Note: the module "R" cannot be unloaded because it was not loaded.

WARNING: ignoring environment value of R_HOME

R Under development (unstable) (2025-05-18 r88216) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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> 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/2025-05-19/deps.csv", 
task.str = "1488", release = "/scratch/th798/data.table-revdeps/2025-05-19/data.table_release_1.17.2.tar.gz", 
master = "/scratch/th798/data.table-revdeps/2025-05-19/data.table_master_1.17.99.c4ea09e099b1833fae0eacb50552bce6f051ed82.tar.gz"
)
> (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers
[1] "/tmp/th798/17369645/R-devel/1488"
> if(requireNamespace("R.cache"))R.cache::getCachePath()
Loading required namespace: R.cache
[1] "/tmp/th798/17369645/R-devel/1488/R.cache"
> task.id <- as.integer(cargs[["task.str"]])
> deps.df <- read.csv(cargs[["deps.csv"]])
> (rev.dep <- deps.df$Package[task.id])
[1] "topics"
> job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id)
> setwd(task.dir)
> .libPaths()
[1] "/tmp/th798/17369645/R-devel/1488/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] "2025-05-19 00:32:06 MST"
> install.time <- system.time({
+   install.packages(rev.dep, dep=TRUE)
+ })
Installing package into '/tmp/th798/17369645/R-devel/1488/library'
(as 'lib' is unspecified)
also installing the dependencies 'DiceDesign', 'sfd', 'hardhat', 'sparsevctrs', 'dials', 'GPfit', 'modelenv', 'recipes', 'parsnip', 'tune', 'workflows', 'yardstick', 'textmineR', 'mallet', 'ngram', 'text', 'vdiffr'

trying URL 'http://cloud.r-project.org/src/contrib/DiceDesign_1.10.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/sfd_0.1.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/hardhat_1.4.1.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/sparsevctrs_0.3.3.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/dials_1.4.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/GPfit_1.0-9.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/modelenv_0.2.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/recipes_1.3.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/parsnip_1.3.1.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/tune_1.3.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/workflows_1.2.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/yardstick_1.3.2.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/textmineR_3.0.5.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/mallet_1.3.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/ngram_3.2.3.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/text_1.5.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/vdiffr_1.0.8.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/topics_0.50.tar.gz'
* installing *source* package 'DiceDesign' ...
** this is package 'DiceDesign' version '1.10'
** package 'DiceDesign' successfully unpacked and MD5 sums checked
** using staged installation
** 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    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c C_StraussDesign.c -o C_StraussDesign.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c C_rss.c -o C_rss.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c DiceDesign_init.c -o DiceDesign_init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o DiceDesign.so C_StraussDesign.o C_rss.o DiceDesign_init.o
installing to /tmp/th798/17369645/R-devel/1488/library/00LOCK-DiceDesign/00new/DiceDesign/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DiceDesign)
* installing *source* package 'sfd' ...
** this is package 'sfd' version '0.1.0'
** package 'sfd' 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
** 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 (sfd)
* installing *source* package 'sparsevctrs' ...
** this is package 'sparsevctrs' version '0.3.3'
** package 'sparsevctrs' successfully unpacked and MD5 sums checked
** using staged installation
** 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    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c altrep-sparse-double.c -o altrep-sparse-double.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c altrep-sparse-integer.c -o altrep-sparse-integer.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c altrep-sparse-logical.c -o altrep-sparse-logical.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c altrep-sparse-string.c -o altrep-sparse-string.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c init.c -o init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c sparse-arithmatic.c -o sparse-arithmatic.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c sparse-dummy.c -o sparse-dummy.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c sparse-extractors.c -o sparse-extractors.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c sparse-utils.c -o sparse-utils.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 sparsevctrs.so altrep-sparse-double.o altrep-sparse-integer.o altrep-sparse-logical.o altrep-sparse-string.o init.o sparse-arithmatic.o sparse-dummy.o sparse-extractors.o sparse-utils.o
installing to /tmp/th798/17369645/R-devel/1488/library/00LOCK-sparsevctrs/00new/sparsevctrs/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** 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 (sparsevctrs)
* installing *source* package 'GPfit' ...
** this is package 'GPfit' version '1.0-9'
** package 'GPfit' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (GPfit)
* installing *source* package 'modelenv' ...
** this is package 'modelenv' version '0.2.0'
** package 'modelenv' 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 (modelenv)
* installing *source* package 'textmineR' ...
** this is package 'textmineR' version '3.0.5'
** package 'textmineR' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
using C++11
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c CalcLikelihoodC.cpp -o CalcLikelihoodC.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c CalcSumSquares.cpp -o CalcSumSquares.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c Dtm2DocsC.cpp -o Dtm2DocsC.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c HellingerMat.cpp -o HellingerMat.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c Hellinger_cpp.cpp -o Hellinger_cpp.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c JSD_cpp.cpp -o JSD_cpp.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c JSDmat.cpp -o JSDmat.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c lda_c_functions.cpp -o lda_c_functions.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -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 textmineR.so CalcLikelihoodC.o CalcSumSquares.o Dtm2DocsC.o HellingerMat.o Hellinger_cpp.o JSD_cpp.o JSDmat.o RcppExports.o lda_c_functions.o
installing to /tmp/th798/17369645/R-devel/1488/library/00LOCK-textmineR/00new/textmineR/libs
** 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
** 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 (textmineR)
* installing *source* package 'mallet' ...
** this is package 'mallet' version '1.3.0'
** package 'mallet' 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
** 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 (mallet)
* installing *source* package 'ngram' ...
** this is package 'ngram' version '3.2.3'
** package 'ngram' successfully unpacked and MD5 sums checked
** using staged installation
** 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 -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c asweka.c -o asweka.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c babble.c -o babble.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c constructor.c -o constructor.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c converters.c -o converters.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c count.c -o count.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c getseed.c -o getseed.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram_native.c -o ngram_native.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c phrase_table.c -o phrase_table.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c print.c -o print.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/counts.c -o ngram/src/counts.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/gen.c -o ngram/src/gen.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/hash.c -o ngram/src/hash.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/lex.c -o ngram/src/lex.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/process.c -o ngram/src/process.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/wordcmp.c -o ngram/src/wordcmp.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/rand/mt/rand_mt.c -o ngram/src/rand/mt/rand_mt.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/rand/mrg/rand_mrg.c -o ngram/src/rand/mrg/rand_mrg.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/rand/rng_interface.c -o ngram/src/rand/rng_interface.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/rand/samplers.c -o ngram/src/rand/samplers.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 ngram.so asweka.o babble.o constructor.o converters.o count.o getseed.o ngram_native.o phrase_table.o print.o ngram/src/counts.o ngram/src/gen.o ngram/src/hash.o ngram/src/lex.o ngram/src/process.o ngram/src/wordcmp.o ngram/src/rand/mt/rand_mt.o ngram/src/rand/mrg/rand_mrg.o ngram/src/rand/rng_interface.o ngram/src/rand/samplers.o
installing to /tmp/th798/17369645/R-devel/1488/library/00LOCK-ngram/00new/ngram/libs
** R
** demo
** 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 (ngram)
* installing *source* package 'vdiffr' ...
** this is package 'vdiffr' version '1.0.8'
** package 'vdiffr' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
using C++11
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c compare.cpp -o compare.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c cpp11.cpp -o cpp11.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c devSVG.cpp -o devSVG.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/cpp11/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c engine_version.cpp -o engine_version.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -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 vdiffr.so compare.o cpp11.o devSVG.o engine_version.o -lpng -lz
installing to /tmp/th798/17369645/R-devel/1488/library/00LOCK-vdiffr/00new/vdiffr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (vdiffr)
* installing *source* package 'hardhat' ...
** this is package 'hardhat' version '1.4.1'
** package 'hardhat' 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 (hardhat)
* installing *source* package 'topics' ...
** this is package 'topics' version '0.50'
** package 'topics' 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 (topics)
* installing *source* package 'dials' ...
** this is package 'dials' version '1.4.0'
** package 'dials' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (dials)
* installing *source* package 'recipes' ...
** this is package 'recipes' version '1.3.0'
** package 'recipes' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (recipes)
* installing *source* package 'parsnip' ...
** this is package 'parsnip' version '1.3.1'
** package 'parsnip' 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 (parsnip)
* installing *source* package 'yardstick' ...
** this is package 'yardstick' version '1.3.2'
** package 'yardstick' successfully unpacked and MD5 sums checked
** using staged installation
** 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    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c mcc-multiclass.c -o mcc-multiclass.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 yardstick.so init.o mcc-multiclass.o
installing to /tmp/th798/17369645/R-devel/1488/library/00LOCK-yardstick/00new/yardstick/libs
** 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
** 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 (yardstick)
* installing *source* package 'workflows' ...
** this is package 'workflows' version '1.2.0'
** package 'workflows' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (workflows)
* installing *source* package 'tune' ...
** this is package 'tune' version '1.3.0'
** package 'tune' 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
** 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 (tune)
* installing *source* package 'text' ...
** this is package 'text' version '1.5'
** package 'text' 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 (text)

The downloaded source packages are in
	'/tmp/th798/17369645/RtmpxVcdAx/downloaded_packages'
> cat("Time to install revdep:\n")
Time to install revdep:
> print(install.time)
   user  system elapsed 
207.480  15.342 318.131 
> print(Sys.time())
[1] "2025-05-19 00:37:24 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] "2025-05-19 00:37:24 MST"
Installing package into '/tmp/th798/17369645/R-devel/1488/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** this is package 'data.table' version '1.17.2'
** 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/th798/17369645/R-devel/1488/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] "2025-05-19 00:37:48 MST"
* using log directory '/tmp/th798/17369645/R-devel/1488/topics.Rcheck'
* using R Under development (unstable) (2025-05-18 r88216)
* 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 'topics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'topics' version '0.50'
* 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 'topics' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

