37: engine$weave(file, quiet = quiet, encoding = enc) 38: doTryCatch(return(expr), name, parentenv, handler) 39: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 40: tryCatchList(expr, classes, parentenv, handlers) 41: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 42: tools::buildVignettes(dir = "/tmp/th798/16120028/R-release/891/mxnorm.Rcheck/vign_test/mxnorm", skip = TRUE, ser_elibs = "/tmp/th798/16120028/Rtmph0lkK7/file25b6ea51a8845.rds") An irrecoverable exception occurred. R is aborting now ... * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 1 NOTE See '/tmp/th798/16120028/R-release/891/mxnorm.Rcheck/00check.log' for details. [1] "2025-03-26 01:36:35 MST" [1] "2025-03-26 01:36:35 MST" Installing package into '/tmp/th798/16120028/R-release/891/library' (as 'lib' is unspecified) * installing *source* package 'data.table' ... ** 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/th798/16120028/R-release/891/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] "2025-03-26 01:36:56 MST" * using log directory '/tmp/th798/16120028/R-release/891/mxnorm.Rcheck' * using R version 4.4.3 (2025-02-28) * 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 'mxnorm/DESCRIPTION' ... OK * this is package 'mxnorm' version '1.0.3' * 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 'mxnorm' 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: 'e1071' 'glue' All declared Imports should be used. * 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ...sh: line 1: 2502863 Segmentation fault (core dumped) LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/home/th798/R/R-release/bin/R' --vanilla > 'mxnorm-Ex.Rout' 2>&1 < 'mxnorm-Ex.R' ERROR Running examples in 'mxnorm-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plot_mx_proportions > ### Title: Visualize variance proportions by marker and table > ### Aliases: plot_mx_proportions > > ### ** Examples > > mx_data = mx_dataset(mxnorm::mx_sample, "slide_id", "image_id", + c("marker1_vals","marker2_vals","marker3_vals"), + c("metadata1_vals")) > mx_data = mx_normalize(mx_data, transform="log10",method="None") > mx_data = run_var_proportions(mx_data, table="both") *** 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$initialize(...) 4: 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3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), p = 0:3000, Dim = c(4L, 3000L), Dimnames = list( c("slide1", "slide2", "slide3", "slide4"), c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", 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1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)) 8: do.call(merPredD$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(marker1_vals = c(15, 11, 12, 11, 12, 11, 16, 12, 11, 10, 15, 14, 14, 13, 14, 11, 12, 16, 16, 13, 13, 12, 9, 11, 13, 14, 14, 11, 11, 11, 13, 12, 13, 12, 13, 10, 13, 11, 13, 12, 13, 11, 15, 14, 13, 13, 14, 13, 8, 14, 12, 13, 15, 11, 13, 15, 13, 10, 11, 14, 14, 15, 11, 14, 13, 11, 13, 13, 11, 12, 11, 12, 11, 14, 15, 12, 14, 14, 11, 10, 10, 14, 15, 14, 11, 12, 13, 12, 14, 12, 12, 16, 14, 11, 12, 9, 10, 12, 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35, 40, 55, 59, 38, 43, 49, 48, 48, 31, 45, 59, 57, 40, 39, 35, 35, 49, 35, 60, 33, 39, 32, 37, 44, 32, 30, 32, 46, 33, 49, 40, 45, 45, 47, 51, 40, 55, 60, 30, 49, 33, 53, 57, 51, 34, 56, 56, 43, 43, 51, 31, 39, 31, 51, 58, 37, 60, 53, 54, 50, 30, 34, 57, 56, 49, 47, 44, 50, 40, 35, 40, 58, 60, 40, 33, 39, 40, 60, 53, 58, 54, 32, 40, 33, 42, 33, 54, 47, 41, 44, 46, 49, 50, 39, 54, 47, 44, 58, 54, 55, 49, 42, 50, 55, 58, 31, 49, 31, 40, 43, 32, 47, 49, 49, 45, 36, 59, 34, 58, 50, 58, 45, 50, 55, 40, 49, 41, 45, 35, 43, 48, 59, 32, 59, 40, 54, 51, 55, 59, 50, 33, 51, 55, 60, 36, 34, 44, 34, 37, 35, 55, 46, 59, 38, 44, 46, 52, 50, 34, 44, 40, 43, 57, 39, 47, 57, 37, 56, 31, 49, 56, 34, 48, 39, 55, 52, 55, 53, 53, 39, 30, 45, 42, 56, 56, 38, 41, 30, 33, 60, 51, 47, 35, 52, 55, 31, 44, 44, 34, 56, 46, 37, 45, 37, 38, 56, 51, 35, 52, 32, 44, 45, 54, 31, 53, 50, 45, 40, 31, 49, 36, 44, 59, 36, 34, 34, 42, 30, 56, 40, 36, 35, 37, 56, 42, 45, 37, 37, 51, 34, 39, 40, 53, 41, 45, 34, 48, 49, 45, 34, 54, 41, 46, 52, 49, 59, 49, 53, 43, 55, 54, 42, 50, 36, 54, 34, 42, 51, 45, 33, 48, 53, 48, 49, 36, 40, 56, 54, 47, 53, 46, 55, 39, 38, 53, 39, 51, 48, 32, 54, 56, 45, 55, 50, 55, 56, 49, 57, 34, 50, 35, 33, 36, 44, 33, 52, 59, 49, 31, 38, 50, 39, 42, 31, 32, 59, 54, 56, 59, 50, 35, 46, 52, 52, 37, 56, 55, 58, 31, 47, 32, 52, 43, 46, 39, 36, 52, 57, 43, 42, 52, 43, 52, 47, 57, 40, 35, 55, 58, 38, 60, 52, 44, 59, 54, 50, 42, 60, 46, 46, 39, 40, 30, 30, 48, 56, 35, 60, 42, 34, 42, 44, 38, 55, 31, 35, 56, 60, 43, 57, 41, 48, 31, 50, 39, 50, 42, 46, 39, 58, 42, 50, 31, 35, 49, 49, 48, 52, 53, 52, 32, 47, 46, 60, 60), slide_id = 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, 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, 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, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 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3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), p = 0:3000, Dim = c(4L, 3000L), Dimnames = list(c("slide1", "slide2", "slide3", "slide4"), 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", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", "111", "112", "113", "114", "115", "116", "117", "118", "119", "120", "121", "122", "123", "124", "125", "126", "127", "128", "129", "130", "131", "132", "133", "134", "135", "136", "137", "138", "139", "140", "141", "142", "143", "144", "145", "146", "147", "148", "149", "150", "151", "152", "153", "154", "155", "156", "157", "158", "159", "160", "161", "162", "163", "164", "165", "166", "167", "168", "169", "170", "171", "172", "173", "174", "175", "176", "177", "178", "179", "180", "181", "182", "183", "184", "185", "186", "187", "188", "189", "190", "191", "192", "193", "194", "195", "196", "197", "198", "199", "200", "201", "202", "203", "204", "205", "206", "207", "208", "209", "210", "211", "212", "213", "214", "215", "216", "217", "218", "219", "220", "221", "222", "223", "224", "225", "226", "227", "228", "229", "230", "231", "232", "233", "234", "235", "236", "237", "238", "239", "240", "241", "242", "243", "244", "245", "246", "247", "248", "249", "250", "251", "252", "253", "254", "255", "256", "257", "258", "259", "260", "261", "262", "263", "264", "265", "266", "267", "268", "269", "270", "271", "272", "273", "274", "275", "276", "277", "278", "279", "280", "281", "282", "283", "284", "285", "286", "287", "288", "289", "290", "291", "292", "293", "294", "295", "296", "297", "298", "299", "300", "301", "302", "303", "304", "305", "306", "307", "308", "309", "310", "311", "312", "313", "314", "315", "316", "317", "318", "319", "320", "321", "322", "323", "324", "325", "326", "327", "328", "329", "330", "331", "332", "333", "334", "335", "336", "337", "338", "339", "340", "341", "342", "343", "344", "345", "346", "347", "348", "349", "350", "351", "352", "353", "354", "355", "356", "357", "358", "359", "360", "361", "362", "363", "364", "365", "366", "367", "368", "369", "370", "371", "372", "373", "374", "375", "376", "377", "378", "379", "380", "381", "382", "383", "384", "385", "386", "387", "388", "389", "390", "391", "392", "393", "394", "395", "396", "397", "398", "399", "400", "401", "402", "403", "404", "405", "406", "407", "408", "409", "410", "411", "412", "413", "414", "415", "416", "417", "418", "419", "420", "421", "422", "423", "424", "425", "426", "427", "428", "429", "430", "431", "432", "433", "434", "435", "436", "437", "438", "439", "440", "441", "442", "443", "444", "445", "446", "447", "448", "449", "450", "451", "452", "453", "454", "455", "456", "457", "458", "459", "460", "461", "462", "463", "464", "465", "466", "467", "468", "469", "470", "471", "472", "473", "474", "475", "476", "477", "478", "479", "480", "481", "482", "483", "484", "485", "486", "487", "488", "489", "490", "491", "492", "493", "494", "495", "496", "497", "498", "499", "500", "501", "502", "503", "504", "505", "506", "507", "508", "509", "510", "511", "512", "513", "514", "515", "516", "517", "518", "519", "520", "521", "522", "523", "524", "525", "526", "527", "528", "529", "530", "531", "532", "533", "534", "535", "536", "537", "538", "539", "540", "541", "542", "543", "544", "545", "546", "547", "548", "549", "550", "551", "552", "553", "554", "555", "556", "557", "558", "559", "560", "561", "562", "563", "564", "565", "566", "567", "568", "569", "570", "571", "572", "573", "574", "575", "576", "577", "578", "579", "580", "581", "582", "583", "584", "585", "586", "587", "588", "589", "590", "591", "592", "593", "594", "595", "596", "597", "598", "599", "600", "601", "602", "603", "604", "605", "606", "607", "608", "609", "610", "611", "612", "613", "614", "615", "616", "617", "618", "619", "620", "621", "622", "623", "624", "625", "626", "627", "628", "629", "630", "631", "632", "633", "634", "635", "636", "637", "638", "639", "640", "641", "642", "643", "644", "645", "646", "647", "648", "649", "650", "651", "652", "653", "654", "655", "656", "657", "658", "659", "660", "661", "662", "663", "664", "665", "666", "667", "668", "669", "670", "671", "672", "673", "674", "675", "676", "677", "678", "679", "680", "681", "682", "683", "684", "685", "686", "687", "688", "689", "690", "691", "692", "693", "694", "695", "696", "697", "698", "699", "700", "701", "702", "703", "704", "705", "706", "707", "708", "709", "710", "711", "712", "713", "714", "715", "716", "717", "718", "719", "720", "721", "722", "723", "724", "725", "726", "727", "728", "729", "730", "731", "732", "733", "734", "735", "736", "737", "738", "739", "740", "741", "742", "743", "744", "745", "746", "747", "748", "749", "750", "751", "752", "753", "754", "755", "756", "757", "758", "759", "760", "761", "762", "763", "764", "765", "766", "767", "768", "769", "770", "771", "772", "773", "774", "775", "776", "777", "778", "779", "780", "781", "782", "783", "784", "785", "786", "787", "788", "789", "790", "791", "792", "793", "794", "795", "796", "797", "798", "799", "800", "801", "802", "803", "804", "805", "806", "807", "808", "809", "810", "811", "812", "813", "814", "815", "816", "817", "818", "819", "820", "821", "822", "823", "824", "825", "826", "827", "828", "829", "830", "831