[1] "2025-05-19 00:40:23 MST"
[1] "2025-05-19 00:40:23 MST"
Installing package into '/tmp/th798/17369645/R-devel/1488/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/th798/17369645/R-devel/1488/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] "2025-05-19 00:40:46 MST"
* using log directory '/tmp/th798/17369645/R-devel/1488/topics.Rcheck'
* using R Under development (unstable) (2025-05-18 r88216)
* 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 'topics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'topics' version '0.50'
* 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 'topics' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

[1] "2025-05-19 00:43:12 MST"
> system(paste(c("diff -u", Rcheck.list), collapse=" "))
> library(data.table, lib.loc=R.home("library"))
> (sig.diff.dt <- myDiff(Rvers))
Key: <checking>
Empty data.table (0 rows and 3 cols): checking,master,release
> 
> ## If there are significant differences, use git bisect to find when
> ## they started.
> if(nrow(sig.diff.dt)){
+   dt.git <- file.path(task.dir, "data.table.git")
+   system(paste("cd ~/R/data.table && git fetch --tags"))
+   system(paste("git clone ~/R/data.table", dt.git))
+   release.tag <- gsub(".tar.gz|.*_", "", cargs[["release"]])
+   rev.parse.cmd <- paste(
+     "cd", dt.git, "&& git rev-parse master")
+   master.sha <- system(rev.parse.cmd, intern=TRUE)
+   merge.base.cmd <- paste(
+     "cd", dt.git, "&& git merge-base master", release.tag)
+   merge.base.sha <- system(merge.base.cmd, intern=TRUE)
+   old.sha <- merge.base.sha
+   run_R <- file.path(proj.dir, "install_dt_then_check_dep.R")
+   sig.diff.dt[, first.bad.commit := NA_character_]
+   sig.diff.dt[, comments := NA_character_]
+   for(diff.i in 1:nrow(sig.diff.dt)){
+     sig.diff.row <- sig.diff.dt[diff.i]
+     bisect.cmd <- paste(
+       "cd", dt.git, "&&",
+       "git bisect start &&",
+       "git bisect old", old.sha, "&&",
+       "git bisect new master &&",
+       "git bisect run",
+       R.home('bin/Rscript'),
+       run_R,
+       shQuote(sig.diff.row$checking),
+       sig.diff.row$release,
+       rev.dep.release.tar.gz,
+       release.tag)
+     print(bisect.cmd)
+     bisect.out <- system(bisect.cmd, intern=TRUE)
+     cat(bisect.out,sep="\n")
+     if(is.null(attr(bisect.out,"status"))){
+       first.bad.sha <- nc::capture_all_str(
+         bisect.out,
+         sha="[0-9a-f]+",
+         " is the first new commit")$sha
+       parent.cmd <- paste(
+         "cd ~/R/data.table && git log --pretty=%P -n 1",
+         first.bad.sha)
+       parent.sha <- system(parent.cmd, intern=TRUE)
+       sig.diff.dt[diff.i, first.bad.commit := first.bad.sha]
+       parent.msg <- paste0("parent=", parent.sha)
+       this.comment <- if(parent.sha==old.sha){
+         paste(parent.msg, "same as git bisect old")
+       }else if(first.bad.sha==master.sha){
+         paste("same as git bisect new=master,", parent.msg)
+       }else{
+         parent.msg
+       }
+       sig.diff.dt[diff.i, comments := this.comment]
+     }
+   }
+   ## add CRAN column.
+   sig.diff.dt[, CRAN := {
+     flavor <- get_flavor(Rvers)
+     details <- data.table(flavor=unique(flavor))[, {
+       base <- "https://www.r-project.org/nosvn/R.check/"
+       u <- paste0(base, flavor, "/", rev.dep, "-00check.txt")
+       check.txt <- tempfile()
+       tryCatch({
+         download.file(u, check.txt, quiet=TRUE)
+       }, error=function(e){
+         NULL
+       })
+       check.lines <- if(file.exists(check.txt)){
+         readLines(check.txt,encoding="UTF-8")
+       }else{
+         ""
+       }
+       repl.lines <- gsub("[\u2018\u2019]", "'", check.lines)
+       ##gsub("[‘’]", "'", check.lines) does not work with LC_ALL=C.
+       myStatus(line.vec=repl.lines)
+     }, by=flavor]
+     select.dt <- data.table(flavor, checking)
+     details[select.dt, msg, on=.(flavor, checking)]
+   }]
+   dir.create(file.path(job.dir, Rvers))
+   diffs.csv <- file.path(job.dir, Rvers, "significant_differences.csv")
+   data.table::fwrite(sig.diff.dt, diffs.csv)
+   print(sig.diff.dt)
+ }
> 
WARNING: ignoring environment value of R_HOME

R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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/2025-05-19/deps.csv", 
task.str = "1488", release = "/scratch/th798/data.table-revdeps/2025-05-19/data.table_release_1.17.2.tar.gz", 
master = "/scratch/th798/data.table-revdeps/2025-05-19/data.table_master_1.17.99.c4ea09e099b1833fae0eacb50552bce6f051ed82.tar.gz"
)
> (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers
[1] "/tmp/th798/17369645/R-release/1488"
> if(requireNamespace("R.cache"))R.cache::getCachePath()
Loading required namespace: R.cache
[1] "/tmp/th798/17369645/R-release/1488/R.cache"
> task.id <- as.integer(cargs[["task.str"]])
> deps.df <- read.csv(cargs[["deps.csv"]])
> (rev.dep <- deps.df$Package[task.id])
[1] "topics"
> job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id)
> setwd(task.dir)
> .libPaths()
[1] "/tmp/th798/17369645/R-release/1488/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] "2025-05-19 00:43:17 MST"
> install.time <- system.time({
+   install.packages(rev.dep, dep=TRUE)
+ })
Installing package into '/tmp/th798/17369645/R-release/1488/library'
(as 'lib' is unspecified)
also installing the dependencies 'DiceDesign', 'sfd', 'hardhat', 'sparsevctrs', 'dials', 'GPfit', 'modelenv', 'recipes', 'rlang', 'parsnip', 'tune', 'workflows', 'yardstick', 'textmineR', 'mallet', 'ngram', 'text'

trying URL 'http://cloud.r-project.org/src/contrib/DiceDesign_1.10.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/sfd_0.1.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/hardhat_1.4.1.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/sparsevctrs_0.3.3.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/dials_1.4.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/GPfit_1.0-9.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/modelenv_0.2.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/recipes_1.3.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/rlang_1.1.6.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/parsnip_1.3.1.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/tune_1.3.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/workflows_1.2.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/yardstick_1.3.2.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/textmineR_3.0.5.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/mallet_1.3.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/ngram_3.2.3.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/text_1.5.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/topics_0.50.tar.gz'
* installing *source* package 'DiceDesign' ...
** this is package 'DiceDesign' version '1.10'
** package 'DiceDesign' successfully unpacked and MD5 sums checked
** using staged installation
** 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    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c C_StraussDesign.c -o C_StraussDesign.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c C_rss.c -o C_rss.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c DiceDesign_init.c -o DiceDesign_init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o DiceDesign.so C_StraussDesign.o C_rss.o DiceDesign_init.o
installing to /tmp/th798/17369645/R-release/1488/library/00LOCK-DiceDesign/00new/DiceDesign/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DiceDesign)
* installing *source* package 'GPfit' ...
** this is package 'GPfit' version '1.0-9'
** package 'GPfit' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (GPfit)
* installing *source* package 'rlang' ...
** this is package 'rlang' version '1.1.6'
** package 'rlang' successfully unpacked and MD5 sums checked
** using staged installation
** 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./rlang/  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fvisibility=hidden -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c capture.c -o capture.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I./rlang/  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fvisibility=hidden -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c internal.c -o internal.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I./rlang/  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fvisibility=hidden -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c rlang.c -o rlang.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I./rlang/  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fvisibility=hidden -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c version.c -o version.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 rlang.so capture.o internal.o rlang.o version.o
installing to /tmp/th798/17369645/R-release/1488/library/00LOCK-rlang/00new/rlang/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rlang)
* installing *source* package 'textmineR' ...
** this is package 'textmineR' version '3.0.5'
** package 'textmineR' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
using C++11
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c CalcLikelihoodC.cpp -o CalcLikelihoodC.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c CalcSumSquares.cpp -o CalcSumSquares.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c Dtm2DocsC.cpp -o Dtm2DocsC.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c HellingerMat.cpp -o HellingerMat.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c Hellinger_cpp.cpp -o Hellinger_cpp.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c JSD_cpp.cpp -o JSD_cpp.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c JSDmat.cpp -o JSDmat.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c lda_c_functions.cpp -o lda_c_functions.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -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 textmineR.so CalcLikelihoodC.o CalcSumSquares.o Dtm2DocsC.o HellingerMat.o Hellinger_cpp.o JSD_cpp.o JSDmat.o RcppExports.o lda_c_functions.o
installing to /tmp/th798/17369645/R-release/1488/library/00LOCK-textmineR/00new/textmineR/libs
** 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
** 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 (textmineR)
* installing *source* package 'mallet' ...
** this is package 'mallet' version '1.3.0'
** package 'mallet' 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
** 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 (mallet)
* installing *source* package 'ngram' ...
** this is package 'ngram' version '3.2.3'
** package 'ngram' successfully unpacked and MD5 sums checked
** using staged installation
** 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 -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c asweka.c -o asweka.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c babble.c -o babble.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c constructor.c -o constructor.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c converters.c -o converters.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c count.c -o count.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c getseed.c -o getseed.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram_native.c -o ngram_native.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c phrase_table.c -o phrase_table.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c print.c -o print.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/counts.c -o ngram/src/counts.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/gen.c -o ngram/src/gen.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/hash.c -o ngram/src/hash.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/lex.c -o ngram/src/lex.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/process.c -o ngram/src/process.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/wordcmp.c -o ngram/src/wordcmp.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/rand/mt/rand_mt.c -o ngram/src/rand/mt/rand_mt.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/rand/mrg/rand_mrg.c -o ngram/src/rand/mrg/rand_mrg.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/rand/rng_interface.c -o ngram/src/rand/rng_interface.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -DNEXTWORDS  -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ngram/src/rand/samplers.c -o ngram/src/rand/samplers.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 ngram.so asweka.o babble.o constructor.o converters.o count.o getseed.o ngram_native.o phrase_table.o print.o ngram/src/counts.o ngram/src/gen.o ngram/src/hash.o ngram/src/lex.o ngram/src/process.o ngram/src/wordcmp.o ngram/src/rand/mt/rand_mt.o ngram/src/rand/mrg/rand_mrg.o ngram/src/rand/rng_interface.o ngram/src/rand/samplers.o
installing to /tmp/th798/17369645/R-release/1488/library/00LOCK-ngram/00new/ngram/libs
** R
** demo
** 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 (ngram)
* installing *source* package 'sfd' ...
** this is package 'sfd' version '0.1.0'
** package 'sfd' 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
** 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 (sfd)
* installing *source* package 'sparsevctrs' ...
** this is package 'sparsevctrs' version '0.3.3'
** package 'sparsevctrs' successfully unpacked and MD5 sums checked
** using staged installation
** 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    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c altrep-sparse-double.c -o altrep-sparse-double.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c altrep-sparse-integer.c -o altrep-sparse-integer.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c altrep-sparse-logical.c -o altrep-sparse-logical.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c altrep-sparse-string.c -o altrep-sparse-string.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c init.c -o init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c sparse-arithmatic.c -o sparse-arithmatic.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c sparse-dummy.c -o sparse-dummy.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c sparse-extractors.c -o sparse-extractors.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c sparse-utils.c -o sparse-utils.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 sparsevctrs.so altrep-sparse-double.o altrep-sparse-integer.o altrep-sparse-logical.o altrep-sparse-string.o init.o sparse-arithmatic.o sparse-dummy.o sparse-extractors.o sparse-utils.o
installing to /tmp/th798/17369645/R-release/1488/library/00LOCK-sparsevctrs/00new/sparsevctrs/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** 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 (sparsevctrs)
* installing *source* package 'modelenv' ...
** this is package 'modelenv' version '0.2.0'
** package 'modelenv' 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 (modelenv)
* installing *source* package 'topics' ...
** this is package 'topics' version '0.50'
** package 'topics' 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 (topics)
* installing *source* package 'hardhat' ...
** this is package 'hardhat' version '1.4.1'
** package 'hardhat' 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 (hardhat)
* installing *source* package 'dials' ...
** this is package 'dials' version '1.4.0'
** package 'dials' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (dials)
* installing *source* package 'recipes' ...
** this is package 'recipes' version '1.3.0'
** package 'recipes' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (recipes)
* installing *source* package 'parsnip' ...
** this is package 'parsnip' version '1.3.1'
** package 'parsnip' 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 (parsnip)
* installing *source* package 'yardstick' ...
** this is package 'yardstick' version '1.3.2'
** package 'yardstick' successfully unpacked and MD5 sums checked
** using staged installation
** 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    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c mcc-multiclass.c -o mcc-multiclass.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 yardstick.so init.o mcc-multiclass.o
installing to /tmp/th798/17369645/R-release/1488/library/00LOCK-yardstick/00new/yardstick/libs
** 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
** 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 (yardstick)
* installing *source* package 'workflows' ...
** this is package 'workflows' version '1.2.0'
** package 'workflows' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (workflows)
* installing *source* package 'tune' ...
** this is package 'tune' version '1.3.0'
** package 'tune' 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
** 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 (tune)
* installing *source* package 'text' ...
** this is package 'text' version '1.5'
** package 'text' 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 (text)