", "832", "833", "834", "835", "836", "837", "838", "839", "840", "841", "842", "843", "844", "845", "846", "847", "848", "849", "850", "851", "852", "853", "854", "855", "856", "857", "858", "859", "860", "861", "862", "863", "864", "865", "866", "867", "868", "869", "870", "871", "872", "873", "874", "875", "876", "877", "878", "879", "880", "881", "882", "883", "884", "885", "886", "887", "888", "889", "890", "891", "892", "893", "894", "895", "896", "897", "898", "899", "900", "901", "902", "903", "904", "905", "906", "907", "908", "909", "910", "911", "912", "913", "914", "915", "916", "917", "918", "919", "920", "921", "922", "923", "924", "925", "926", "927", "928", "929", "930", "931", "932", "933", "934", "935", "936", "937", "938", "939", "940", "941", "942", "943", "944", "945", "946", "947", "948", "949", "950", "951", "952", "953", "954", "955", "956", "957", "958", "959", "960", "961", "962", "963", "964", "965", "966", "967", "968", "969", "970", "971", "972", "973", "974", "975", "976", "977", "978", "979", "980", "981", "982", "983", "984", "985", "986", "987", "988", "989", "990", "991", "992", "993", "994", "995", "996", "997", "998", "999", "1000", "1001", "1002", "1003", "1004", "1005", "1006", "1007", "1008", "1009", "1010", "1011", "1012", "1013", "1014", "1015", "1016", "1017", "1018", "1019", "1020", "1021", "1022", "1023", "1024", "1025", "1026", "1027", "1028", "1029", "1030", "1031", "1032", "1033", "1034", "1035", "1036", "1037", "1038", "1039", "1040", "1041", "1042", "1043", "1044", "1045", "1046", "1047", "1048", "1049", "1050", "1051", "1052", "1053", "1054", "1055", "1056", "1057", "1058", "1059", "1060", "1061", "1062", "1063", "1064", "1065", "1066", "1067", "1068", "1069", "1070", "1071", "1072", "1073", "1074", "1075", "1076", "1077", "1078", "1079", "1080", "1081", "1082", "1083", "1084", "1085", "1086", "1087", "1088", "1089", "1090", "1091", "1092", "1093", "1094", "1095", "1096", "1097", "1098", "1099", "1100", "1101", "1102", "1103", "1104", "1105", "1106", "1107", "1108", "1109", "1110", "1111", "1112", "1113", "1114", "1115", "1116", "1117", "1118", "1119", "1120", "1121", "1122", "1123", "1124", "1125", "1126", "1127", "1128", "1129", "1130", "1131", "1132", "1133", "1134", "1135", "1136", "1137", "1138", "1139", "1140", "1141", "1142", "1143", "1144", "1145", "1146", "1147", "1148", "1149", "1150", "1151", "1152", "1153", "1154", "1155", "1156", "1157", "1158", "1159", "1160", "1161", "1162", "1163", "1164", "1165", "1166", "1167", "1168", "1169", "1170", "1171", "1172", "1173", "1174", "1175", "1176", "1177", "1178", "1179", "1180", "1181", "1182", "1183", "1184", "1185", "1186", "1187", "1188", "1189", "1190", "1191", "1192", "1193", "1194", "1195", "1196", "1197", "1198", "1199", "1200", "1201", "1202", "1203", "1204", "1205", "1206", "1207", "1208", "1209", "1210", "1211", "1212", "1213", "1214", "1215", "1216", "1217", "1218", "1219", "1220", "1221", "1222", "1223", "1224", "1225", "1226", "1227", "1228", "1229", "1230", "1231", "1232", "1233", "1234", "1235", "1236", "1237", "1238", "1239", "1240", "1241", "1242", "1243", "1244", "1245", "1246", 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1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), factors = list())), nl = c(slide_id = 4L)), 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(f, data = dat, ...) 12: get_var_proportions(mx_data, metadata_cols, table = "raw", m = marker, formula_override) 13: run_var_proportions(mx_data, table = "both") An irrecoverable exception occurred. R is aborting now ... * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.R'/home/th798/R/R-release/bin/BATCH: line 60: 2503094 Segmentation fault (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 ERROR Running the tests in 'tests/testthat.R' failed. Complete output: > library(testthat) > library(mxnorm) Warning message: In check_dep_version() : ABI version mismatch: lme4 was built with Matrix ABI version 1 Current Matrix ABI version is 2 Please re-install lme4 from source or restore original 'Matrix' package > > test_check("mxnorm") *** caught segfault *** address (nil), cause 'unknown' Traceback: 1: .Call(merPredDCreate, as(X, "matrix"), Lambdat, LamtUt, Lind, RZX, Ut, Utr, V, VtV, Vtr, Xwts, Zt, beta0, delb, delu, theta, u0) 2: initializePtr() 3: .Object$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, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 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3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), p = 0:3000, Dim = c(4L, 3000L), Dimnames = list( c("slide1", "slide2", "slide3", "slide4"), 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", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", "111", "112", "113", "114", "115", "116", "117", "118", "119", "120", "121", "122", "123", "124", "125", "126", "127", "128", "129", "130", "131", "132", "133", "134", "135", "136", "137", "138", "139", "140", "141", "142", "143", "144", "145", "146", "147", "148", "149", "150", "151", "152", "153", "154", "155", "156", "157", "158", "159", "160", "161", "162", "163", "164", "165", "166", "167", "168", "169", "170", "171", "172", "173", "174", "175", "176", "177", "178", "179", "180", "181", "182", "183", "184", "185", "186", "187", "188", "189", "190", "191", "192", "193", "194", "195", "196", "197", "198", "199", "200", "201", "202", "203", "204", "205", "206", "207", "208", "209", "210", "211", "212", "213", "214", "215", "216", "217", "218", "219", "220", "221", "222", "223", "224", "225", "226", "227", "228", "229", "230", "231", "232", "233", "234", "235", "236", "237", "238", "239", "240", "241", "242", "243", "244", "245", "246", "247", "248", "249", "250", "251", "252", "253", "254", "255", "256", "257", "258", "259", "260", "261", "262", "263", "264", "265", "266", "267", "268", "269", "270", "271", "272", "273", "274", "275", "276", "277", "278", "279", "280", "281", "282", "283", "284", "285", "286", "287", "288", "289", "290", "291", "292", "293", "294", "295", "296", "297", "298", "299", "300", "301", "302", "303", "304", "305", "306", "307", "308", "309", "310", "311", "312", "313", "314", "315", "316", "317", "318", "319", "320", "321", "322", "323", "324", "325", "326", "327", "328", "329", "330", "331", "332", "333", "334", "335", "336", "337", "338", "339", "340", "341", "342", "343", "344", "345", "346", "347", "348", "349", "350", "351", "352", "353", "354", "355", "356", "357", "358", "359", "360", "361", "362", "363", "364", "365", "366", "367", "368", "369", "370", "371", "372", "373", "374", "375", "376", "377", "378", "379", "380", "381", "382", "383", "384", "385", "386", "387", "388", "389", "390", "391", "392", "393", "394", "395", "396", "397", "398", "399", "400", "401", "402", "403", "404", "405", "406", "407", "408", "409", "410", "411", "412", "413", "414", "415", "416", "417", "418", "419", "420", "421", "422", "423", "424", "425", "426", "427", "428", "429", "430", "431", "432", "433", "434", "435", "436", "437", "438", "439", "440", "441", "442", "443", "444", "445", "446", "447", "448", "449", "450", "451", "452", "453", "454", "455", "456", "457", "458", "459", "460", "461", "462", "463", "464", "465", "466", "467", "468", "469", "470", "471", "472", "473", "474", "475", "476", "477", "478", "479", "480", "481", "482", "483", "484", "485", "486", "487", "488", "489", "490", "491", "492", "493", "494", "495", "496", "497", "498", "499", "500", "501", "502", "503", "504", "505", "506", "507", "508", "509", "510", "511", "512", "513", "514", "515", "516", "517", "518", "519", "520", "521", "522", "523", "524", "525", "526", "527", "528", "529", "530", "531", "532", "533", "534", "535", "536", "537", "538", "539", "540", "541", "542", "543", "544", "545", "546", "547", "548", "549", "550", "551", "552", "553", "554", "555", "556", "557", "558", "559", "560", "561", "562", "563", "564", "565", "566", "567", "568", "569", "570", "571", "572", "573", "574", "575", "576", "577", "578", "579", "580", "581", "582", "583", "584", "585", "586", "587", "588", "589", "590", "591", "592", "593", "594", "595", "596", "597", "598", "599", "600", "601", "602", "603", "604", "605", "606", "607", "608", "609", "610", "611", "612", "613", "614", "615", "616", "617", "618", "619", "620", "621", "622", "623", "624", "625", "626", "627", "628", "629", "630", "631", "632", "633", "634", "635", "636", "637", "638", "639", "640", "641", "642", "643", "644", "645", "646", "647", "648", "649", "650", "651", "652", "653", "654", "655", "656", "657", "658", "659", "660", "661", "662", "663", "664", "665", "666", "667", "668", "669", "670", "671", "672", "673", "674", "675", "676", "677", "678", "679", "680", "681", "682", "683", "684", "685", "686", "687", "688", "689", "690", "691", "692", "693", "694", "695", "696", "697", "698", "699", "700", "701", "702", "703", "704", "705", "706", "707", "708", "709", "710", "711", "712", "713", "714", "715", "716", "717", "718", "719", "720", "721", "722", "723", "724", "725", "726", "727", "728", "729", "730", "731", "732", "733", "734", "735", "736", "737", "738", "739", "740", "741", "742", "743", "744", "745", "746", "747", "748", "749", "750", "751", "752", "753", "754", "755", "756", "757", "758", "759", "760", "761", "762", "763", "764", "765", "766", "767", "768", "769", "770", "771", "772", "773", "774", "775", "776", "777", "778", "779", "780", "781", "782", "783", "784", "785", "786", "787", "788", "789", "790", "791", "792", "793", "794", "795", "796", "797", "798", "799", "800", "801", "802", "803", "804", "805", "806", "807", "808", "809", "810", "811", "812", "813", "814", "815", "816", "817", "818", "819", "820", "821", "822", "823", "824", "825", "826", "827", "828", "829", "830", "831", "832", "833", "834", "835", "836", "837", "838", "839", "840", "841", "842", "843", "844", "845", "846", "847", "848", "849", "850", "851", "852", "853", "854", "855", "856", "857", "858", "859", "860", "861", "862", "863", "864", "865", "866", "867", "868", "869", "870", "871", "872", "873", "874", "875", "876", "877", "878", "879", "880", "881", "882", "883", "884", "885", "886", "887", "888", "889", "890", "891", "892", "893", "894", "895", "896", "897", "898", "899", "900", "901", "902", "903", "904", "905", "906", "907", "908", "909", "910