The downloaded source packages are in
	'/tmp/th798/17369645/Rtmpi4XZXm/downloaded_packages'
> cat("Time to install revdep:\n")
Time to install revdep:
> print(install.time)
   user  system elapsed 
224.207  15.230 249.835 
> print(Sys.time())
[1] "2025-05-19 00:47:27 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] "2025-05-19 00:47:27 MST"
Installing package into '/tmp/th798/17369645/R-release/1488/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** this is package 'data.table' version '1.17.2'
** 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/th798/17369645/R-release/1488/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] "2025-05-19 00:47:50 MST"
* using log directory '/tmp/th798/17369645/R-release/1488/topics.Rcheck'
* using R version 4.5.0 (2025-04-11)
* 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 'topics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'topics' version '0.50'
* 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 'topics' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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
* 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 ... ERROR
Error(s) in re-building vignettes:
--- re-building 'extended_installation_guide.Rmd' using rmarkdown
--- finished re-building 'extended_installation_guide.Rmd'

sh: line 1: 1036112 Segmentation fault      (core dumped) '/home/th798/R/R-release/bin/R' --vanilla --no-echo > '/tmp/th798/17369645/RtmppYoOtL/filefceb651f6a512' 2>&1 < '/tmp/th798/17369645/RtmppYoOtL/filefceb627bd8357'
--- re-building 'topics.Rmd' using rmarkdown
May 19, 2025 12:49:56 AM cc.mallet.topics.ParallelTopicModel <init>
INFO: Mallet LDA: 20 topics, 5 topic bits, 11111 topic mask
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel initializeHistograms
INFO: max tokens: 18
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel initializeHistograms
INFO: total tokens: 5789
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <10> LL/token: -10.54928
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <20> LL/token: -10.4368
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <30> LL/token: -10.46242
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <40> LL/token: -10.4171
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.25	worthless sad weak quiet melancholy lazy normal 
1	0.25	sad alone isolated upset numb pessimistic critical 
2	0.25	anxiety fear sad_tired snappy frozen optimism family 
3	0.25	stressed worried helpless pointless busy insomnia frustrated 
4	0.25	happy content calm optimistic relaxed cheerful grateful 
5	0.25	tired lethargic slow overwhelmed restless neutral hungry 
6	0.25	hopeful peace mindful great happy_optimistic grey lethargy 
7	0.25	bored worried anxious loved fine failure free 
8	0.25	hopeless sad blue low miserable dejected na 
9	0.25	lonely gloomy lost sad_lonely yes sleepy lonely_sad 
10	0.25	upset unhappy worry tearful pain anxious sad_upset 
11	0.25	happy sadness hopeful joyful emotional tears loneliness 
12	0.25	empty suicidal darkness despairing sad_empty fragile depressed_sad 
13	0.25	strong coping dark active distressed family carefree 
14	0.25	angry useless isolated self anxious lonely_isolated grumpy 
15	0.25	sad tired low unmotivated sad_low heavy confused 
16	0.25	joy agitated antisocial joyless okay drinking change 
17	0.25	excited motivated apathetic hopeless flat wonderful balanced 
18	0.25	sad depressed alone exhausted crying troubled bothered 
19	0.25	nervous positive unhappy fearful bleak tired irritable 

May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <50> LL/token: -10.38957
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <60> LL/token: -10.42703
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <70> LL/token: -10.39149
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <80> LL/token: -10.39257
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <90> LL/token: -10.373
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.25	sad worthless hopeless melancholy ok suicidal pathetic 
1	0.25	nervous helpless frozen distressed tears coping desperate 
2	0.25	fear anxiety loneliness life hopelessness death waiting 
3	0.25	stressed insomnia fine pointless antisocial joyless snappy 
4	0.25	happy content calm relaxed optimistic cheerful loved 
5	0.25	tired lethargic overwhelmed numb slow agitated restless 
6	0.25	happy joy peace love tired happy_optimistic smiling 
7	0.25	anxious worried bored sad frustrated listless confused 
8	0.25	hopeless sad alone miserable low pessimistic negative 
9	0.25	lonely lost crying sad_lonely anger lonely_sad sad_numb 
10	0.25	upset unhappy weak tearful exhausted moody apathetic 
11	0.25	joyful sadness hopeful despair happy active tiredness 
12	0.25	empty alone pain numb free fatigued depressed 
13	0.25	family worry angry smile unhappy dog cool 
14	0.25	isolated angry gloomy useless self quiet dejected 
15	0.25	low tired sad unmotivated scared unhappy sad_low 
16	0.25	sadness emotional failure dark heavy sleepy bright 
17	0.25	excited motivated strong normal busy okay sometimes 
18	0.25	sad hopeful depressed troubled bothered frightened carefree 
19	0.25	positive sad drained bleak yes fearful blue 

May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <100> LL/token: -10.36726
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <110> LL/token: -10.37766
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <120> LL/token: -10.38785
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <130> LL/token: -10.35184
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <140> LL/token: -10.38075
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.25	useless worthless hopeless sad confident dull pathetic 
1	0.25	nervous self family ok loss thinking self_esteem 
2	0.25	fear anxiety frozen darkness hopelessness cool withdrawn 
3	0.25	stressed fatigued antisocial busy sometimes tired sad_angry 
4	0.25	happy content calm optimistic relaxed cheerful joyful 
5	0.25	tired lethargic numb overwhelmed irritable lazy neutral 
6	0.25	happy joy bleak peace love smile smiling 
7	0.25	anxious worried bored insomnia distressed bored_listless worried_anxious 
8	0.25	sad hopeless blue low pessimistic miserable negative 
9	0.25	lonely depressed worthless lost sad_lonely crying helpless 
10	0.25	upset unhappy exhausted weak worry moody anxious 
11	0.25	sadness pain melancholy despair bright loneliness frustration 
12	0.25	alone empty yes heavy bored sad_empty trying 
13	0.25	dark frustrated life desperate bad resigned stress 
14	0.25	isolated gloomy unhappy quiet apathetic bored miserable 
15	0.25	sad low tired unmotivated slow sad_low low_tired 
16	0.25	worried tearful failure dejected coping emotional restless 
17	0.25	excited motivated strong agitated free alive glad 
18	0.25	sad angry troubled depressed bothered disturbed low 
19	0.25	hopeful positive fearful flat mindful demotivated pointless 

May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <150> LL/token: -10.39719
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <160> LL/token: -10.3788
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <170> LL/token: -10.36414
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <180> LL/token: -10.3433
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <190> LL/token: -10.36913
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.25	hopeless sad empty bleak flat pointless demotivated 
1	0.25	nervous restless stress frozen sleepless contemplative pain 
2	0.25	fear anger fatigue normal guilt sad_unmotivated dreariness 
3	0.25	tired worried stressed angry fatigued ok irritable 
4	0.25	happy content calm relaxed optimistic cheerful active 
5	0.25	lethargic numb exhausted tired overwhelmed drained hungry 
6	0.25	happy joy family peace love antisocial smile 
7	0.25	anxious bored worried lonely scared insomnia listless 
8	0.25	blue miserable bored failure na negative na_na 
9	0.25	lonely worthless sad useless lost crying weak 
10	0.25	unhappy upset worry moody gloomy melancholy sad_upset 
11	0.25	sadness despair dark tears loneliness somewhat sleep 
12	0.25	alone isolated disturbed loved hopelessness dog bad 
13	0.25	pain low balanced optimism sometimes work confident_hopeful 
14	0.25	sad isolated gloomy quiet despondent despairing weary 
15	0.25	low sad tired unmotivated sad_low yes slow 
16	0.25	helpless tearful dejected frustrated broken fragile edgy 
17	0.25	motivated strong agitated excited fine free carefree 
18	0.25	sad depressed anxiety angry tired anxious fearful 
19	0.25	hopeful apathetic confused great life mindful trying 

May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <200> LL/token: -10.33757
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <210> LL/token: -10.31999
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <220> LL/token: -10.35006
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <230> LL/token: -10.33597
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <240> LL/token: -10.33511
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.25	hopeless empty pain sad irritable flat lifeless 
1	0.25	unhappy nervous bleak restless miserable hopelessness antisocial 
2	0.25	fear neutral anger tiredness disinterested thinking withdrawn 
3	0.25	tired worried stressed anxiety drained emotional fatigued 
4	0.25	happy content calm relaxed optimistic cheerful joyful 
5	0.25	tired exhausted numb lonely overwhelmed lethargic yes 
6	0.25	happy joy family coping peace love smile 
7	0.25	bored anxious worried scared insomnia lonely listless 
8	0.25	blue gloomy miserable na despondent fine na_na 
9	0.25	lonely worthless sad useless isolated lost weak 
10	0.25	upset sad unhappy worry tearful pessimistic melancholy 
11	0.25	sadness despair failure dark frozen darkness sometimes 
12	0.25	alone angry sad isolated okay sluggish guilt 
13	0.25	lethargic ok lazy trying work anxious_stressed level 
14	0.25	quiet apathetic lonely joyless lonely_tired grey optimism 
15	0.25	low sad unmotivated tired slow sad_low negative 
16	0.25	helpless dejected pointless frustrated confused broken grief 
17	0.25	motivated excited heavy agitated strong free glad 
18	0.25	sad depressed anxious fearful troubled bothered tense 
19	0.25	hopeful mindful great confident stable hopeful_optimistic busy 

May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.08028] 
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <250> LL/token: -9.91364
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <260> LL/token: -10.11753
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <270> LL/token: -10.09343
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <280> LL/token: -10.1188
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <290> LL/token: -10.11641
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.24601	alone hopeless sad tired numb distracted negative 
1	0.22356	unhappy gloomy stressed moody agitated death happy_balanced 
2	0.2196	sad lonely anxious low exhausted busy tears 
3	0.25341	bored miserable apathetic flat blue miserable_sad tired_bored 
4	0.2672	happy content calm relaxed hopeful optimistic excited 
5	0.24732	overwhelmed emotional uneasy heavy lethargy sleep irritability 
6	0.21337	happy joy family peace love smiling joy_happy 
7	0.23758	anxious worried tired lethargic stressed hungry alone 
8	0.22784	na na_na fearful anxious anxiety useless na_na_na 
9	0.25758	lonely sad worthless hopeless isolated useless exhausted 
10	0.25443	upset unhappy sad fear melancholy tired nervous 
11	0.2156	sadness worried failure pointless despair loneliness strong 
12	0.23935	helpless upset wonderful bored_listless inconsolable unloved grumpy 
13	0.21328	blue weak despairing dreariness triggered guilt drained 
14	0.2216	pain insomnia fear heavy worry steady grey 
15	0.27545	sad tired low angry depressed unmotivated unhappy 
16	0.22495	worried carefree coping numb overwhelming upbeat sometimes 
17	0.22785	sadness broken crying edgy teary broken_dejected difficult 
18	0.2374	sad bothered troubled tense anger frightened excited_happy 
19	0.22696	dark blue_tired alert end ok irritable agitated 

May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.11797] 
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <300> LL/token: -10.09088
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <310> LL/token: -10.12712
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <320> LL/token: -10.08908
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <330> LL/token: -10.11842
May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <340> LL/token: -10.08338
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.22589	bored drained listless bored_listless angry lonely_bored covid 
1	0.20739	sad sadness broken dejected mixed snappy broken_dejected 
2	0.18865	pointless overwhelmed concerned unsociable loneliness_life cheerful life 
3	0.23518	fear nervous coping apathetic tears blue low 
4	0.30747	happy content calm relaxed optimistic hopeful excited 
5	0.2229	alone tired emotional neutral ok anger afraid 
6	0.18559	joy happy family peace love happy_optimistic smile 
7	0.23727	disturbed work calm_cool stable unloved lacking hopeless 
8	0.19942	na na_na na_na_na overwhelmed grateful level joy_smiling_enjoyment 
9	0.28929	lonely sad hopeless worthless bored useless self 
10	0.25957	worried worry restless jolly isolated short inconsolable 
11	0.19184	alone distracted hopeful useful purposeful aggressive frozen 
12	0.21511	frightened distressed quiet miserable nervous empty_numb grumpy 
13	0.18522	meh dog doubtful repetitive darkness irritable future 
14	0.19571	happy blue flat great wonderful fragile miserable 
15	0.33386	sad tired low upset anxious unhappy lonely 
16	0.19214	hopeless dull anger pain worthless inactive despairing 
17	0.20127	sadness empty helpless alone tearful useless_worthless empty_tired 
18	0.21568	yes supported missing energy uninterested sad_distressed sleep 
19	0.20147	blue lethargic trying emotionless despondent busy scared 

May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.1383] 
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <350> LL/token: -10.09403
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <360> LL/token: -10.01065
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <370> LL/token: -10.05585
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <380> LL/token: -10.03154
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <390> LL/token: -10.04184
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.19463	stress family miserable happy headache alive fearful 
1	0.18795	joy overwhelmed hopeful death blank insomnia family 
2	0.16573	bleak short change painful waiting lifeless triggered 
3	0.21241	focused inactive driven mixed useful purposeful emotional 
4	0.34054	happy content calm optimistic relaxed excited hopeful 
5	0.19343	sadness nervous troubled angry frustration despair sleepless 
6	0.17468	smiling enjoyment joy mindful hopeless_desperate futile enjoyment_bliss 
7	0.21126	upset tearful fragile apathetic sadness antisocial despondent 
8	0.17311	na pain na_na na_na_na inconsolable mindful_hopeful glum 
9	0.33186	sad hopeless lonely worthless useless isolated sad_lonely 
10	0.23069	fear bothered bored flat emotional anger tearful 
11	0.1721	worry mindful hopeful tired_unmotivated unsettled stable laughter 
12	0.18194	lethargy uninterested energy bored_tired tired_motivated_prepared prepared motivated_prepared 
13	0.16446	fulfilled dejected despair lethargy_sad energy_miserable question_last one 
14	0.16875	heavy elated_jolly elated wonderful sad_worried locked yes 
15	0.46977	sad tired low anxious worried unhappy alone 
16	0.16875	coping trying dog meaningless quiet agitated hope 
17	0.17551	sorrow maybe failure tearful thoughtful lonely smiling_enjoyment 
18	0.1924	blue active carefree grey ok miserable grumpy_blue 
19	0.17306	sluggish disinterested burden lethargic resilient_cheerful_buoyant doubting_concerned doubting 

May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.15331] 
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <400> LL/token: -9.9999
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <410> LL/token: -9.95792
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <420> LL/token: -9.9964
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <430> LL/token: -9.98962
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <440> LL/token: -9.96221
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.16972	positive troubled bothered optimism anxious disturbed troubled_bothered 
1	0.16597	joy smiling enjoyment peace love dog confined 
2	0.1525	life normal frustration hurt work demotivated worried 
3	0.18555	helpless agitated edgy unhappy_upset grumpy desperate tired_sad 
4	0.36033	happy content calm hopeful optimistic relaxed excited 
5	0.17238	yes worried_sad loneliness hopeless_tired question doubting_concerned cheerful_buoyant 
6	0.15447	elated_jolly antisocial coping hopeful_optimistic distracted sad_hopeless pleased 
7	0.18225	apathetic anxiety sorry laughter irritability bored average 
8	0.14653	na fear na_na na_na_na emotional critical despondent 
9	0.35795	lonely isolated hopeless worthless useless sad pointless 
10	0.19505	heavy anxiety happiness frustration alone_irrelevant_irriatble meaningful futility 
11	0.15417	fatigue upbeat tiredness well_coping_focused managing_active coping_focused_managing relaxing_optimistic_enthusiastic 
12	0.15623	scared despair heavy family balanced lonely_bored ok 
13	0.14816	dark struggling coping family content enthusiastic_bored irriatble_sad 
14	0.15219	self dejected relaxed_happy self_esteem esteem neutral broken 
15	0.62626	sad tired low worried upset lonely alone 
16	0.14744	trying self focused miserable teary content_optimistic overwhelmed 
17	0.16032	blue tired_lethargic cool hopeless_bleak sad_melancholy anger failure 
18	0.1659	sadness sad pain worry frozen tears failure 
19	0.14917	sadness energy abandoned blue surviving help grumpy_blue 