", "911", "912", "913", "914", "915", "916", "917", "918", "919", "920", "921", "922", "923", "924", "925", "926", "927", "928", "929", "930", "931", "932", "933", "934", "935", "936", "937", "938", "939", "940", "941", "942", "943", "944", "945", "946", "947", "948", "949", "950", "951", "952", "953", "954", "955", "956", "957", "958", "959", "960", "961", "962", "963", "964", "965", "966", "967", "968", "969", "970", "971", "972", "973", "974", "975", "976", "977", "978", "979", "980", "981", "982", "983", "984", "985", "986", "987", "988", "989", "990", "991", "992", "993", "994", "995", "996", "997", "998", "999", "1000", "1001", "1002", "1003", "1004", "1005", "1006", "1007", "1008", "1009", "1010", "1011", "1012", "1013", "1014", "1015", "1016", "1017", "1018", "1019", "1020", "1021", "1022", "1023", "1024", "1025", "1026", "1027", "1028", "1029", "1030", "1031", "1032", "1033", "1034", "1035", "1036", "1037", "1038", "1039", "1040", "1041", "1042", "1043", "1044", "1045", "1046", "1047", "1048", "1049", "1050", "1051", "1052", "1053", "1054", "1055", "1056", "1057", "1058", "1059", "1060", "1061", "1062", "1063", "1064", "1065", "1066", "1067", "1068", "1069", "1070", "1071", "1072", "1073", "1074", "1075", "1076", "1077", "1078", "1079", "1080", "1081", "1082", "1083", "1084", "1085", "1086", "1087", "1088", "1089", "1090", "1091", "1092", "1093", "1094", "1095", "1096", "1097", "1098", "1099", "1100", "1101", "1102", "1103", "1104", "1105", "1106", "1107", "1108", "1109", "1110", "1111", "1112", "1113", "1114", "1115", "1116", "1117", "1118", "1119", "1120", "1121", "1122", "1123", "1124", "1125", "1126", "1127", "1128", "1129", "1130", "1131", "1132", "1133", "1134", "1135", "1136", "1137", "1138", "1139", "1140", "1141", "1142", "1143", "1144", "1145", "1146", "1147", "1148", "1149", "1150", "1151", "1152", "1153", "1154", "1155", "1156", "1157", "1158", "1159", "1160", "1161", "1162", "1163", "1164", "1165", "1166", "1167", "1168", "1169", "1170", "1171", "1172", "1173", "1174", "1175", "1176", "1177", "1178", "1179", "1180", "1181", "1182", "1183", "1184", "1185", "1186", "1187", "1188", "1189", "1190", "1191", "1192", "1193", "1194", "1195", "1196", "1197", "1198", "1199", "1200", "1201", "1202", "1203", "1204", "1205", "1206", "1207", "1208", "1209", "1210", "1211", "1212", "1213", "1214", "1215", "1216", "1217", "1218", "1219", "1220", "1221", "1222", "1223", "1224", "1225", "1226", "1227", "1228", "1229", "1230", "1231", "1232", "1233", "1234", "1235", "1236", "1237", "1238", "1239", "1240", "1241", "1242", "1243", "1244", "1245", "1246", "1247", "1248", "1249", "1250", "1251", "1252", "1253", "1254", "1255", "1256", "1257", "1258", "1259", "1260", "1261", "1262", "1263", "1264", "1265", "1266", "1267", "1268", "1269", "1270", "1271", "1272", "1273", "1274", 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"2525", "2526", "2527", "2528", "2529", "2530", "2531", "2532", "2533", "2534", "2535", "2536", "2537", "2538", "2539", "2540", "2541", "2542", "2543", "2544", "2545", "2546", "2547", "2548", "2549", "2550", "2551", "2552", "2553", "2554", "2555", "2556", "2557", "2558", "2559", "2560", "2561", "2562", "2563", "2564", "2565", "2566", "2567", "2568", "2569", "2570", "2571", "2572", "2573", "2574", "2575", "2576", "2577", "2578", "2579", "2580", "2581", "2582", "2583", "2584", "2585", "2586", "2587", "2588", "2589", "2590", "2591", "2592", "2593", "2594", "2595", "2596", "2597", "2598", "2599", "2600", "2601", "2602", "2603", "2604", "2605", "2606", "2607", "2608", "2609", "2610", "2611", "2612", "2613", "2614", "2615", "2616", "2617", "2618", "2619", "2620", "2621", "2622", "2623", "2624", "2625", "2626", "2627", "2628", "2629", "2630", "2631", "2632", "2633", "2634", "2635", "2636", "2637", "2638", "2639", "2640", "2641", "2642", "2643", "2644", "2645", "2646", "2647", "2648", "2649", 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"2775", "2776", "2777", "2778", "2779", "2780", "2781", "2782", "2783", "2784", "2785", "2786", "2787", "2788", "2789", "2790", "2791", "2792", "2793", "2794", "2795", "2796", "2797", "2798", "2799", "2800", "2801", "2802", "2803", "2804", "2805", "2806", "2807", "2808", "2809", "2810", "2811", "2812", "2813", "2814", "2815", "2816", "2817", "2818", "2819", "2820", "2821", "2822", "2823", "2824", "2825", "2826", "2827", "2828", "2829", "2830", "2831", "2832", "2833", "2834", "2835", "2836", "2837", "2838", "2839", "2840", "2841", "2842", "2843", "2844", "2845", "2846", "2847", "2848", "2849", "2850", "2851", "2852", "2853", "2854", "2855", "2856", "2857", "2858", "2859", "2860", "2861", "2862", "2863", "2864", "2865", "2866", "2867", "2868", "2869", "2870", "2871", "2872", "2873", "2874", "2875", "2876", "2877", "2878", "2879", "2880", "2881", "2882", "2883", "2884", "2885", "2886", "2887", "2888", "2889", "2890", "2891", "2892", "2893", "2894", "2895", "2896", "2897", "2898", "2899", 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1L, 1L, 1L), n = 3000L, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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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(marker1_vals = c(15, 11, 12, 11, 12, 11, 16, 12, 11, 10, 15, 14, 14, 13, 14, 11, 12, 16, 16, 13, 13, 12, 9, 11, 13, 14, 14, 11, 11, 11, 13, 12, 13, 12, 13, 10, 13, 11, 13, 12, 13, 11, 15, 14, 13, 13, 14, 13, 8, 14, 12, 13, 15, 11, 13, 15, 13, 10, 11, 14, 14, 15, 11, 14, 13, 11, 13, 13, 11, 12, 11, 12, 11, 14, 15, 12, 14, 14, 11, 10, 10, 14, 15, 14, 11, 12, 13, 12, 14, 12, 12, 16, 14, 11, 12, 9, 10, 12, 10, 12, 12, 11, 9, 13, 13, 10, 12, 14, 15, 11, 11, 12, 12, 11, 11, 12, 13, 12, 14, 11, 12, 15, 12, 12, 12, 15, 13, 17, 12, 13, 12, 14, 8, 13, 13, 14, 12, 12, 16, 14, 12, 11, 13, 12, 13, 16, 13, 15, 11, 14, 13, 11, 14, 12, 13, 10, 10, 13, 13, 16, 13, 9, 12, 16, 10, 13, 13, 11, 12, 12, 13, 12, 12, 13, 14, 10, 15, 14, 12, 13, 12, 13, 12, 15, 12, 10, 12, 14, 8, 12, 15, 14, 13, 10, 15, 10, 12, 12, 11, 11, 14, 15, 11, 11, 11, 11, 13, 15, 10, 9, 11, 14, 12, 13, 11, 12, 13, 13, 12, 11, 10, 11, 14, 10, 12, 12, 13, 17, 11, 9, 11, 13, 12, 12, 14, 17, 12, 10, 11, 12, 14, 12, 12, 12, 10, 12, 11, 13, 12, 12, 11, 10, 13, 10, 12, 12, 15, 16, 13, 12, 12, 15, 14, 14, 12, 12, 12, 11, 12, 14, 12, 10, 13, 14, 10, 15, 12, 11, 13, 11, 15, 12, 13, 11, 11, 12, 12, 13, 16, 15, 12, 13, 15, 13, 15, 10, 12, 12, 11, 16, 17, 11, 13, 12, 12, 11, 15, 14, 13, 12, 10, 12, 12, 13, 12, 11, 11, 11, 11, 15, 13, 13, 10, 11, 10, 11, 10, 9, 13, 13, 8, 10, 11, 14, 12, 11, 9, 12, 13, 11, 10, 12, 9, 13, 12, 15, 13, 15, 11, 14, 12, 12, 10, 10, 9, 12, 10, 15, 14, 18, 11, 16, 10, 11, 12, 15, 14, 9, 14, 12, 12, 8, 10, 12, 13, 14, 13, 13, 14, 15, 11, 12, 13, 11, 13, 12, 14, 11, 11, 10, 10, 16, 12, 13, 14, 13, 11, 10, 11, 12, 12, 17, 16, 10, 13, 13, 10, 12, 11, 19, 14, 10, 14, 12, 11, 10, 13, 11, 13, 12, 13, 10, 12, 13, 9, 13, 15, 14, 11, 10, 10, 10, 14, 14, 13, 15, 10, 14, 15, 15, 12, 13, 16, 8, 11, 13, 15, 13, 11, 12, 9, 12, 12, 11, 12, 11, 13, 10, 14, 9, 12, 10, 13, 12, 15, 13, 10, 9, 12, 13, 14, 14, 11, 16, 12, 11, 14, 13, 12, 13, 14, 14, 11, 12, 12, 14, 14, 11, 14, 14, 14, 15, 12, 13, 11, 15, 15, 11, 12, 11, 12, 11, 13, 13, 12, 11, 14, 13, 13, 14, 12, 15, 14, 12, 11, 12, 14, 11, 15, 14, 14, 12, 14, 13, 10, 12, 11, 12, 12, 11, 11, 10, 11, 10, 12, 15, 12, 12, 12, 16, 14, 11, 11, 12, 11, 12, 8, 13, 13, 11, 13, 12, 10, 12, 12, 12, 12, 11, 12, 14, 13, 16, 12, 15, 12, 15, 14, 13, 12, 11, 11, 12, 13, 11, 14, 12, 12, 12, 11, 12, 13, 16, 13, 11, 12, 13, 11, 9, 13, 11, 13, 13, 15, 13, 13, 13, 12, 11, 14, 12, 13, 16, 11, 15, 11, 14, 13, 13, 15, 12, 11, 13, 18, 11, 10, 12, 11, 13, 11, 13, 13, 14, 12, 12, 16, 9, 14, 14, 13, 12, 13, 12, 14, 15, 13, 10, 10, 13, 9, 11, 14, 10, 15, 13, 9, 11, 11, 11, 13, 12, 12, 13, 10, 9, 11, 12, 8, 14, 11, 12, 12, 10, 15, 14, 9, 11, 12, 10, 14, 14, 14, 10, 11, 13, 11, 13, 12, 13, 10, 11, 10, 11, 10, 13, 11, 13, 11, 11, 11, 16, 11, 14, 13, 13, 11, 15, 12, 12, 13, 11, 14, 14, 9, 18, 14, 12, 13, 10, 8, 13, 13, 10, 13, 13, 15, 13, 14, 11, 11, 13, 11, 13, 16, 13, 14, 14, 12, 12, 15, 13, 15, 12, 11, 15, 13, 13, 11, 15, 10, 12, 10, 14, 11, 14, 12, 14, 13, 15, 13, 17, 18, 24, 24, 23, 23, 20, 17, 25, 17, 25, 14, 21, 20, 19, 22, 26, 26, 21, 22, 22, 20, 16, 19, 15, 15, 17, 32, 23, 23, 22, 18, 18, 23, 22, 17, 18, 18, 19, 23, 21, 17, 16, 27, 25, 20, 16, 18, 23, 18, 15, 16, 25, 20, 22, 17, 21, 17, 21, 21, 20, 17, 21, 20, 18, 21, 20, 20, 17, 18, 30, 21, 18, 17, 20, 21, 20, 22, 21, 22, 21, 25, 17, 20, 20, 24, 18, 19, 23, 22, 24, 16, 21, 17, 24, 17, 19, 22, 16, 21, 19, 20, 20, 17, 21, 24, 16, 23, 22, 17, 21, 24, 21, 19, 20, 17, 21, 14, 21, 19, 18, 23, 18, 16, 23, 20, 16, 21, 25, 20, 24, 15, 24, 18, 21, 14, 22, 17, 20, 25, 21, 21, 14, 17, 14, 20, 22, 16, 22, 26, 25, 20, 19, 17, 17, 19, 19, 22, 29, 20, 26, 21, 26, 20, 26, 21, 19, 19, 18, 19, 20, 20, 19, 15, 21, 26, 16, 21, 19, 19, 17, 15, 19, 19, 14, 22, 22, 22, 20, 25, 17, 21, 23, 23, 16, 21, 21, 23, 23, 13, 22, 23, 18, 23, 21, 23, 20, 26, 20, 18, 21, 21, 22, 19, 19, 17, 19, 21, 22, 15, 19, 24, 19, 22, 23, 17, 18, 23, 18, 18, 16, 23, 25, 19, 22, 25, 19, 18, 24, 23, 19, 19, 17, 18, 21, 20, 19, 19, 21, 27, 23, 27, 18, 21, 22, 20, 17, 21, 22, 19, 27, 16, 17, 25, 17, 21, 24, 24, 22, 14, 20, 22, 16, 13, 21, 19, 18, 19, 16, 26, 22, 22, 14, 18, 16, 26, 28, 22, 19, 15, 23, 15, 18, 31, 20, 26, 17, 16, 15, 18, 16, 22, 18, 23, 21, 22, 16, 19, 19, 22, 18, 21, 19, 18, 22, 19, 20, 19, 15, 25, 17, 18, 25, 23, 24, 21, 19, 20, 15, 17, 19, 21, 20, 19, 24, 20, 17, 23, 18, 18, 16, 21, 20, 22, 20, 16, 17, 18, 15, 23, 23, 17, 19, 20, 24, 16, 15, 21, 20, 23, 18, 23, 19, 20, 23, 20, 15, 18, 13, 20, 19, 18, 19, 20, 23, 22, 20, 21, 20, 23, 24, 16, 16, 23, 17, 17, 20, 20, 19, 22, 18, 24, 19, 20, 17, 25, 24, 18, 17, 18, 18, 21, 22, 16, 18, 19, 18, 14, 25, 18, 20, 26, 22, 15, 20, 16, 22, 17, 17, 17, 19, 23, 23, 23, 24, 21, 20, 17, 22, 25, 20, 21, 22, 17, 23, 16, 16, 20, 25, 22, 23, 18, 21, 21, 23, 20, 18, 19, 19, 15, 22, 19, 22, 14, 18, 18, 21, 22, 22, 20, 22, 19, 22, 20, 28, 18, 23, 16, 22, 20, 19, 22, 18, 21, 20, 16, 16, 19, 16, 21, 24, 20, 18, 23, 19, 18, 28, 19, 20, 17, 17, 16, 16, 24, 18, 17, 21, 19, 22, 21, 22, 18, 18, 19, 21, 17, 15, 15, 22, 19, 22, 15, 18, 24, 22, 18, 20, 22, 21, 20, 14, 16, 19, 19, 19, 20, 18, 22, 20, 21, 19, 23, 22, 18, 28, 17, 20, 25, 24, 18, 23, 19, 20, 25, 20, 19, 20, 15, 16, 21, 18, 