May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.1635] 
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <450> LL/token: -9.98591
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <460> LL/token: -9.92413
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <470> LL/token: -9.89601
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <480> LL/token: -9.92328
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <490> LL/token: -9.90131
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.15646	disturbed sadness dreariness lacking trouble isolation tearful 
1	0.15386	coping content_optimistic elated_jolly useful purposeful isolated_sad low_unhappy 
2	0.13439	stress steady positive quiet accepting gloomy loneliness 
3	0.16358	sad_numb helpless contemplative emotional peaceful gloomy worried 
4	0.37798	happy content calm relaxed optimistic hopeful excited 
5	0.15892	empty snappy teary heavy apathy stressed_moody low_devastated 
6	0.13957	tears life struggling weary loneliness_life happiness motivated_prepared 
7	0.16227	demotivated enthusiastic thought sad_low_unhappy unhappy_gloomy fear confused 
8	0.13394	na na_na na_na_na blue_tired despondent restless relaxation 
9	0.34009	nervous fear troubled anxiety neutral bothered tense 
10	0.16909	dark lively joyless heavy carefree tiredness afraid 
11	0.1366	random sleep flat average frustration miserable question_last_one 
12	0.14228	calm calm_cool painful desperate isolated worried bleak 
13	0.13707	sometimes change slow bright content_fulfilled love agitated_grumpy 
14	0.13694	fatigue suicidal distressed tiredness frustration joy_smiling normal_standard 
15	0.74647	sad tired lonely low anxious hopeless unhappy 
16	0.13906	agitated distracted drained critical_agitated agitated_grumpy_blue tired_cincerned anxious_pressurized_drained 
17	0.14131	pain tensed failure worry hopelessness tired_exhausted antisocial 
18	0.15671	sadness uninterested loss despair lazy fragile end 
19	0.13323	abandoned worthless_self restless miserable happy_tired_cincerned cincerned exercising 

May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.18319] 
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <500> LL/token: -9.89981
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <510> LL/token: -9.86441
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <520> LL/token: -9.8564
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <530> LL/token: -9.86544
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <540> LL/token: -9.88115
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.14248	tired_unmotivated critical isolated_angry gloomy nice happy_nice empty 
1	0.14105	smile anxious_stressed sad_lonely_isolated mindful_hopeful emotional cheerful question_last_one 
2	0.12685	steady sorrow sometimes joy miserable_sad meaningful_happy meaningful 
3	0.14766	suicidal crying quiet surviving help alone_irrelevant thoughtful_contemplative_considered 
4	0.37991	happy content calm hopeful relaxed optimistic excited 
5	0.14188	loneliness death sadness_loneliness smiling_enjoyment_bliss lethargic_lonely stressed_anxious_pressurized pressurized_drained 
6	0.1297	family heavy grey failure love worried pointless 
7	0.1432	sadness hopelessness despairing low_unhappy slightly enthusiastic darkness 
8	0.12473	scared na na_na agitated na_na_na locked lethargy 
9	0.29142	bothered jolly unmotivated_sad distracted busy emotional anger 
10	0.14851	joy insomnia love joy_happy grief laughter guilt 
11	0.12932	overwhelmed troubled family critical_agitated agitated_grumpy_blue agitated_grumpy focused_managing 
12	0.13033	stress broken insomnia happy_smiling abandoned welcome_satisfied welcome 
13	0.12327	tiredness bad emptiness stress normal unhappy_gloomy moody 
14	0.12696	miserable snappy light content irriatble_sad stressed_moody short_sweaty 
15	0.85654	sad tired lonely low hopeless worried anxious 
16	0.13203	unloved morose weary tired_motivated_prepared tired_motivated prepared bored_tired_motivated 
17	0.1338	fatigue doubtful shame_embarrassment_environment embarrassment_environment_achievement sadness_hopelessness_end hopelessness_end_confusion despair_sadness 
18	0.14846	sadness frozen tears antisocial desperate sad_empty eager 
19	0.12579	buoyant overwhelmed_tired trying lethargy_sad_energy doubting buoyant_doubting_concerned fine_normal_standard 

May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.19956] 
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <550> LL/token: -9.88062
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <560> LL/token: -9.81542
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <570> LL/token: -9.83269
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <580> LL/token: -9.7997
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <590> LL/token: -9.80976
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.1326	confident fluctuating uncertain optimistic_enthusiastic low_blue_anxious lethargy_futility heavy_dread_lethargy 
1	0.13188	dark hopeful fearful energised working amused buoyant_doubting_concerned 
2	0.11883	coping worthless_self afraid work fatigued empty fulfilled_inspired_creative 
3	0.13573	mindful inconsolable overwhelming_sad question_last_one question last resilient 
4	0.38464	happy content calm optimistic relaxed hopeful excited 
5	0.13254	sad_low_unhappy devastated trying fear happy sad_low_blue low_devastated_hopeless 
6	0.11916	fear edgy smiling_enjoyment_bliss relaxing exercising_contacting enthusiastic_exercising contacting 
7	0.13363	despair alive agitated grief troubled_bothered supported tears 
8	0.11428	na na_na na_na_na lifeless exhausted_lifeless uneasy trouble 
9	0.24404	emotional fatigue lethargic hungry pain joyless sad_numb 
10	0.13377	lacking light scared isolation sadness life tired_cincerned 
11	0.11857	sleepless tired_lethargic lonley busy capable frustration well 
12	0.12199	static family happy low_blue upset_low low_bad heavy_dread 
13	0.11738	lazy maybe shame sadness_loneliness lonely bored_tired_motivated irriatble_sad 
14	0.12105	strong doubtful contemplative downhearted darkness bored_tired troubled 
15	0.92781	sad tired lonely low hopeless worried anxious 
16	0.12174	snappy depressed_low calm_cool joy agitated_grumpy_blue joy_smiling_enjoyment one 
17	0.12577	gloomy sometimes death heavy optimism darkness sad_hopeless 
18	0.14711	frightened distressed bothered troubled frustrated hopelessness balanced 
19	0.11902	strong pointless worthless lethargic_lonely unstable_unhappy unhappy_sad_weak depressed_unstable 

May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.20209] 
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <600> LL/token: -9.85447
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <610> LL/token: -9.82284
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <620> LL/token: -9.84237
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <630> LL/token: -9.80204
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <640> LL/token: -9.80782
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.12662	meh repetitive help relaxing optimistic_enthusiastic exercising_contacting lonely_meh 
1	0.12458	na na_na na_na_na family agitated vulnerable work 
2	0.11488	snappy level guilt medication overthinking focused_managing_active question_last_one 
3	0.12679	tense_sad stable tired_anxious apathetic sometimes hopeless_worthless lonely_worthless 
4	0.38721	happy content relaxed calm hopeful optimistic excited 
5	0.12666	fear agitated_grumpy lethargy_sad_energy upset_low inspired_creative_happy inspired_creative fulfilled_inspired 
6	0.11081	ok great empty question_last fulfilled_inspired_creative creative_happy_calm creative 
7	0.12571	waiting broken_dejected dejected honest resilient_cheerful_buoyant resilient_cheerful low_devastated_hopeless 
8	0.10839	sad_tearful suicidal sad_distressed pathetic disturbed grumpy_blue critical_agitated_grumpy 
9	0.20542	worry sadness mindful loneliness trying tears darkness 
10	0.12766	grumpy downhearted maybe morose irritability family apathetic 
11	0.1125	sadness joyless coping desperate crying failure laziness 
12	0.11353	optimism strength sometimes angry well_coping_focused well_coping happy_tired_cincerned 
13	0.11266	dog grief laughter bored_tired_motivated cheerful_buoyant_doubting anxious_stressed_moody past_shame_embarrassment 
14	0.11209	lively random better tiredness doubting_concerned buoyant_doubting stress_occasional_tiredness 
15	0.97652	sad tired lonely low hopeless worried unhappy 
16	0.11637	driven stress coping hungry sleep cincerned doubful 
17	0.12479	coping recklessness lethargy demotivated pointless hopelessness lethargy_sad 
18	0.14183	bleak thinking elated_jolly elated self_esteem esteem doubtful 
19	0.11212	fear depressed_sad mixed overwhelmed_tired alert lonely_isolated love 

May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.20541] 
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <650> LL/token: -9.79254
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <660> LL/token: -9.81146
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <670> LL/token: -9.76528
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <680> LL/token: -9.78481
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <690> LL/token: -9.77501
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.1226	sometimes loss stressed agitated_grumpy_blue managing_active managing coping_focused_managing 
1	0.11775	na na_na na_na_na melancholic tired_motivated_prepared enthusiastic_bored_tired enthusiastic_exercising 
2	0.11173	fine flat hatred worthless_self great sad_tired prepared 
3	0.11909	meh unmotivated_sad repetitive frustrated tearful worried bored_tired_motivated 
4	0.38262	happy content calm hopeful relaxed optimistic excited 
5	0.12091	fatigue unmotivated crying grumpy_blue stress_occasional_tiredness inspired sweaty_agitated_restless 
6	0.10976	upbeat emotionless low_tired loss life irrelevant_irriatble relaxing_optimistic 
7	0.12419	sadness despair confident stress tense tears isolation 
8	0.1064	distracted low_tired resilient crushing_heavy crushing unpredictable_doubtful exhausted_overwhelmed 
9	0.18219	heavy balanced painful overwhelmed uneasy sad_angry happy_tired_cincerned 
10	0.12066	driven distracted carefree strong_excited agitated_grumpy irriatble_sad stressed_moody_demotivated 
11	0.10943	purposeful sorrow trying pointless hopelessness well focused_managing_active 
12	0.10861	antisocial anxiety afraid crushing_heavy_dread gloomy_tense home dog_partner_job 
13	0.10723	family mindful lonely_isolated glad confusion lethargy_sad_energy welcome_satisfied 
14	0.10896	heavy lethargy frustration nervous motivated_prepared sad_energy_miserable irrelevant 
15	0.98008	sad tired lonely low hopeless anxious worried 
16	0.11163	loneliness fine hope downtrodden work worry last 
17	0.12005	ok calm_cool better hungry frustration tired bleak 
18	0.13392	sleep neutral grey somewhat darkness irritability worry 
19	0.10959	emotional uninterested lonely_tired lazy tired_exhausted unsettled triggered 