20, 19, 22, 20, 25, 20, 17, 22, 18, 14, 20, 19, 19, 23, 28, 17, 24, 16, 26, 17, 15, 20, 19, 20, 18, 24, 22, 21, 21, 24, 23, 20, 18, 25, 17, 27, 18, 24, 20, 23, 26, 23, 19, 23, 17, 21, 19, 24, 17, 19, 23, 18, 22, 22, 21, 17, 23, 22, 23, 18, 14, 15, 14, 26, 25, 23, 21, 20, 24, 15, 17, 25, 19, 19, 18, 17, 20, 25, 15, 17, 26, 22, 18, 18, 19, 22, 23, 27, 17, 16, 18, 24, 29, 14, 21, 19, 16, 18, 14, 21, 24, 27, 20, 17, 25, 18, 16, 25, 16, 17, 21, 20, 18, 19, 31, 24, 21, 23, 18, 13, 21, 20, 18, 21, 17, 18, 26, 22, 24, 21, 16, 15, 22, 18, 17, 20, 19, 28, 16, 22, 19, 20, 18, 23, 14, 22, 22, 24, 25, 17, 19, 21, 21, 20, 18, 17, 29, 23, 23, 19, 26, 24, 16, 20, 19, 23, 18, 20, 22, 18, 17, 23, 18, 24, 18, 19, 23, 18, 19, 22, 22, 20, 22, 21, 18, 19, 22, 21, 20, 18, 16, 19, 19, 18, 15, 24, 20, 25, 23, 24, 96, 85, 90, 93, 92, 98, 93, 76, 93, 93, 96, 97, 70, 96, 88, 95, 89, 88, 96, 92, 76, 84, 89, 81, 83, 99, 95, 84, 92, 77, 97, 93, 91, 98, 87, 96, 95, 78, 90, 89, 99, 94, 94, 95, 95, 96, 99, 98, 95, 95, 93, 99, 96, 96, 92, 87, 98, 89, 96, 96, 84, 94, 94, 93, 94, 87, 95, 89, 96, 97, 95, 90, 99, 95, 88, 95, 87, 98, 97, 99, 100, 99, 97, 90, 90, 84, 74, 84, 96, 95, 99, 99, 84, 84, 83, 80, 80, 67, 80, 93, 96, 98, 73, 91, 100, 83, 97, 76, 98, 96, 69, 98, 99, 93, 88, 77, 89, 90, 98, 93, 97, 99, 99, 96, 88, 98, 70, 93, 91, 95, 97, 98, 96, 98, 92, 89, 79, 79, 98, 90, 93, 96, 84, 85, 96, 70, 89, 89, 77, 86, 70, 90, 53, 95, 82, 97, 95, 81, 85, 96, 97, 96, 94, 92, 92, 89, 88, 99, 100, 100, 98, 89, 98, 100, 97, 100, 98, 98, 82, 98, 99, 96, 91, 92, 88, 94, 99, 99, 96, 75, 80, 79, 96, 87, 100, 87, 93, 88, 98, 81, 91, 86, 97, 93, 77, 97, 92, 85, 91, 93, 93, 90, 91, 98, 100, 99, 96, 95, 87, 97, 98, 91, 87, 94, 85, 100, 99, 96, 85, 100, 90, 100, 91, 80, 97, 61, 58, 83, 93, 99, 94, 90, 95, 85, 98, 94, 81, 99, 95, 64, 94, 86, 90, 88, 97, 94, 81, 89, 96, 97, 90, 98, 93, 98, 95, 95, 100, 95, 94, 96, 100, 99, 100, 81, 98, 99, 86, 81, 99, 90, 77, 99, 97, 99, 79, 94, 92, 95, 90, 99, 94, 84, 83, 95, 94, 93, 86, 99, 99, 98, 75, 93, 96, 91, 92, 100, 91, 86, 100, 92, 95, 99, 79, 83, 84, 93, 84, 97, 94, 95, 93, 89, 91, 98, 99, 87, 79, 87, 97, 89, 84, 90, 99, 86, 100, 82, 98, 91, 88, 85, 97, 91, 82, 98, 66, 80, 97, 95, 79, 99, 94, 91, 93, 94, 90, 96, 99, 79, 92, 81, 90, 93, 89, 85, 82, 91, 88, 81, 95, 95, 93, 95, 95, 86, 96, 94, 99, 99, 82, 84, 86, 96, 98, 94, 86, 100, 91, 96, 97, 99, 97, 91, 97, 95, 78, 98, 93, 90, 99, 90, 91, 90, 96, 98, 96, 85, 88, 89, 77, 96, 91, 87, 97, 97, 95, 61, 91, 93, 81, 99, 98, 95, 96, 96, 85, 64, 97, 96, 96, 91, 90, 96, 91, 95, 97, 97, 99, 93, 74, 96, 85, 96, 99, 97, 100, 99, 94, 94, 100, 65, 92, 93, 85, 95, 95, 86, 95, 97, 99, 91, 78, 91, 89, 94, 99, 92, 82, 100, 91, 99, 97, 97, 96, 94, 85, 96, 84, 92, 96, 98, 96, 96, 94, 91, 73, 100, 100, 97, 86, 98, 92, 90, 92, 83, 97, 92, 94, 94, 93, 87, 96, 93, 96, 93, 96, 89, 89, 96, 94, 100, 89, 92, 98, 86, 93, 98, 99, 87, 85, 93, 92, 93, 97, 97, 98, 57, 95, 87, 95, 100, 87, 91, 94, 79, 76, 94, 98, 83, 98, 87, 97, 100, 83, 92, 98, 94, 95, 91, 97, 83, 99, 95, 99, 96, 90, 75, 95, 100, 94, 84, 94, 96, 97, 94, 66, 95, 83, 89, 100, 72, 96, 94, 96, 83, 97, 84, 88, 97, 92, 89, 81, 99, 93, 92, 95, 84, 74, 88, 81, 95, 97, 89, 82, 86, 92, 83, 83, 92, 93, 99, 78, 93, 85, 98, 99, 99, 97, 82, 89, 94, 99, 83, 95, 96, 75, 73, 97, 91, 84, 95, 78, 96, 61, 100, 77, 93, 81, 96, 96, 93, 99, 97, 91, 96, 89, 71, 92, 100, 100, 96, 80, 94, 90, 100, 100, 97, 86, 93, 74, 86, 99, 82, 94, 99, 95, 96, 78, 92, 74, 83, 94, 89, 66, 95, 94, 90, 83, 98, 90, 91, 96, 95, 86, 99, 99, 100, 88, 80, 91, 99, 86, 94, 92, 86, 100, 98, 93, 97, 77, 75, 100, 97, 98, 93, 86, 97, 100, 88, 97, 95, 98, 95, 90, 80, 95, 88, 78, 98, 94, 94, 80, 92, 100, 93, 96, 98, 93, 93, 93, 91, 68, 95, 100, 96, 87, 81, 97, 92, 85, 59, 73, 98, 94, 72, 88, 77, 86, 99, 98, 93, 88, 82, 96, 85, 91, 100, 81, 87, 94, 96, 57, 30, 37, 46, 47, 50, 32, 60, 38, 48, 49, 42, 45, 50, 58, 37, 58, 54, 57, 32, 32, 44, 38, 41, 46, 53, 34, 40, 43, 41, 55, 49, 44, 42, 54, 50, 39, 44, 55, 56, 56, 49, 58, 39, 54, 58, 59, 49, 51, 38, 40, 48, 54, 40, 54, 32, 36, 60, 43, 36, 52, 42, 34, 54, 38, 40, 42, 34, 41, 41, 53, 58, 45, 44, 35, 43, 53, 46, 52, 49, 34, 33, 45, 33, 50, 58, 40, 32, 57, 42, 45, 60, 57, 60, 40, 43, 46, 40, 58, 49, 44, 38, 43, 43, 33, 30, 54, 34, 51, 41, 53, 30, 47, 52, 48, 41, 32, 50, 55, 30, 33, 39, 41, 44, 50, 32, 51, 34, 30, 53, 56, 37, 39, 36, 50, 39, 43, 50, 46, 30, 39, 55, 31, 53, 45, 42, 42, 42, 48, 39, 30, 57, 46, 59, 60, 52, 40, 46, 55, 54, 58, 37, 45, 45, 60, 30, 32, 49, 30, 38, 45, 30, 31, 52, 53, 33, 51, 39, 46, 47, 51, 43, 45, 44, 41, 40, 47, 39, 40, 35, 30, 35, 48, 50, 60, 34, 30, 39, 45, 59, 49, 60, 38, 35, 35, 42, 34, 40, 57, 47, 44, 55, 57, 49, 44, 36, 46, 60, 55, 31, 54, 54, 30, 60, 37, 30, 41, 45, 46, 36, 35, 51, 33, 48, 30, 53, 34, 34, 42, 42, 59, 58, 60, 54, 56, 38, 54, 60, 55, 55, 58, 37, 37, 43, 52, 38, 59, 31, 45, 46, 50, 44, 30, 51, 37, 31, 60, 52, 40, 55, 34, 53, 60, 39, 37, 34, 54, 37, 53, 47, 50, 35, 48, 53, 41, 46, 33, 36, 45, 51, 37, 46, 30, 51, 48, 34, 34, 31, 56, 33, 39, 40, 42, 50, 56, 52, 49, 40, 39, 50, 48, 42, 58, 34, 37, 44, 32, 48, 50, 34, 55, 34, 34, 49, 56, 48, 45, 31, 43, 49, 43, 38, 54, 41, 52, 43, 60, 39, 41, 38, 38, 40, 58, 35, 35, 40, 55, 59, 38, 43, 49, 48, 48, 31, 45, 59, 57, 40, 39, 35, 35, 49, 35, 60, 33, 39, 32, 37, 44, 32, 30, 32, 46, 33, 49, 40, 45, 45, 47, 51, 40, 55, 60, 30, 49, 33, 53, 57, 51, 34, 56, 56, 43, 43, 51, 31, 39, 31, 51, 58, 37, 60, 53, 54, 50, 30, 34, 57, 56, 49, 47, 44, 50, 40, 35, 40, 58, 60, 40, 33, 39, 40, 60, 53, 58, 54, 32, 40, 33, 42, 33, 54, 47, 41, 44, 46, 49, 50, 39, 54, 47, 44, 58, 54, 55, 49, 42, 50, 55, 58, 31, 49, 31, 40, 43, 32, 47, 49, 49, 45, 36, 59, 34, 58, 50, 58, 45, 50, 55, 40, 49, 41, 45, 35, 43, 48, 59, 32, 59, 40, 54, 51, 55, 59, 50, 33, 51, 55, 60, 36, 34, 44, 34, 37, 35, 55, 46, 59, 38, 44, 46, 52, 50, 34, 44, 40, 43, 57, 39, 47, 57, 37, 56, 31, 49, 56, 34, 48, 39, 55, 52, 55, 53, 53, 39, 30, 45, 42, 56, 56, 38, 41, 30, 33, 60, 51, 47, 35, 52, 55, 31, 44, 44, 34, 56, 46, 37, 45, 37, 38, 56, 51, 35, 52, 32, 44, 45, 54, 31, 53, 50, 45, 40, 31, 49, 36, 44, 59, 36, 34, 34, 42, 30, 56, 40, 36, 35, 37, 56, 42, 45, 37, 37, 51, 34, 39, 40, 53, 41, 45, 34, 48, 49, 45, 34, 54, 41, 46, 52, 49, 59, 49, 53, 43, 55, 54, 42, 50, 36, 54, 34, 42, 51, 45, 33, 48, 53, 48, 49, 36, 40, 56, 54, 47, 53, 46, 55, 39, 38, 53, 39, 51, 48, 32, 54, 56, 45, 55, 50, 55, 56, 49, 57, 34, 50, 35, 33, 36, 44, 33, 52, 59, 49, 31, 38, 50, 39, 42, 31, 32, 59, 54, 56, 59, 50, 35, 46, 52, 52, 37, 56, 55, 58, 31, 47, 32, 52, 43, 46, 39, 36, 52, 57, 43, 42, 52, 43, 52, 47, 57, 40, 35, 55, 58, 38, 60, 52, 44, 59, 54, 50, 42, 60, 46, 46, 39, 40, 30, 30, 48, 56, 35, 60, 42, 34, 42, 44, 38, 55, 31, 35, 56, 60, 43, 57, 41, 48, 31, 50, 39, 50, 42, 46, 39, 58, 42, 50, 31, 35, 49, 49, 48, 52, 53, 52, 32, 47, 46, 60, 60), slide_id = 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, 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, 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, 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, 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, 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, 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, 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, 1L, 1L, 1L, 1L, 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3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), p = 0:3000, Dim = c(4L, 3000L), Dimnames = list( c("slide1", "slide2", "slide3", "slide4"), 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", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", 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3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), p = 0:3000, Dim = c(4L, 3000L), Dimnames = list(c("slide1", "slide2", "slide3", "slide4"), 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", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", 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"206", "207", "208", "209", "210", "211", "212", "213", "214", "215", "216", "217", "218", "219", "220", "221", "222", "223", "224", "225", "226", "227", "228", "229", "230", "231", "232", "233", "234", "235", "236", "237", "238", "239", "240", "241", "242", "243", "244", "245", "246", "247", "248", "249", "250", "251", "252", "253", "254", "255", "256", "257", "258", "259", "260", "261", "262", "263", "264", "265", "266", "267", "268", "269", "270", "271", "272", "273", "274", "275", "276", "277", "278", "279", "280", "281", "282", "283", "284", "285", "286", "287", "288", "289", "290", "291", "292", "293", "294", "295", "296", "297", "298", "299", "300", "301", "302", "303", "304", "305", "306", "307", "308", "309", "310", "311", "312", "313", "314", "315", "316", "317", "318", "319", "320", "321", "322", "323", "324", "325", "326", "327", "328", "329", "330", "331", "332", "333", "334", "335", "336", "337", "338", "339", "340", "341", "342", "343", "344", "345", "346", "347", "348", "349", "350", "351", "352", "353", "354", "355", "356", "357", "358", "359", "360", "361", "362", "363", "364", "365", "366", "367", "368", "369", "370", "371", "372", "373", "374", "375", "376", "377", "378", "379", "380", "381", "382", "383", "384", "385", "386", "387", "388", "389", "390", "391", "392", "393", "394", "395", "396", "397", "398", "399", "400", "401", "402", "403", "404", "405", "406", "407", "408", "409", "410", "411", "412", "413", "414", "415", "416", "417", "418", "419", "420", "421", "422", "423", "424", "425", "426", "427", "428", "429", "430", "431", "432", "433", "434", "435", "436", "437", "438", "439", "440", "441", "442", "443", "444", "445", "446", "447", "448", "449", "450", "451", "452", "453", "454", "455", "456", "457", "458", "459", "460", "461", "462", "463", "464", "465", "466", "467", "468", "469", "470", "471", "472", "473", "474", "475", "476", "477", "478", "479", "480", "481", "482", "483", "484", "485", "486", "487", "488", "489", "490", "491", "492", "493", "494", "495", "496", "497", "498", "499", "500", "501", "502", "503", "504", "505", "506", "507", "508", "509", "510", "511", "512", "513", "514", "515", "516", "517", "518", "519", "520", "521", "522", "523", "524", "525", "526", "527", "528", "529", "530", "531", "532", "533", "534", "535", "536", "537", "538", "539", "540", "541", "542", "543", "544