May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.20484] 
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <700> LL/token: -9.75143
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <710> LL/token: -9.77931
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <720> LL/token: -9.73048
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <730> LL/token: -9.76813
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <740> LL/token: -9.74105
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.11735	peace great unhappy_gloomy anger love anxiety sweaty_agitated 
1	0.11256	na na_na na_na_na hopeless_sad triggered fatigued happy 
2	0.10733	uncertain dreariness sad_loss fatigue sleep accepting critical_agitated 
3	0.11326	lively joyless death heavy tears fear fine 
4	0.3812	happy content calm hopeful relaxed optimistic excited 
5	0.11116	quiet restless bothered helpless emotional stressed_anxious_pressurized anxious_pressurized 
6	0.10956	sadness yes contacting optimistic_joy_honest welcome_satisfied environment_achievement embarrassment 
7	0.1184	bothered melancholy bored unwanted sadness frustrated amused 
8	0.10315	bored_listless joy cincerned lethargy_sad low_devastated_hopeless devastated_hopeless_numb fine_normal_standard 
9	0.15922	bleak talking smile free tiredness demotivated joyful_happy 
10	0.11894	family dejected guilt procrastination insomnia crying flat 
11	0.10674	elated_jolly okay relaxing_optimistic_enthusiastic exercising doubting_concerned carefree_fortunate sad_family_tired 
12	0.10272	balanced anger tense troubled blue numb hopeless_numb 
13	0.10629	dog sad_upset optimistic_joy stressed_moody anxious_stressed_moody sweaty_agitated_restless sweaty 
14	0.10093	smiling despondent happy_smiling bliss optimistic well_coping joy_smiling_enjoyment 
15	0.98447	sad tired lonely low hopeless worried anxious 
16	0.11025	disinterested static broken fragile irritable sad_lonely overthinking 
17	0.11369	mindful pointless stressed smiling_enjoyment tired_cincerned cincerned_normal meaningful 
18	0.12428	suicidal ok enjoyment_bliss tensed relaxation work dark 
19	0.10986	elated grey tense jolly unsociable enjoyment happy_joy 

May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.21118] 
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <750> LL/token: -9.78595
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <760> LL/token: -9.74117
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <770> LL/token: -9.75641
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <780> LL/token: -9.76302
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <790> LL/token: -9.74084
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.1114	upset_tired happy_balanced guilt lethargy shame sadness nice 
1	0.10773	na na_na irritable joy love na_na_na edgy 
2	0.10445	routine free reckless tired_lethargic_diet moody_sleep lethargic_diet_moody diet_moody_sleep 
3	0.11142	lazy dog emptiness maybe bright tiredness tired_motivated_prepared 
4	0.37381	happy content calm hopeful relaxed optimistic excited 
5	0.10619	sadness prepared motivated_prepared resilient_cheerful doubting_concerned low_devastated_hopeless depressed_low_devastated 
6	0.10343	sad_low_unhappy motivation fluctuating alone_sad smiling_enjoyment low_blue moody_demotivated 
7	0.1168	distracted somewhat despair lethargy_sad_energy irrelevant optimistic_joy_honest occasional 
8	0.10165	family fragile busy gloomy dejected life miserable 
9	0.14248	happy restless overwhelmed peace critical_agitated_grumpy agitated_grumpy_blue question 
10	0.11522	disturbed short grumpy lifeless heavy isolation agitated 
11	0.10406	ok bored_tired upset_low_bad fulfilled_inspired sitting_avoidance sitting low_quiet 
12	0.09999	level lonely_bored ok excited_happy tired_drained anxious_stressed_moody lethargic_lonely_meh 
13	0.10358	tired_bored struggling normal broken optimism stressed_anxious_pressurized pressurized 
14	0.09945	frozen darkness gloomy excited lonely_meh reckless_tired_worthless fearful_reckless_tired 
15	0.97518	sad tired lonely low hopeless anxious worried 
16	0.10771	dark distressed cheerful tiredness great frustration grumpy_blue 
17	0.10804	family relaxed well_coping_focused coping_focused_managing tired_cincerned_normal happy_tired_cincerned cincerned_normal 
18	0.12052	sadness joyless useful afraid sad_tired low_sad hopelessness 
19	0.10995	wonderful stress lacking well managing_active tiredness_stable stress_occasional 

May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.221] 
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <800> LL/token: -9.74475
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <810> LL/token: -9.7748
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <820> LL/token: -9.73956
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <830> LL/token: -9.70987
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <840> LL/token: -9.74443
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.11048	overwhelmed quiet free thoughtful tired_motivated_prepared motivated_prepared enthusiastic_bored_tired 
1	0.10804	na na_na na_na_na fatigue happy_balanced yes somewhat 
2	0.10612	lazy exhausted_lifeless uninterested sometimes life despair tired_cincerned_normal 
3	0.1093	sadness contemplative headache smiling_enjoyment upset_low_bad upset_low contemplative_considered_appreciative 
4	0.36816	happy calm content relaxed optimistic excited active 
5	0.1007	sleepless overwhelmed insomnia morose darkness joy_honest resilient_cheerful_buoyant 
6	0.10174	sadness sluggish happy_joy_smiling question_last one last_one low_blue 
7	0.10741	heavy tense irritable despondent ok failure upset 
8	0.10611	suicidal poor trying uninterested worthless_self okay cheerful 
9	0.12982	flat lonely_sad repetitive laughter yes love fun 
10	0.11144	self upset lonely energy_miserable buoyant_doubting unpredictable_doubtful exhausted_overwhelmed 
11	0.10036	lively unhappy_gloomy strong coping_focused_managing question_last_one question low_devastated 
12	0.09827	heavy joyless sad_numb disinterested grey lethargy pointless 
13	0.10076	monotonous critical agitated loneliness sadness great uncertain 
14	0.09533	darkness content critical_agitated_grumpy partner_job home_dog_partner home_dog shame_embarrassment_environment 
15	0.95851	sad tired low lonely hopeless worried anxious 
16	0.10672	broken dejected edgy isolated_sad sorry guilt broken_dejected 
17	0.10217	neutral bothered weakness uncontrollable enthusiastic_exercising_contacting stressed_anxious drained_helpless 
18	0.11645	despair hopelessness pain sadness covid exhausted concern_stress_occasional 
19	0.10579	self_esteem supported lonely_crying frozen jolly quiet worried 

May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.21735] 
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <850> LL/token: -9.75613
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <860> LL/token: -9.73484
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <870> LL/token: -9.71793
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <880> LL/token: -9.70708
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <890> LL/token: -9.76688
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.10979	snappy resigned active sadness happy_sad happy_optimistic_joy resilient_cheerful_buoyant 
1	0.0985	na na_na na_na_na dejected sadness coping loneliness 
2	0.10182	failure peace great optimistic_enthusiastic_exercising low_blue_anxious moody_demotivated_unhappy anxious_stressed_moody 
3	0.10181	gloomy joy trapped smiling_enjoyment_bliss upset_low mobile itchy 
4	0.3646	happy content calm optimistic relaxed hopeful excited 
5	0.10155	tears dreariness antisocial frozen disturbed free resilient 
6	0.09853	glum inconsolable struggling grumpy moody inadequate weary 
7	0.09982	life stress tiredness grumpy_blue well managing_active focused_managing_active 
8	0.10177	locked lacking hopeless_bleak tense gloomy prepared motivated_prepared 
9	0.11942	sadness cool darkness listless apathetic alone_lonely lethargy_sad 
10	0.10372	hurt worthless_useless sleepless gloomy worthless agitated_grumpy sad_energy 
11	0.09876	worthless bored heavy self worthless_self weak alone_irrelevant 
12	0.10199	edgy neutral coping bad end sadness tiredness 
13	0.0978	normal fine despair fine_normal agitated tired_cincerned cincerned 
14	0.09645	emptiness thought strength bliss pathetic tired_motivated_prepared tired_motivated 
15	0.94344	sad tired lonely low hopeless worried anxious 
16	0.10604	overwhelmed grief bored_listless heavy uncertain nervous irriatble_sad 
17	0.09561	death alone_irrelevant_irriatble normal_standard calm_thoughtful gloomy_tense_sad tired_lethargic_diet energetic_active 
18	0.11284	anger useful self_esteem light agitated bored_tired_motivated question_last 
19	0.10323	work low_slow futile managing reckless_tired hopeful_energetic_active hopeful_energetic 

May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.22179] 
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <900> LL/token: -9.70502
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <910> LL/token: -9.70014
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <920> LL/token: -9.73723
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <930> LL/token: -9.71808
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <940> LL/token: -9.67047
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.10021	joyless distracted jumpy scared fine disturbed hope 
1	0.09667	na na_na na_na_na sleepless fatigue failure procrastination 
2	0.09775	disinterested grumpy_blue happy_joy_smiling doubting_concerned futility crushing_heavy guilty_emotional 
3	0.09542	anxiety doubtful isolated_angry vulnerable peace tired_motivated motivated_prepared 
4	0.35587	happy content calm hopeful relaxed optimistic excited 
5	0.09913	broken_dejected frozen scared embarrassment unmotivated_happy_sad unmotivated_happy unstable_unhappy_sad 
6	0.09893	sad_worried prepared irriatble irrelevant_irriatble_sad fortunate_happy distracted_unbothered fear_restless_emotional 
7	0.09799	suicidal fulfilled dejected optimistic_enthusiastic_exercising optimistic_enthusiastic exercising_contacting enthusiastic_exercising 
8	0.10097	hungry frightened routine accepting loneliness flat demotivated 
9	0.11325	missing uneasy pain useless tired cincerned_normal irrelevant_irriatble 
10	0.10345	lethargy irrelevant thoughtful_contemplative contemplative_considered calm_thoughtful unwillingness_gloomy_tense hopeless_miserable 
11	0.09791	purposeful happy_hopeful static work well_coping_focused lethargy_sad resilient_cheerful 
12	0.09786	headache sleep gloomy failure despair well_coping focused_managing_active 
13	0.09828	dreariness heavy managing_active managing sad_energy_miserable energy_miserable question 
14	0.09374	wonderful overwhelming_sad busy despair irriatble_sad sad_low_blue low_blue_anxious 
15	0.92698	sad tired lonely low hopeless worried anxious 
16	0.10602	neutral despondent crying sometimes peace relaxing tiredness_stable 
17	0.09514	tired_exhausted unsettled thinking irritated family weak tired 
18	0.11088	contemplative anxious tiredness frustration appreciative concern_stress_occasional concern_stress 
19	0.09599	dog covid optimism devastated_hopeless fulfilled_inspired sad_family_tired sad_family 