", "545", "546", "547", "548", "549", "550", "551", "552", "553", "554", "555", "556", "557", "558", "559", "560", "561", "562", "563", "564", "565", "566", "567", "568", "569", "570", "571", "572", "573", "574", "575", "576", "577", "578", "579", "580", "581", "582", "583", "584", "585", "586", "587", "588", "589", "590", "591", "592", "593", "594", "595", "596", "597", "598", "599", "600", "601", "602", "603", "604", "605", "606", "607", "608", "609", "610", "611", "612", "613", "614", "615", "616", "617", "618", "619", "620", "621", "622", "623", "624", "625", "626", "627", "628", "629", "630", "631", "632", "633", "634", "635", "636", "637", "638", "639", "640", "641", "642", "643", "644", "645", "646", "647", "648", "649", "650", "651", "652", "653", "654", "655", "656", "657", "658", "659", "660", "661", "662", "663", "664", "665", "666", "667", "668", "669", "670", "671", "672", "673", "674", "675", "676", "677", "678", "679", "680", "681", "682", "683", "684", "685", "686", "687", "688", "689", "690", "691", "692", "693", "694", "695", "696", "697", "698", "699", "700", "701", "702", "703", "704", "705", "706", "707", "708", "709", "710", "711", "712", "713", "714", "715", "716", "717", "718", "719", "720", "721", "722", "723", "724", "725", "726", "727", "728", "729", "730", "731", "732", "733", "734", "735", "736", "737", "738", "739", "740", "741", "742", "743", "744", "745", "746", "747", "748", "749", "750", "751", "752", "753", "754", "755", "756", "757", "758", "759", "760", "761", "762", "763", "764", "765", "766", "767", "768", "769", "770", "771", "772", "773", "774", "775", "776", "777", "778", "779", "780", "781", "782", "783", "784", "785", "786", "787", "788", "789", "790", "791", "792", "793", "794", "795", "796", "797", "798", "799", "800", "801", "802", "803", "804", "805", "806", "807", "808", "809", "810", "811", "812", "813", "814", "815", "816", "817", "818", "819", "820", "821", "822", "823", "824", "825", "826", "827", "828", "829", "830", "831", "832", "833", "834", "835", "836", "837", "838", "839", "840", "841", "842", "843", "844", "845", "846", "847", "848", "849", "850", "851", "852", "853", "854", "855", "856", "857", "858", "859", "860", "861", "862", "863", "864", "865", "866", "867", "868", "869", "870", "871", "872", "873", "874", "875", "876", "877", "878", "879", "880", "881", "882", "883", "884", "885", "886", "887", "888", "889", "890", "891", "892", "893", "894", "895", "896", "897", "898", "899", "900", "901", "902", "903", "904", "905", "906", "907", "908", "909", "910", "911", "912", "913", "914", "915", "916", "917", "918", "919", "920", "921", "922", "923", "924", "925", "926", "927", "928", "929", "930", "931", "932", "933", "934", "935", "936", "937", "938", "939", "940", "941", "942", "943", "944", "945", "946", "947", "948", "949", "950", "951", "952", "953", "954", "955", "956", "957", "958", "959", "960", "961", "962", "963", "964", "965", "966", "967", "968", "969", "970", "971", "972", "973", "974", "975", "976", "977", "978", "979", "980", "981", "982", "983", "984", "985", "986", "987", "988", "989", "990", "991", "992", "993", "994", "995", "996", "997", "998", "999", "1000", "1001", "1002", "1003", "1004", "1005", "1006", "1007", "1008", "1009", "1010", "1011", "1012", "1013", "1014", "1015", "1016", "1017", "1018", "1019", "1020", "1021", "1022", "1023", "1024", "1025", "1026", "1027", "1028", "1029", "1030", "1031", "1032", "1033", "1034", "1035", "1036", "1037", "1038", "1039", "1040", "1041", "1042", "1043", "1044", "1045", "1046", "1047", "1048", "1049", "1050", "1051", "1052", "1053", "1054", "1055", "1056", "1057", "1058", "1059", "1060", "1061", "1062", "1063", "1064", "1065", "1066", "1067", "1068", "1069", "1070", "1071", "1072", "1073", "1074", "1075", "1076", "1077", "1078", "1079", "1080", "1081", "1082", "1083", "1084", "1085", "1086", "1087", "1088", "1089", "1090", "1091", "1092", "1093", "1094", "1095", "1096", "1097", "1098", "1099", "1100", "1101", "1102", "1103", "1104", "1105", "1106", "1107", "1108", "1109", "1110", "1111", "1112", "1113", "1114", "1115", "1116", "1117", "1118", "1119", "1120", "1121", "1122", "1123", "1124", "1125", "1126", "1127", "1128", "1129", "1130", "1131", "1132", "1133", "1134", "1135", "1136", "1137", "1138", "1139", "1140", "1141", "1142", "1143", "1144", "1145", "1146", "1147", "1148", "1149", "1150", "1151", "1152", "1153", "1154", "1155", "1156", "1157", "1158", "1159", "1160", "1161", "1162", "1163", "1164", "1165", "1166", "1167", "1168", "1169", "1170", "1171", "1172", "1173", "1174", "1175", "1176", "1177", "1178", "1179", "1180", "1181", "1182", "1183", "1184", "1185", "1186", "1187", "1188", "1189", "1190", "1191", "1192", "1193", "1194", "1195", "1196", "1197", "1198", "1199", "1200", "1201", "1202", "1203", "1204", "1205", "1206", "1207", "1208", "1209", "1210", "1211", "1212", "1213", "1214", "1215", "1216", "1217", "1218", "1219", "1220", "1221", "1222", "1223", "1224", "1225", "1226", "1227", "1228", "1229", "1230", "1231", "1232", "1233", "1234", "1235", "1236", "1237", "1238", "1239", "1240", "1241", "1242", "1243", "1244", "1245", "1246", "1247", "1248", "1249", "1250", "1251", "1252", "1253", "1254", "1255", "1256", "1257", "1258", "1259", "1260", "1261", "1262", "1263", "1264", "1265", "1266", "1267", "1268", "1269", "1270", "1271", "1272", "1273", "1274", "1275", "1276", "1277", "1278", "1279", "1280", "1281", "1282", "1283", "1284", "1285", "1286", "1287", "1288", "1289", "1290", "1291", "1292", "1293", "1294", "1295", "1296", "1297", "1298", "1299", "1300", "1301", "1302", "1303", "1304", "1305", 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1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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(slide_id = 4L)), 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(f, data = dat, ...) 12: get_var_proportions(mx_data, metadata_cols, table = "raw", m = marker, formula_override) 13: run_var_proportions(mx_data, table = "both") 14: eval(code, test_env) 15: eval(code, test_env) 16: 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) 17: doTryCatch(return(expr), name, parentenv, handler) 18: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 19: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 20: doTryCatch(return(expr), name, parentenv, handler) 21: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 22: tryCatchList(expr, classes, parentenv, handlers) 23: 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) { }) 24: test_code(desc, code, env = parent.frame(), default_reporter = local_interactive_reporter()) 25: test_that("plotting works", { mx_data = mx_dataset(mxnorm::mx_sample, "slide_id", "image_id", c("marker1_vals", "marker2_vals", "marker3_vals"), c("metadata1_vals")) mx_data = mx_normalize(mx_data, transform = "log10", method = "None") expect_error(plot_mx_proportions(mx_data)) expect_error(plot_mx_proportions(rnorm(100))) mx_data = run_var_proportions(mx_data, table = "both") expect_equal(class(plot_mx_proportions(mx_data)), c("gg", "ggplot"))}) 26: eval(code, test_env) 27: eval(code, test_env) 28: 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) 29: doTryCatch(return(expr), name, parentenv, handler) 30: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 31: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 32: doTryCatch(return(expr), name, parentenv, handler) 33: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 34: tryCatchList(expr, classes, parentenv, handlers) 35: 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) { }) 36: test_code(test = NULL, code = exprs, env = env, default_reporter = StopReporter$new()) 37: source_file(path, env = env(env), desc = desc, error_call = error_call) 38: FUN(X[[i]], ...) 39: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call) 40: doTryCatch(return(expr), name, parentenv, handler) 41: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 42: tryCatchList(expr, classes, parentenv, handlers) 43: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) 44: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)) 45: 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) 46: 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) 47: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") 48: test_check("mxnorm") 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 ...sh: line 1: 2503370 Segmentation fault (core dumped) '/home/th798/R/R-release/bin/R' --vanilla --no-echo > '/tmp/th798/16120028/R-release/891/mxnorm.Rcheck/build_vignettes.log' 2>&1 < '/tmp/th798/16120028/Rtmp71C7u8/file2614485baae512' ERROR Error(s) in re-building vignettes: --- re-building 'mxnorm-vignette.Rmd' using rmarkdown *** 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, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 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3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), p = 0:3000, Dim = c(4L, 3000L), Dimnames = list( c("slide1", "slide2", "slide3", "slide4"), 