May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.22087] 
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <950> LL/token: -9.71316
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <960> LL/token: -9.69979
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <970> LL/token: -9.70197
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <980> LL/token: -9.71049
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <990> LL/token: -9.71284
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.09835	happy_calm upset_emotional motivated insomnia_tired emotional sad_hopeless pain 
1	0.09272	nervous na_na overwhelmed okay sometimes contented_optimistic fine_normal_standard 
2	0.09983	normal family tired_cincerned_normal optimistic_joy_honest optimistic_joy joy_honest honest 
3	0.09613	calm_cool apathetic uncertain depressed happy_tired_cincerned irriatble_sad alone_irrelevant 
4	0.35625	happy content calm optimistic relaxed excited hopeful 
5	0.0992	pain lazy burden unhappy_gloomy withdrawn loss strong_excited 
6	0.09665	yes frozen weary disinterested upset_tired poor busy 
7	0.09523	disturbed mixed future agitated upset_low_bad short_sweaty agitated_restless 
8	0.09291	heavy fearful aggressive fatigue darkness emotional content_fulfilled 
9	0.1116	smile inactive antisocial lonely_lost despondent unhappy_weak good 
10	0.09627	despair end anxiety stressed_anxious_pressurized hopelessness_end_confusion hopelessness_end unmotivated_happy_sad 
11	0.09469	resigned alone joyful_happy question_last_one question_last happy_optimistic_joy stressed_moody_demotivated 
12	0.09514	worried_anxious ok sad_distressed agitated life optimistic_enthusiastic_exercising meaningful 
13	0.09497	locked fear failure critical_agitated feeling hopeful_energetic fulfilled_motivated 
14	0.08949	useful teary apathetic well_coping_focused well managing_active managing 
15	0.90789	sad tired lonely low hopeless worried anxious 
16	0.09825	thinking broken fear relaxed worry irrelevant_irriatble_sad alone_irrelevant_irriatble 
17	0.09343	tired_lethargic cool unloved fragile distressed isolated_hopeless average 
18	0.10642	na_na_na carefree unhappy_upset numb agitated_grumpy_blue exercising standard_average_flat 
19	0.09114	self hopeful confined random happy_balanced trapped sad_empty 

May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.22529] 
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <1000> LL/token: -9.7144
May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
Total time: 2 seconds

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: wordcloud_boxes(data_points = points_valid_first, boxes = boxes,     boxes_text = boxes_text, text_boxes = text_boxes, bigboxes = bigboxes,     boxes_masks = boxes_masks, boxes_mask = boxes_mask, mask_boxes = mask_boxes,     mask_group = mask_group, angle_group = angle_group, max_angle_group = x$data$max_angle_group[1],     xlim = range(x$limits$x), ylim = range(x$limits$y), eccentricity = x$eccentricity,     rstep = x$rstep, tstep = x$tstep, perc_step = x$perc_step,     max_steps = x$max_steps, rm_outside = x$rm_outside, shape = x$shape)
 2: makeContent.textwordcloudtree(x)
 3: makeContent(x)
 4: drawGTree(x)
 5: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
 6: grid.draw.gTree(x$children[[i]], recording = FALSE)
 7: grid.draw(x$children[[i]], recording = FALSE)
 8: drawGTree(x)
 9: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
10: grid.draw.gTree(x$children[[i]], recording = FALSE)
11: grid.draw(x$children[[i]], recording = FALSE)
12: drawGTree(x)
13: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
14: grid.draw.gTree(x$children[[i]], recording = FALSE)
15: grid.draw(x$children[[i]], recording = FALSE)
16: drawGTree(x)
17: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
18: grid.draw.gTree(gtable)
19: grid.draw(gtable)
20: print.ggplot(x)
21: (function (x, ...) UseMethod("print"))(x)
22: print.default(x)
23: print(x)
24: normal_print(x)
25: knit_print.default(x, ...)
26: knit_print(x, ...)
27: withVisible(knit_print(x, ...))
28: fun(x, options = options)
29: value_fun(ev$value, ev$visible)
30: withVisible(value_fun(ev$value, ev$visible))
31: withCallingHandlers(withVisible(value_fun(ev$value, ev$visible)),     warning = wHandler, error = eHandler, message = mHandler)
32: handle(pv <- withCallingHandlers(withVisible(value_fun(ev$value,     ev$visible)), warning = wHandler, error = eHandler, message = mHandler))
33: evaluate_call(expr, parsed$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)
34: evaluate::evaluate(...)
35: 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$render, options))
36: in_dir(input_dir(), expr)
37: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
38: eng_r(options)
39: block_exec(params)
40: call_block(x)
41: process_group(group)
42: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
43: 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)))})
44: 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)
45: process_file(text, output)
46: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
47: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
48: vweave_rmarkdown(...)
49: engine$weave(file, quiet = quiet, encoding = enc)
50: doTryCatch(return(expr), name, parentenv, handler)
51: tryCatchOne(expr, names, parentenv, handlers[[1L]])
52: tryCatchList(expr, classes, parentenv, handlers)
53: tryCatch({    engine$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)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
54: tools:::.buildOneVignette("topics.Rmd", "/tmp/th798/17369645/R-release/1488/topics.Rcheck/vign_test/topics",     TRUE, FALSE, "topics", "UTF-8", "/tmp/th798/17369645/RtmppYoOtL/filefceb62414a207.rds")
An irrecoverable exception occurred. R is aborting now ...
SUMMARY: processing the following file failed:
  'topics.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  '/tmp/th798/17369645/R-release/1488/topics.Rcheck/00check.log'
for details.

[1] "2025-05-19 00:50:08 MST"
[1] "2025-05-19 00:50:08 MST"
Installing package into '/tmp/th798/17369645/R-release/1488/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-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/th798/17369645/R-release/1488/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] "2025-05-19 00:50:29 MST"
* using log directory '/tmp/th798/17369645/R-release/1488/topics.Rcheck'
* using R version 4.5.0 (2025-04-11)
* 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 'topics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'topics' version '0.50'
* 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 'topics' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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
* 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 ... ERROR
Error(s) in re-building vignettes:
--- re-building 'extended_installation_guide.Rmd' using rmarkdown
--- finished re-building 'extended_installation_guide.Rmd'

sh: line 1: 1042601 Segmentation fault      (core dumped) '/home/th798/R/R-release/bin/R' --vanilla --no-echo > '/tmp/th798/17369645/RtmpQsjco6/filefe5c6566df6a0' 2>&1 < '/tmp/th798/17369645/RtmpQsjco6/filefe5c644bb3cd9'
--- re-building 'topics.Rmd' using rmarkdown
May 19, 2025 12:52:33 AM cc.mallet.topics.ParallelTopicModel <init>
INFO: Mallet LDA: 20 topics, 5 topic bits, 11111 topic mask
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel initializeHistograms
INFO: max tokens: 18
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel initializeHistograms
INFO: total tokens: 5789
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <10> LL/token: -10.54928
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <20> LL/token: -10.4368
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <30> LL/token: -10.46242
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <40> LL/token: -10.4171
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.25	worthless sad weak quiet melancholy lazy normal 
1	0.25	sad alone isolated upset numb pessimistic critical 
2	0.25	anxiety fear sad_tired snappy frozen optimism family 
3	0.25	stressed worried helpless pointless busy insomnia frustrated 
4	0.25	happy content calm optimistic relaxed cheerful grateful 
5	0.25	tired lethargic slow overwhelmed restless neutral hungry 
6	0.25	hopeful peace mindful great happy_optimistic grey lethargy 
7	0.25	bored worried anxious loved fine failure free 
8	0.25	hopeless sad blue low miserable dejected na 
9	0.25	lonely gloomy lost sad_lonely yes sleepy lonely_sad 
10	0.25	upset unhappy worry tearful pain anxious sad_upset 
11	0.25	happy sadness hopeful joyful emotional tears loneliness 
12	0.25	empty suicidal darkness despairing sad_empty fragile depressed_sad 
13	0.25	strong coping dark active distressed family carefree 
14	0.25	angry useless isolated self anxious lonely_isolated grumpy 
15	0.25	sad tired low unmotivated sad_low heavy confused 
16	0.25	joy agitated antisocial joyless okay drinking change 
17	0.25	excited motivated apathetic hopeless flat wonderful balanced 
18	0.25	sad depressed alone exhausted crying troubled bothered 
19	0.25	nervous positive unhappy fearful bleak tired irritable 

May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <50> LL/token: -10.38957
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <60> LL/token: -10.42703
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <70> LL/token: -10.39149
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <80> LL/token: -10.39257
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <90> LL/token: -10.373
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.25	sad worthless hopeless melancholy ok suicidal pathetic 
1	0.25	nervous helpless frozen distressed tears coping desperate 
2	0.25	fear anxiety loneliness life hopelessness death waiting 
3	0.25	stressed insomnia fine pointless antisocial joyless snappy 
4	0.25	happy content calm relaxed optimistic cheerful loved 
5	0.25	tired lethargic overwhelmed numb slow agitated restless 
6	0.25	happy joy peace love tired happy_optimistic smiling 
7	0.25	anxious worried bored sad frustrated listless confused 
8	0.25	hopeless sad alone miserable low pessimistic negative 
9	0.25	lonely lost crying sad_lonely anger lonely_sad sad_numb 
10	0.25	upset unhappy weak tearful exhausted moody apathetic 
11	0.25	joyful sadness hopeful despair happy active tiredness 
12	0.25	empty alone pain numb free fatigued depressed 
13	0.25	family worry angry smile unhappy dog cool 
14	0.25	isolated angry gloomy useless self quiet dejected 
15	0.25	low tired sad unmotivated scared unhappy sad_low 
16	0.25	sadness emotional failure dark heavy sleepy bright 
17	0.25	excited motivated strong normal busy okay sometimes 
18	0.25	sad hopeful depressed troubled bothered frightened carefree 
19	0.25	positive sad drained bleak yes fearful blue 