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", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", "111", "112", "113", "114", "115", "116", "117", "118", "119", "120", "121", "122", "123", "124", "125", "126", "127", "128", "129", "130", "131", "132", "133", "134", "135", "136", "137", "138", "139", "140", "141", "142", "143", "144", "145", "146", "147", "148", "149", "150", "151", "152", "153", "154", "155", "156", "157", "158", "159", "160", "161", "162", "163", "164", "165", "166", "167", "168", "169", "170", "171", "172", "173", "174", "175", "176", "177", "178", "179", "180", "181", "182", "183", "184", "185", "186", "187", "188", "189", "190", "191", "192", "193", "194", "195", "196", "197", "198", "199", "200", "201", "202", "203", "204", "205", "206", "207", "208", "209", "210", "211", "212", "213", "214", "215", "216", "217", "218", "219", "220", "221", "222", "223", "224", "225", "226", "227", "228", "229", "230", "231", "232", "233", "234", "235", "236", "237", "238", "239", "240", "241", "242", "243", "244", "245", "246", "247", "248", "249", "250", "251", "252", "253", "254", "255", "256", "257", "258", "259", "260", "261", "262", "263", "264", "265", "266", "267", "268", "269", "270", "271", "272", "273", "274", "275", "276", "277", "278", "279", "280", "281", "282", "283", "284", "285", "286", "287", "288", "289", "290", "291", "292", "293", "294", "295", "296", "297", "298", "299", "300", "301", "302", "303", "304", "305", "306", "307", "308", "309", "310", "311", "312", "313", "314", "315", "316", "317", "318", "319", "320", "321", "322", "323", "324", "325", "326", "327", "328", "329", "330", "331", "332", "333", "334", "335", "336", "337", "338", "339", "340", "341", "342", "343", "344", "345", "346", "347", "348", "349", "350", "351", "352", "353", "354", "355", "356", "357", "358", "359", "360", "361", "362", "363", "364", "365", "366", "367", "368", "369", "370", "371", "372", "373", "374", "375", "376", "377", "378", "379", "380", "381", "382", "383", "384", "385", "386", "387", "388", "389", "390", "391", "392", "393", "394", "395", "396", "397", "398", "399", "400", "401", "402", "403", "404", "405", "406", "407", "408", "409", "410", "411", "412", "413", "414", "415", "416", "417", "418", "419", "420", "421", "422", "423", "424", "425", "426", "427", "428", "429", "430", "431", "432", "433", "434", "435", "436", "437", "438", "439", "440", "441", "442", "443", "444", "445", "446", "447", "448", "449", "450", "451", "452", "453", "454", "455", "456", "457", "458", "459", "460", "461", "462", "463", "464", "465", "466", "467", "468", "469", "470", "471", "472", "473", "474", "475", "476", "477", "478", "479", "480", "481", "482", "483", "484", "485", "486", "487", "488", "489", "490", "491", "492", "493", "494", "495", "496", "497", "498", "499", "500", "501", "502", "503", "504", "505", "506", "507", "508", "509", "510", "511", "512", "513", "514", "515", "516", "517", "518", "519", "520", "521", "522", "523", "524", "525", "526", "527", "528", "529", "530", "531", "532", "533", "534", "535", "536", "537", "538", "539", "540", "541", "542", "543", "544", "545", "546", "547", "548", "549", "550", "551", "552", "553", "554", "555", "556", "557", "558", "559", "560", "561", "562", "563", "564", "565", "566", "567", "568", "569", "570", "571", "572", "573", "574", "575", "576", "577", "578", "579", "580", "581", "582", "583", "584", "585", "586", "587", "588", "589", "590", "591", "592", "593", "594", "595", "596", "597", "598", "599", "600", "601", "602", "603", "604", "605", "606", "607", "608", "609", "610", "611", "612", "613", "614", "615", "616", "617", "618", "619", "620", "621", "622", "623", "624", "625", "626", "627", "628", "629", "630", "631", "632", "633", "634", "635", "636", "637", "638", "639", "640", "641", "642", "643", "644", "645", "646", "647", "648", "649", "650", "651", "652", "653", "654", "655", "656", "657", "658", "659", "660", "661", "662", "663", "664", "665", "666", "667", "668", "669", "670", "671", "672", "673", "674", "675", "676", "677", "678", "679", "680", "681", "682", "683", "684", "685", "686", "687", "688", "689", "690", "691", "692", "693", "694", "695", "696", "697", "698", "699", "700", "701", "702", "703", "704", "705", "706", "707", "708", "709", "710", "711", "712", "713", "714", "715", "716", "717", "718", "719", "720", "721", "722", "723", "724", "725", "726", "727", "728", "729", "730", "731", "732", "733", "734", "735", "736", "737", "738", "739", "740", "741", "742", "743", "744", "745", "746", "747", "748", "749", "750", "751", "752", "753", "754", "755", "756", "757", "758", "759", "760", "761", "762", "763", "764", "765", "766", "767", "768", "769", "770", "771", "772", "773", "774", "775", "776", "777", "778", "779", "780", "781", "782", "783", "784", "785", "786", "787", "788", "789", "790", "791", "792", "793", "794", "795", "796", "797", "798", "799", "800", "801", "802", "803", "804", "805", "806", "807", "808", "809", "810", "811", "812", "813", "814", "815", "816", "817", "818", "819", "820", "821", "822", "823", "824", "825", "826", "827", "828", "829", "830", "831", "832", "833", "834", "835", "836", "837", "838", "839", "840", "841", "842", "843", "844", "845", "846", "847", "848", "849", "850", "851", "852", "853", "854", "855", "856", "857", "858", "859", "860", "861", "862", "863", "864", "865", "866", "867", "868", "869", "870", "871", "872", "873", "874", "875", "876", "877", "878", "879", "880", "881", "882", "883", "884", "885", "886", "887", "888", "889", "890", "891", "892", "893", "894", "895", "896", "897", "898", "899", "900", "901", "902", "903", "904", "905", "906", "907", "908", "909", "910", "911", "912", "913", "914", "915", "916", "917", "918", "919", "920", "921", "922", "923", "924", "925", "926", "927", "928", "929", "930", "931", "932", "933", "934", "935", "936", "937", "938", "939", "940", "941", "942", "943", "944", "945", "946", "947", "948", "949", "950", "951", "952", "953", "954", "955", "956", "957", "958", "959", "960", "961", "962", "963", "964", "965", "966", "967", "968", "969", "970", "971", "972", "973", "974", "975", "976", "977", "978", "979", "980", "981", "982", "983", "984", "985", "986", "987", "988", "989", "990", "991", "992", "993", "994", "995", "996", "997", "998", "999", "1000", "1001", "1002", "1003", "1004", "1005", "1006", "1007", "1008", "1009", "1010", "1011", "1012", "1013", "1014", "1015", "1016", "1017", "1018", "1019", "1020", "1021", "1022", "1023", "1024", "1025", "1026", "1027", "1028", "1029", "1030", "1031", "1032", "1033", "1034", "1035", "1036", "1037", "1038", "1039", "1040", "1041", "1042", "1043", "1044", "1045", "1046", "1047", "1048", "1049", "1050", "1051", "1052", "1053", "1054", "1055", "1056", "1057", "1058", "1059", "1060", "1061", "1062", "1063", "1064", "1065", "1066", "1067", "1068", "1069", "1070", "1071", "1072", "1073", "1074", "1075", "1076", "1077", "1078", "1079", "1080", "1081", "1082", "1083", "1084", "1085", "1086", "1087", "1088", "1089", "1090", "1091", "1092", "1093", "1094", "1095", "1096", "1097", "1098", "1099", "1100", "1101", "1102", "1103", "1104", "1105", "1106", "1107", "1108", "1109", "1110", "1111", "1112", "1113", "1114", "1115", "1116", "1117", "1118", "1119", "1120", "1121", "1122", "1123", "1124", "1125", "1126", "1127", "1128", "1129", "1130", "1131", "1132", "1133", "1134", "1135", "1136", "1137", "1138", "1139", "1140", "1141", "1142", "1143", "1144", "1145", "1146", "1147", "1148", "1149", "1150", "1151", "1152", "1153", "1154", "1155", "1156", "1157", "1158", "1159", "1160", "1161", "1162", "1163", "1164", "1165", "1166", "1167", "1168", "1169", "1170", "1171", "1172", "1173", "1174", "1175", "1176", "1177", "1178", "1179", "1180", "1181", "1182", "1183", "1184", "1185", "1186", "1187", "1188", "1189", "1190", "1191", "1192", "1193", "1194", "1195", "1196", "1197", "1198", "1199", "1200", "1201", "1202", "1203", "1204", "1205", "1206", "1207", "1208", "1209", "1210", "1211", "1212", "1213", "1214", "1215", "1216", "1217", "1218", "1219", "1220", "1221", "1222", "1223", "1224", "1225", "1226", "1227", "1228", "1229", "1230", "1231", "1232", "1233", "1234", "1235", "1236", "1237", "1238", "1239", "1240", "1241", "1242", "1243", "1244", "1245", "1246", "1247", "1248", "1249", "1250", "1251", "1252", "1253", "1254", "1255", "1256", "1257", "1258", "1259", "1260", "1261", "1262", "1263", 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"2514", "2515", "2516", "2517", "2518", "2519", "2520", "2521", "2522", "2523", "2524", "2525", "2526", "2527", "2528", "2529", "2530", "2531", "2532", "2533", "2534", "2535", "2536", "2537", "2538", "2539", "2540", "2541", "2542", "2543", "2544", "2545", "2546", "2547", "2548", "2549", "2550", "2551", "2552", "2553", "2554", "2555", "2556", "2557", "2558", "2559", "2560", "2561", "2562", "2563", "2564", "2565", "2566", "2567", "2568", "2569", "2570", "2571", "2572", "2573", "2574", "2575", "2576", "2577", "2578", "2579", "2580", "2581", "2582", "2583", "2584", "2585", "2586", "2587", "2588", "2589", "2590", "2591", "2592", "2593", "2594", "2595", "2596", "2597", "2598", "2599", "2600", "2601", "2602", "2603", "2604", "2605", "2606", "2607", "2608", "2609", "2610", "2611", "2612", "2613", "2614", "2615", "2616", "2617", "2618", "2619", "2620", "2621", "2622", "2623", "2624", "2625", "2626", "2627", "2628", "2629", "2630", "2631", "2632", "2633", "2634", "2635", "2636", "2637", "2638", 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"2764", "2765", "2766", "2767", "2768", "2769", "2770", "2771", "2772", "2773", "2774", "2775", "2776", "2777", "2778", "2779", "2780", "2781", "2782", "2783", "2784", "2785", "2786", "2787", "2788", "2789", "2790", "2791", "2792", "2793", "2794", "2795", "2796", "2797", "2798", "2799", "2800", "2801", "2802", "2803", "2804", "2805", "2806", "2807", "2808", "2809", "2810", "2811", "2812", "2813", "2814", "2815", "2816", "2817", "2818", "2819", "2820", "2821", "2822", "2823", "2824", "2825", "2826", "2827", "2828", "2829", "2830", "2831", "2832", "2833", "2834", "2835", "2836", "2837", "2838", "2839", "2840", "2841", "2842", "2843", "2844", "2845", "2846", "2847", "2848", "2849", "2850", "2851", "2852", "2853", "2854", "2855", "2856", "2857", "2858", "2859", "2860", "2861", "2862", "2863", "2864", "2865", "2866", "2867", "2868", "2869", "2870", "2871", "2872", "2873", "2874", "2875", "2876", "2877", "2878", "2879", "2880", "2881", "2882", "2883", "2884", "2885", "2886", "2887", "2888", 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4L), Dimnames = list(NULL, NULL), x = c(1, 1, 1, 1), factors = list()), Lind = c(1L, 1L, 1L, 1L), n = 3000L, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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(marker1_vals = c(15, 11, 12, 11, 12, 11, 16, 12, 11, 10, 15, 14, 14, 13, 14, 11, 12, 16, 16, 13, 13, 12, 9, 11, 13, 14, 14, 11, 11, 11, 13, 12, 13, 12, 13, 10, 13, 11, 13, 12, 13, 11, 15, 14, 13, 13, 14, 13, 8, 14, 12, 13, 15, 11, 13, 15, 13, 10, 11, 14, 14, 15, 11, 14, 13, 11, 13, 13, 11, 12, 11, 12, 11, 14, 15, 12, 14, 14, 11, 10, 10, 14, 15, 14, 11, 12, 13, 12, 14, 12, 12, 16, 14, 11, 12, 9, 10, 12, 10, 12, 12, 11, 9, 13, 13, 10, 12, 14, 15, 11, 11, 12, 12, 11, 11, 12, 13, 12, 14, 11, 12, 15, 12, 12, 12, 15, 13, 17, 12, 13, 12, 14, 8, 13, 13, 14, 12, 12, 16, 14, 12, 11, 13, 12, 13, 16, 13, 15, 11, 14, 13, 11, 14, 12, 13, 10, 10, 13, 13, 16, 13, 9, 12, 16, 10, 13, 13, 11, 12, 12, 13, 12, 12, 13, 14, 10, 15, 14, 12, 13, 12, 13, 12, 15, 12, 10, 12, 14, 8, 12, 15, 14, 13, 10, 15, 10, 12, 12, 11, 11, 14, 15, 11, 11, 11, 11, 13, 15, 10, 9, 11, 14, 12, 13, 11, 12, 13, 13, 12, 11, 10, 11, 14, 10, 12, 12, 13, 17, 11, 9, 11, 13, 12, 12, 14, 17, 12, 10, 11, 12, 14, 12, 12, 12, 10, 12, 11, 13, 12, 12, 11, 10, 13, 10, 12, 12, 15, 16, 13, 12, 12, 15, 14, 14, 12, 12, 12, 11, 12, 14, 12, 10, 13, 14, 10, 15, 12, 11, 13, 11, 15, 12, 13, 11, 11, 12, 12, 13, 16, 15, 12, 13, 15, 13, 15, 10, 12, 12, 11, 16, 17, 11, 13, 12, 12, 11, 15, 14, 13, 12, 10, 12, 12, 13, 12, 11, 11, 11, 11, 15, 13, 13, 10, 11, 10, 11, 10, 9, 13, 13, 8, 10, 11, 14, 12, 11, 9, 12, 13, 11, 10, 12, 9, 13, 12, 15, 13, 15, 11, 14, 12, 12, 10, 10, 9, 12, 10, 15, 14, 18, 11, 16, 10, 11, 12, 15, 14, 9, 14, 12, 12, 8, 10, 12, 13, 14, 13, 13, 14, 15, 11, 12, 13, 11, 13, 12, 14, 11, 11, 10, 10, 16, 12, 13, 14, 13, 11, 10, 11, 12, 12, 17, 16, 10, 13, 13, 10, 12, 11, 19, 14, 10, 14, 12, 11, 10, 13, 11, 13, 12, 13, 10, 12, 13, 9, 13, 15, 14, 11, 10, 10, 10, 14, 14, 13, 15, 10, 14, 15, 15, 12, 13, 16, 8, 11, 13, 15, 13, 11, 12, 9, 12, 12, 11, 12, 11, 13, 10, 14, 9, 12, 10, 13, 12, 15, 13, 10, 9, 12, 13, 14, 14, 11, 16, 12, 11, 14, 13, 12, 13, 14, 14, 11, 12, 12, 14, 14, 11, 14, 14, 14, 15, 12, 13, 11, 15, 15, 11, 12, 11, 12, 11, 13, 13, 12, 11, 14, 13, 13, 14, 12, 15, 14, 12, 11, 12, 14, 11, 15, 14, 14, 12, 14, 13, 10, 12, 11, 12, 12, 11, 11, 10, 11, 10, 12, 15, 12, 12, 12, 16, 14, 11, 11, 12, 11, 12, 8, 13, 13, 11, 13, 12, 10, 12, 12, 12, 12, 11, 12, 14, 13, 16, 12, 15, 12, 15, 14, 13, 12, 11, 11, 12, 13, 11, 14, 12, 12, 12, 11, 12, 13, 16, 13, 11, 12, 13, 11, 9, 13, 11, 13, 13, 15, 13, 13, 13, 12, 11, 14, 12, 13, 16, 11, 15, 11, 14, 13, 13, 15, 12, 11, 13, 18, 11, 10, 12, 11, 13, 11, 13, 13, 14, 12, 12, 16, 9, 14, 14, 13, 12, 13, 12, 14, 15, 13, 10, 10, 13, 9, 11, 14, 10, 15, 13, 9, 11, 11, 11, 13, 12, 12, 13, 10, 9, 11, 12, 8, 14, 11, 12, 12, 10, 15, 14, 9, 11, 12, 10, 14, 14, 14, 10, 11, 13, 11, 13, 12, 13, 10, 11, 10, 11, 10, 13, 11, 13, 11, 11, 11, 16, 11, 14, 13, 13, 11, 15, 12, 12, 13, 11, 14, 14, 9, 18, 14, 12, 13, 10, 8, 13, 13, 10, 13, 13, 15, 13, 14, 11, 11, 13, 11, 13, 16, 13, 14, 14, 12, 12, 15, 13, 15, 12, 11, 15, 13, 13, 11, 15, 10, 12, 10, 14, 11, 14, 12, 14, 13, 15, 13, 17, 18, 24, 24, 23, 23, 20, 17, 25, 17, 25, 14, 21, 20, 19, 22, 26, 26, 21, 22, 22, 20, 16, 19, 15, 15, 17, 32, 23, 23, 22, 18, 18, 23, 22, 17, 18, 18, 19, 23, 21, 17, 16, 27, 25, 20, 16, 18, 23, 18, 15, 16, 25, 20, 22, 17, 21, 17, 21, 21, 20, 17, 21, 20, 18, 21, 20, 20, 17, 18, 30, 21, 18, 17, 20, 21, 20, 22, 21, 22, 21, 25, 17, 20, 20, 24, 18, 19, 23, 22, 24, 16, 21, 17, 24, 17, 19, 22, 16, 21, 19, 20, 20, 17, 21, 24, 16, 23, 22, 17, 21, 24, 21, 19, 20, 17, 21, 14, 21, 19, 18, 23, 18, 16, 23, 20, 16, 21, 25, 20, 24, 15, 24, 18, 21, 14, 22, 17, 20, 25, 21, 21, 14, 17, 14, 20, 22, 16, 22, 26, 25, 20, 19, 17, 17, 19, 19, 22, 29, 20, 26, 21, 26, 20, 26, 21, 19, 19, 18, 19, 20, 20, 19, 15, 21, 26, 16, 21, 19, 19, 17, 15, 19, 19, 14, 22, 22, 22, 20, 25, 17, 21, 23, 23, 16, 21, 21, 23, 23, 13, 22, 23, 18, 23, 21, 23, 20, 26, 20, 18, 21, 21, 22, 19, 19, 17, 19, 21, 22, 15, 19, 24, 19, 22, 23, 17, 18, 23, 18, 18, 16, 23, 25, 19, 22, 25, 19, 18, 24, 23, 19, 19, 17, 18, 21, 20, 19, 19, 21, 27, 23, 27, 18, 21, 22, 20, 17, 21, 22, 19, 27, 16, 17, 25, 17, 21, 24, 24, 22, 14, 20, 22, 16, 13, 21, 19, 18, 19, 16, 26, 22, 22, 14, 18, 16, 26, 28, 22, 19, 15, 23, 15, 18, 31, 20, 26, 17, 16, 15, 18, 16, 22, 18, 23, 21, 22, 16, 19, 19, 22, 18, 21, 19, 18, 22, 19, 20, 19, 15, 25, 17, 18, 25, 23, 24, 21, 19, 20, 15, 17, 19, 21, 20, 19, 24, 20, 17, 23, 18, 18, 16, 21, 20, 22, 20, 16, 17, 18, 15, 23, 23, 17, 19, 20, 24, 16, 15, 21, 20, 23, 18, 23, 19, 20, 23, 20, 15, 18, 13, 20, 19, 18, 19, 20, 23, 22, 20, 21, 20, 23, 24, 16, 16, 23, 17, 17, 20, 20, 19, 22, 18, 24, 19, 20, 17, 25, 24, 18, 17, 18, 18, 21, 22, 16, 18, 19, 18, 14, 25, 18, 20, 26, 22, 15, 20, 16, 22, 17, 17, 17, 19, 23, 23, 23, 24, 21, 20, 17, 22, 25, 20, 21, 22, 17, 23, 16, 16, 20, 25, 22, 23, 18, 21, 21, 23, 20, 18, 19, 19, 15, 22, 19, 22, 14, 18, 18, 21, 22, 22, 20, 22, 19, 22, 20, 28, 18, 23, 16, 22, 20, 19, 22, 18, 21, 20, 16, 16, 19, 16, 21, 24, 20, 18, 23, 19, 18, 28, 19, 20, 17, 17, 16, 16, 24, 18, 17, 21, 19, 22, 21, 22, 18, 18, 19, 21, 17, 15, 15, 22, 19, 22, 15, 18, 24, 22, 18, 20, 22, 21, 20, 14, 16, 19, 19, 19, 20, 18, 22, 20, 21, 19, 23, 22, 18, 28, 17, 20, 25, 24, 18, 23, 19, 20, 25, 20, 19, 20, 15, 16, 21, 18, 20, 19, 22, 20, 25, 20, 17, 22, 18, 14, 20, 19, 19, 23, 28, 17, 24, 16, 26, 17, 15, 20, 19, 20, 18, 24, 22, 21, 21, 24, 23, 20, 18, 25, 17, 27, 18, 24, 20, 23, 26, 23, 19, 23, 17, 21, 19, 24, 17, 19, 23, 18, 22, 22, 21, 17, 23, 22, 23, 18, 14, 15, 14, 26, 25, 23, 21, 20, 24, 15, 17, 25, 19, 19, 18, 17, 20, 25, 15, 17, 26, 22, 18, 18, 19, 22, 23, 27, 17, 16, 18, 24, 29, 14, 21, 19, 16, 18, 14, 21, 24, 27, 20, 17, 25, 18, 16, 25, 16, 17, 21, 20, 18, 19, 31, 24, 21, 23, 18, 13, 21, 20, 18, 21, 17, 18, 26, 22, 24, 21, 16, 15, 22, 18, 17, 20, 19, 28, 16, 22, 19, 20, 18, 23, 14, 22, 22, 24, 25, 17, 19, 21, 21, 20, 18, 17, 29, 23, 23, 19, 26, 24, 16, 20, 19, 23, 18, 20, 22, 18, 17, 23, 18, 24, 18, 19, 23, 18, 19, 22, 22, 20, 22, 21, 18, 19, 22, 21, 20, 18, 16, 19, 19, 18, 15, 24, 20, 25, 23, 24, 96, 85, 90, 93, 92, 98, 93, 76, 93, 93, 96, 97, 70, 96, 88, 95, 89, 88, 96, 92, 76, 84, 89, 81, 83, 99, 95, 84, 92, 77, 97, 93, 91, 98, 87, 96, 95, 78, 90, 89, 99, 94, 94, 95, 95, 96, 99, 98, 95, 95, 93, 99, 96, 96, 92, 87, 98, 89, 96, 96, 84, 94, 94, 93, 94, 87, 95, 89, 96, 97, 95, 90, 99, 95, 88, 95, 87, 98, 97, 99, 100, 99, 97, 90, 90, 84, 74, 84, 96, 95, 99, 99, 84, 84, 83, 80, 80, 67, 80, 93, 96, 98, 73, 91, 100, 83, 97, 76, 98, 96, 69, 98, 99, 93, 88, 77, 89, 90, 98, 93, 97, 99, 99, 96, 88, 98, 70, 93, 91, 95, 97, 98, 96, 98, 92, 89, 79, 79, 98, 90, 93, 96, 84, 85, 96, 70, 89, 89, 77, 86, 70, 90, 53, 95, 82, 97, 95, 81, 85, 96, 97, 96, 94, 92, 92, 89, 88, 99, 100, 100, 98, 89, 98, 100, 97, 100, 98, 98, 82, 98, 99, 96, 91, 92, 88, 94, 99, 99, 96, 75, 80, 79, 96, 87, 100, 87, 93, 88, 98, 81, 91, 86, 97, 93, 77, 97, 92, 85, 91, 93, 93, 90, 91, 98, 100, 99, 96, 95, 87, 97, 98, 91, 87, 94, 85, 100, 99, 96, 85, 100, 90, 100, 91, 80, 97, 61, 58, 83, 93, 99, 94, 90, 95, 85, 98, 94, 81, 99, 95, 64, 94, 86, 90, 88, 97, 94, 81, 89, 96, 97, 90, 98, 93, 98, 95, 95, 100, 95, 94, 96, 100, 99, 100, 81, 98, 99, 86, 81, 99, 90, 77, 99, 97, 99, 79, 94, 92, 95, 90, 99, 94, 84, 83, 95, 94, 93, 86, 99, 99, 98, 75, 93, 96, 91, 92, 100, 91, 86, 100, 92, 95, 99, 79, 83, 84, 93, 84, 97, 94, 95, 93, 89, 91, 98, 99, 87, 79, 87, 97, 89, 84, 90, 99, 86, 100, 82, 98, 91, 88, 85, 97, 91, 82, 98, 66, 80, 97, 95, 79, 99, 94, 91, 93, 94, 90, 96, 99, 79, 92, 81, 90, 93, 89, 85, 82, 91, 88, 81, 95, 95, 93, 95, 95, 86, 96, 94, 99, 99, 82, 84, 86, 96, 98, 94, 86, 100, 91, 96, 97, 99, 97, 91, 97, 95, 78, 98, 93, 90, 99, 90, 91, 90, 96, 98, 96, 85, 88, 89, 77, 96, 91, 87, 97, 97, 95, 61, 91, 93, 81, 99, 98, 95, 96, 96, 85, 64, 97, 96, 96, 91, 90, 96, 91, 95, 97, 97, 99, 93, 74, 96, 85, 96, 99, 97, 100, 99, 94, 94, 100, 65, 92, 93, 85, 95, 95, 86, 95, 97, 99, 91, 78, 91, 89, 94, 99, 92, 82, 100, 91, 99, 97, 97, 96, 94, 85, 96, 84, 92, 96, 98, 96, 96, 94, 91, 73, 100, 100, 97, 86, 98, 92, 90, 92, 83, 97, 92, 94, 94, 93, 87, 96, 93, 96, 93, 96, 89, 89, 96, 94, 100, 89, 92, 98, 86, 93, 98, 99, 87, 85, 93, 92, 93, 97, 97, 98, 57, 95, 87, 95, 100, 87, 91, 94, 79, 76, 94, 98, 83, 98, 87, 97, 100, 83, 92, 98, 94, 95, 91, 97, 83, 99, 95, 99, 96, 90, 75, 95, 100, 94, 84, 94, 96, 97, 94, 66, 95, 83, 89, 100, 72, 96, 94, 96, 83, 97, 84, 88, 97, 92, 89, 81, 99, 93, 92, 95, 84, 74, 88, 81, 95, 97, 89, 82, 86, 92, 83, 83, 92, 93, 99, 78, 93, 85, 98, 99, 99, 97, 82, 89, 94, 99, 83, 95, 96, 75, 73, 97, 91, 84, 95, 78, 96, 61, 100, 77, 93, 81, 96, 96, 93, 99, 97, 91, 96, 89, 71, 92, 100, 100, 96, 80, 94, 90, 100, 100, 97, 86, 93, 74, 86, 99, 82, 94, 99, 95, 96, 78, 92, 74, 83, 94, 89, 66, 95, 94, 90, 83, 98, 90, 91, 96, 95, 86, 99, 99, 100, 88, 80, 91, 99, 86, 94, 92, 86, 100, 98, 93, 97, 77, 75, 100, 97, 98, 93, 86, 97, 100, 88, 97, 95, 98, 95, 90, 80, 95, 88, 78, 98, 94, 94, 80, 92, 100, 93, 96, 98, 93, 93, 93, 91, 68, 95, 100, 96, 87, 81, 97, 92, 85, 59, 73, 98, 94, 72, 88, 77, 86, 99, 98, 93, 88, 82, 96, 85, 91, 100, 81, 87, 94, 96, 57, 30, 37, 46, 47, 50, 32, 60, 38, 48, 49, 42, 45, 50, 58, 37, 58, 54, 57, 32, 32, 44, 38, 41, 46, 53, 34, 40, 43, 41, 55, 49, 44, 42, 54, 50, 39, 44, 55, 56, 56, 49, 58, 39, 54, 58, 59, 49, 51, 38, 40, 48, 54, 40, 54, 32, 36, 60, 43, 36, 52, 42, 34, 54, 38, 40, 42, 34, 41, 41, 53, 58, 45, 44, 35, 43, 53, 46, 52, 49, 34, 33, 45, 33, 50, 58, 40, 32, 57, 42, 45, 60, 57, 60, 40, 43, 46, 40, 58, 49, 44, 38, 43, 43, 33, 30, 54, 34, 51, 41, 53, 30, 47, 52, 48, 41, 32, 50, 55, 30, 33, 39, 41, 44, 50, 32, 51, 34, 30, 53, 56, 37, 39, 36, 50, 39, 43, 50, 46, 30, 39, 55, 31, 53, 45, 42, 42, 42, 48, 39, 30, 57, 46, 59, 60, 52, 40, 46, 55, 54, 58, 37, 45, 45, 60, 30, 32, 49, 30, 38, 45, 30, 31, 52, 53, 33, 51, 39, 46, 47, 51, 43, 45, 44, 41, 40, 47, 39, 40, 35, 30, 35, 48, 50, 60, 34, 30, 39, 45, 59, 49, 60, 38, 35, 35, 42, 34, 40, 57, 47, 44, 55, 57, 49, 44, 36, 46, 60, 55, 31, 54, 54, 30, 60, 37, 30, 41, 45, 46, 36, 35, 51, 33, 48, 30, 53, 34, 34, 42, 42, 59, 58, 60, 54, 56, 38, 54, 60, 55, 55, 58, 37, 37, 43, 52, 38, 59, 31, 45, 46, 50, 44, 30, 51, 37, 31, 60, 52, 40, 55, 34, 53, 60, 39, 37, 34, 54, 37, 53, 47, 50, 35, 48, 53, 41, 46, 33, 36, 45, 51, 37, 46, 30, 51, 48, 34, 34, 31, 56, 33, 39, 40, 42, 50, 56, 52, 49, 40, 39, 50, 48, 42, 58, 34, 37, 44, 32, 48, 50, 34, 55, 34, 34, 49, 56, 48, 45, 31, 43, 49, 43, 38, 54, 41, 52, 43, 60, 39, 41, 38, 38, 40, 58, 35, 35, 40, 55, 59, 38, 43, 49, 48, 48, 31, 45, 59, 57, 40, 39, 35, 35, 49, 35, 60, 33, 39, 32, 37, 44, 32, 30, 32, 46, 33, 49, 40, 45, 45, 47, 51, 40, 55, 60, 30, 49, 33, 53, 57, 51, 34, 56, 56, 43, 43, 51, 31, 39, 31, 51, 58, 37, 60, 53, 54, 50, 30, 34, 57, 56, 49, 47, 44, 50, 40, 35, 40, 58, 60, 40, 33, 39, 40, 60, 53, 58, 54, 32, 40, 33, 42, 33, 54, 47, 41, 44, 46, 49, 50, 39, 54, 47, 44, 58, 54, 55, 49, 42, 50, 55, 58, 31, 49, 31, 40, 43, 32, 47, 49, 49, 45, 36, 59, 34, 58, 50, 58, 45, 50, 55, 40, 49, 41, 45, 35, 43, 48, 59, 32, 59, 40, 54, 51, 55, 59, 50, 33, 51, 55, 60, 36, 34, 44, 34, 37, 35, 55, 46, 59, 38, 44, 46, 52, 50, 34, 44, 40, 43, 57, 39, 47, 57, 37, 56, 31, 49, 56, 34, 48, 39, 55, 52, 55, 53, 53, 39, 30, 45, 42, 56, 56, 38, 41, 30, 33, 60, 51, 47, 35, 52, 55, 31, 44, 44, 34, 56, 46, 37, 45, 37, 38, 56, 51, 35, 52, 32, 44, 45, 54, 31, 53, 50, 45, 40, 31, 49, 36, 44, 59, 36, 34, 34, 42, 30, 56, 40, 36, 35, 37, 56, 42, 45, 37, 37, 51, 34, 39, 40, 53, 41, 45, 34, 48, 49, 45, 34, 54, 41, 46, 52, 49, 59, 49, 53, 43, 55, 54, 42, 50, 36, 54, 34, 42, 51, 45, 33, 48, 53, 48, 49, 36, 40, 56, 54, 47, 53, 46, 55, 39, 38, 53, 39, 51, 48, 32, 54, 56, 45, 55, 50, 55, 56, 49, 57, 34, 50, 35, 33, 36, 44, 33, 52, 59, 49, 31, 38, 50, 39, 42, 31, 32, 59, 54, 56, 59, 50, 35, 46, 52, 52, 37, 56, 55, 58, 31, 47, 32, 52, 43, 46, 39, 36, 52, 57, 43, 42, 52, 43, 52, 47, 57, 40, 35, 55, 58, 38, 60, 52, 44, 59, 54, 50, 42, 60, 46, 46, 39, 40, 30, 30, 48, 56, 35, 60, 42, 34, 42, 44, 38, 55, 31, 35, 56, 60, 43, 57, 41, 48, 31, 50, 39, 50, 42, 46, 39, 58, 42, 50, 31, 35, 49, 49, 48, 52, 53, 52, 32, 47, 46, 60, 60), slide_id = 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, 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, 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, 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, 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, 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, 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, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 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3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), p = 0:3000, Dim = c(4L, 3000L), Dimnames = list( c("slide1", "slide2", "slide3", "slide4"), 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", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", 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3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), p = 0:3000, Dim = c(4L, 3000L), Dimnames = list(c("slide1", "slide2", "slide3", "slide4"), 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", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", 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"337", "338", "339", "340", "341", "342", "343", "344", "345", "346", "347", "348", "349", "350", "351", "352", "353", "354", "355", "356", "357", "358", "359", "360", "361", "362", "363", "364", "365", "366", "367", "368", "369", "370", "371", "372", "373", "374", "375", "376", "377", "378", "379", "380", "381", "382", "383", "384", "385", "386", "387", "388", "389", "390", "391", "392", "393", "394", "395", "396", "397", "398", "399", "400", "401", "402", "403", "404", "405", "406", "407", "408", "409", "410", "411", "412", "413", "414", "415", "416", "417", "418", "419", "420", "421", "422", "423", "424", "425", "426", "427", "428", "429", "430", "431", "432", "433", "434", "435", "436", "437", "438", "439", "440", "441", "442", "443", "444", "445", "446", "447", "448", "449", "450", "451", "452", "453", "454", "455", "456", "457", "458", "459", "460", "461", "462", "463", "464", "465", "466", "467", "468", "469", "470", "471", "472", "473", "474", "475", "476", "477", "478", "479", "480", "481", "482", "483", "484", "485", "486", "487", "488", "489", "490", "491", "492", "493", "494", "495", "496", "497", "498", "499", "500", "501", "502", "503", "504", "505", "506", "507", "508", "509", "510", "511", "512", "513", "514", "515", "516", "517", "518", "519", "520", "521", "522", "523", "524", "525", "526", "527", "528", "529", "530", "531", "532", "533", "534", "535", "536", "537", "538", "539", "540", "541", "542", "543", "544", "545", "546", "547", "548", "549", "550", "551", "552", "553", "554", "555", "556", "557", "558", "559", "560", "561", "562", "563", "564", "565", "566", "567", "568", "569", "570", "571", "572", "573", "574", "575", "576", "577", "578", "579", "580", "581", "582", "583", "584", "585", "586", "587", "588", "589", "590", "591", "592", "593", "594", "595", "596", "597", "598", "599", "600", "601", "602", "603", "604", "605", "606", "607", "608", "609", "610", "611", "612", "613", "614", "615", "616", "617", "618", "619", "620", "621", "622", "623", "624", "625", "626", "627", "628", "629", "630", "631", "632", "633", "634", "635", "636", "637", "638", "639", "640", "641", "642", "643", "644", "645", "646", "647", "648", "649", "650", "651", "652", "653", "654", "655", "656", "657", "658", "659", "660", "661", "662", "663", "664", "665", "666", "667", "668", "669", "670", "671", "672", "673", "674", "675", "676", "677", "678", "679", "680", "681", "682", "683", "684", "685", "686", "687", "688", "689", "690", "691", "692", "693", "694", "695", "696", "697", "698", "699", "700", "701", "702", "703", "704", "705", "706", "707", "708", "709", "710", "711", "712", "713", "714", "715", "716", "717", "718", "719", "720", "721", "722", "723", "724", "725", "726", "727", "728", "729", "730", "731", "732", "733", "734", "735", "736", "737", "738", "739", "740", "741", "742", "743", "744", "745", "746", "747", "748", "749", "750", "751", "752", "753", "754", "755", "756", "757", "758", "759", "760", "761", "762", "763", "764", "765", "766", "767", "768", "769", "770", "771", "772", "773", "774", "775", "776", "777", "778", "779", "780", "781", "782", "783", "784", "785", "786", "787", "788", "789", "790", "791", "792", "793", "794", "795", "796", "797", "798", "799", "800", "801", "802", "803", "804", "805", "806", "807", "808", "809", "810", "811", "812", "813", "814", "815", "816", "817", "818", "819", "820", "821", "822", "823", "824", "825", "826", "827", "828", "829", "830", "831", "832", "833", "834", "835", "836", "837", "838", "839", "840", "841", "842", "843", "844", "845", "846", "847", "848", "849", "850", "851", "852", "853", "854", "855", "856", "857", "858", "859", "860", "861", "862", "863", "864", "865", "866", "867", "868", "869", "870", "871", "872", "873", "874", "875", "876", "877", "878", "879", "880", "881", "882", "883", "884", "885", "886", "887", "888", "889", "890", "891", "892", "893", "894", "895", "896", "897", "898", "899", "900", "901", "902", "903", "904", "905", "906", "907", "908", "909", "910", "911", "912", "913", "914", "915", "916", "917", "918", "919", "920", "921", "922", "923", "924", "925", "926", "927", "928", "929", "930", "931", "932", "933", "934", "935", "936", "937", "938", "939", "940", "941", "942", "943", "944", "945", "946", "947", "948", "949", "950", "951", "952", "953", "954", "955", "956", "957", "958", "959", "960", "961", "962", "963", "964", "965", "966", "967", "968", "969", "970", "971", "972", "973", "974", "975", "976", "977", "978", "979", "980", "981", "982", "983", "984", "985", "986", "987", "988", "989", "990", "991", "992", "993", "994", "995", "996", "997", "998", "999", "1000", "1001", "1002", "1003", "1004", "1005", "1006", "1007", "1008", "1009", "1010", "1011", "1012", "1013", "1014", "1015", "1016", "1017", "1018", "1019", "1020", "1021", "1022", "1023", "1024", "1025", "1026", "1027", "1028", "1029", "1030", "1031", "1032", "1033", "1034", "1035", "1036", "1037", "1038", "1039", "1040", "1041", "1042", "1043", "1044", 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1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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(slide_id = 4L)), 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(f, data = dat, ...) 12: get_var_proportions(mx_data, metadata_cols, table = "raw", m = marker, formula_override) 13: run_var_proportions(mx_data, table = "both", metadata_cols = NULL, formula_override = NULL, save_models = FALSE) 14: eval(expr, envir, enclos) 15: eval(expr, envir, enclos) 16: eval_with_user_handlers(expr, envir, enclos, user_handlers) 17: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)) 18: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler) 19: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)) 20: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))) 21: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing) 22: evaluate::evaluate(...) 23: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)) 24: in_dir(input_dir(), expr) 25: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))) 26: eng_r(options) 27: block_exec(params) 28: call_block(x) 29: process_group(group) 30: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)) 31: withCallingHandlers(expr, error = function(e) { loc = if (is.function(fun)) trimws(fun(label)) else "" if (loc != "") loc = sprintf(" at lines %s", loc) message(one_string(handler(e, loc)))}) 32: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(e, loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc) 33: process_file(text, output) 34: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet) 35: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...) 36: vweave_rmarkdown(...) 37: engine$weave(file, quiet = quiet, encoding = enc) 38: doTryCatch(return(expr), name, parentenv, handler) 39: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 40: tryCatchList(expr, classes, parentenv, handlers) 41: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) 42: tools::buildVignettes(dir = "/tmp/th798/16120028/R-release/891/mxnorm.Rcheck/vign_test/mxnorm", skip = TRUE, ser_elibs = "/tmp/th798/16120028/Rtmp71C7u8/file2614486fde5bd6.rds") An irrecoverable exception occurred. R is aborting now ... * checking PDF version of manual ... OK * DONE Status: 3 ERRORs, 1 NOTE See '/tmp/th798/16120028/R-release/891/mxnorm.Rcheck/00check.log' for details. [1] "2025-03-26 01:38:59 MST" > system(paste(c("diff -u", Rcheck.list), collapse=" ")) --- R_version_4.4.3_2025-02-28/release_1.17.0.Rcheck/00check.log 2025-03-26 01:36:35.276009100 -0700 +++ R_version_4.4.3_2025-02-28/master_1.17.99.77b43940971091a63baeccf65ec3b2d729dc3a57.Rcheck/00check.log 2025-03-26 01:38:59.360886615 -0700 @@ -211,7 +211,7 @@ 39: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 40: tryCatchList(expr, classes, parentenv, handlers) 41: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))}) -42: tools::buildVignettes(dir = "/tmp/th798/16120028/R-release/891/mxnorm.Rcheck/vign_test/mxnorm", skip = TRUE, ser_elibs = "/tmp/th798/16120028/Rtmph0lkK7/file25b6ea51a8845.rds") +42: tools::buildVignettes(dir = "/tmp/th798/16120028/R-release/891/mxnorm.Rcheck/vign_test/mxnorm", skip = TRUE, ser_elibs = "/tmp/th798/16120028/Rtmp71C7u8/file2614486fde5bd6.rds") An irrecoverable exception occurred. R is aborting now ... * checking PDF version of manual ... OK > 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) + } >