May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <100> LL/token: -10.36726
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <110> LL/token: -10.37766
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <120> LL/token: -10.38785
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <130> LL/token: -10.35184
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <140> LL/token: -10.38075
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.25	useless worthless hopeless sad confident dull pathetic 
1	0.25	nervous self family ok loss thinking self_esteem 
2	0.25	fear anxiety frozen darkness hopelessness cool withdrawn 
3	0.25	stressed fatigued antisocial busy sometimes tired sad_angry 
4	0.25	happy content calm optimistic relaxed cheerful joyful 
5	0.25	tired lethargic numb overwhelmed irritable lazy neutral 
6	0.25	happy joy bleak peace love smile smiling 
7	0.25	anxious worried bored insomnia distressed bored_listless worried_anxious 
8	0.25	sad hopeless blue low pessimistic miserable negative 
9	0.25	lonely depressed worthless lost sad_lonely crying helpless 
10	0.25	upset unhappy exhausted weak worry moody anxious 
11	0.25	sadness pain melancholy despair bright loneliness frustration 
12	0.25	alone empty yes heavy bored sad_empty trying 
13	0.25	dark frustrated life desperate bad resigned stress 
14	0.25	isolated gloomy unhappy quiet apathetic bored miserable 
15	0.25	sad low tired unmotivated slow sad_low low_tired 
16	0.25	worried tearful failure dejected coping emotional restless 
17	0.25	excited motivated strong agitated free alive glad 
18	0.25	sad angry troubled depressed bothered disturbed low 
19	0.25	hopeful positive fearful flat mindful demotivated pointless 

May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <150> LL/token: -10.39719
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <160> LL/token: -10.3788
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <170> LL/token: -10.36414
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <180> LL/token: -10.3433
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <190> LL/token: -10.36913
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.25	hopeless sad empty bleak flat pointless demotivated 
1	0.25	nervous restless stress frozen sleepless contemplative pain 
2	0.25	fear anger fatigue normal guilt sad_unmotivated dreariness 
3	0.25	tired worried stressed angry fatigued ok irritable 
4	0.25	happy content calm relaxed optimistic cheerful active 
5	0.25	lethargic numb exhausted tired overwhelmed drained hungry 
6	0.25	happy joy family peace love antisocial smile 
7	0.25	anxious bored worried lonely scared insomnia listless 
8	0.25	blue miserable bored failure na negative na_na 
9	0.25	lonely worthless sad useless lost crying weak 
10	0.25	unhappy upset worry moody gloomy melancholy sad_upset 
11	0.25	sadness despair dark tears loneliness somewhat sleep 
12	0.25	alone isolated disturbed loved hopelessness dog bad 
13	0.25	pain low balanced optimism sometimes work confident_hopeful 
14	0.25	sad isolated gloomy quiet despondent despairing weary 
15	0.25	low sad tired unmotivated sad_low yes slow 
16	0.25	helpless tearful dejected frustrated broken fragile edgy 
17	0.25	motivated strong agitated excited fine free carefree 
18	0.25	sad depressed anxiety angry tired anxious fearful 
19	0.25	hopeful apathetic confused great life mindful trying 

May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <200> LL/token: -10.33757
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <210> LL/token: -10.31999
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <220> LL/token: -10.35006
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <230> LL/token: -10.33597
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <240> LL/token: -10.33511
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.25	hopeless empty pain sad irritable flat lifeless 
1	0.25	unhappy nervous bleak restless miserable hopelessness antisocial 
2	0.25	fear neutral anger tiredness disinterested thinking withdrawn 
3	0.25	tired worried stressed anxiety drained emotional fatigued 
4	0.25	happy content calm relaxed optimistic cheerful joyful 
5	0.25	tired exhausted numb lonely overwhelmed lethargic yes 
6	0.25	happy joy family coping peace love smile 
7	0.25	bored anxious worried scared insomnia lonely listless 
8	0.25	blue gloomy miserable na despondent fine na_na 
9	0.25	lonely worthless sad useless isolated lost weak 
10	0.25	upset sad unhappy worry tearful pessimistic melancholy 
11	0.25	sadness despair failure dark frozen darkness sometimes 
12	0.25	alone angry sad isolated okay sluggish guilt 
13	0.25	lethargic ok lazy trying work anxious_stressed level 
14	0.25	quiet apathetic lonely joyless lonely_tired grey optimism 
15	0.25	low sad unmotivated tired slow sad_low negative 
16	0.25	helpless dejected pointless frustrated confused broken grief 
17	0.25	motivated excited heavy agitated strong free glad 
18	0.25	sad depressed anxious fearful troubled bothered tense 
19	0.25	hopeful mindful great confident stable hopeful_optimistic busy 

May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.08028] 
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <250> LL/token: -9.91364
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <260> LL/token: -10.11753
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <270> LL/token: -10.09343
May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <280> LL/token: -10.1188
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <290> LL/token: -10.11641
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.24601	alone hopeless sad tired numb distracted negative 
1	0.22356	unhappy gloomy stressed moody agitated death happy_balanced 
2	0.2196	sad lonely anxious low exhausted busy tears 
3	0.25341	bored miserable apathetic flat blue miserable_sad tired_bored 
4	0.2672	happy content calm relaxed hopeful optimistic excited 
5	0.24732	overwhelmed emotional uneasy heavy lethargy sleep irritability 
6	0.21337	happy joy family peace love smiling joy_happy 
7	0.23758	anxious worried tired lethargic stressed hungry alone 
8	0.22784	na na_na fearful anxious anxiety useless na_na_na 
9	0.25758	lonely sad worthless hopeless isolated useless exhausted 
10	0.25443	upset unhappy sad fear melancholy tired nervous 
11	0.2156	sadness worried failure pointless despair loneliness strong 
12	0.23935	helpless upset wonderful bored_listless inconsolable unloved grumpy 
13	0.21328	blue weak despairing dreariness triggered guilt drained 
14	0.2216	pain insomnia fear heavy worry steady grey 
15	0.27545	sad tired low angry depressed unmotivated unhappy 
16	0.22495	worried carefree coping numb overwhelming upbeat sometimes 
17	0.22785	sadness broken crying edgy teary broken_dejected difficult 
18	0.2374	sad bothered troubled tense anger frightened excited_happy 
19	0.22696	dark blue_tired alert end ok irritable agitated 

May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.11797] 
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <300> LL/token: -10.09088
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <310> LL/token: -10.12712
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <320> LL/token: -10.08908
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <330> LL/token: -10.11842
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <340> LL/token: -10.08338
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.22589	bored drained listless bored_listless angry lonely_bored covid 
1	0.20739	sad sadness broken dejected mixed snappy broken_dejected 
2	0.18865	pointless overwhelmed concerned unsociable loneliness_life cheerful life 
3	0.23518	fear nervous coping apathetic tears blue low 
4	0.30747	happy content calm relaxed optimistic hopeful excited 
5	0.2229	alone tired emotional neutral ok anger afraid 
6	0.18559	joy happy family peace love happy_optimistic smile 
7	0.23727	disturbed work calm_cool stable unloved lacking hopeless 
8	0.19942	na na_na na_na_na overwhelmed grateful level joy_smiling_enjoyment 
9	0.28929	lonely sad hopeless worthless bored useless self 
10	0.25957	worried worry restless jolly isolated short inconsolable 
11	0.19184	alone distracted hopeful useful purposeful aggressive frozen 
12	0.21511	frightened distressed quiet miserable nervous empty_numb grumpy 
13	0.18522	meh dog doubtful repetitive darkness irritable future 
14	0.19571	happy blue flat great wonderful fragile miserable 
15	0.33386	sad tired low upset anxious unhappy lonely 
16	0.19214	hopeless dull anger pain worthless inactive despairing 
17	0.20127	sadness empty helpless alone tearful useless_worthless empty_tired 
18	0.21568	yes supported missing energy uninterested sad_distressed sleep 
19	0.20147	blue lethargic trying emotionless despondent busy scared 

May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.1383] 
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <350> LL/token: -10.09403
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <360> LL/token: -10.01065
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <370> LL/token: -10.05585
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <380> LL/token: -10.03154
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <390> LL/token: -10.04184
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.19463	stress family miserable happy headache alive fearful 
1	0.18795	joy overwhelmed hopeful death blank insomnia family 
2	0.16573	bleak short change painful waiting lifeless triggered 
3	0.21241	focused inactive driven mixed useful purposeful emotional 
4	0.34054	happy content calm optimistic relaxed excited hopeful 
5	0.19343	sadness nervous troubled angry frustration despair sleepless 
6	0.17468	smiling enjoyment joy mindful hopeless_desperate futile enjoyment_bliss 
7	0.21126	upset tearful fragile apathetic sadness antisocial despondent 
8	0.17311	na pain na_na na_na_na inconsolable mindful_hopeful glum 
9	0.33186	sad hopeless lonely worthless useless isolated sad_lonely 
10	0.23069	fear bothered bored flat emotional anger tearful 
11	0.1721	worry mindful hopeful tired_unmotivated unsettled stable laughter 
12	0.18194	lethargy uninterested energy bored_tired tired_motivated_prepared prepared motivated_prepared 
13	0.16446	fulfilled dejected despair lethargy_sad energy_miserable question_last one 
14	0.16875	heavy elated_jolly elated wonderful sad_worried locked yes 
15	0.46977	sad tired low anxious worried unhappy alone 
16	0.16875	coping trying dog meaningless quiet agitated hope 
17	0.17551	sorrow maybe failure tearful thoughtful lonely smiling_enjoyment 
18	0.1924	blue active carefree grey ok miserable grumpy_blue 
19	0.17306	sluggish disinterested burden lethargic resilient_cheerful_buoyant doubting_concerned doubting 

May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.15331] 
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <400> LL/token: -9.9999
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <410> LL/token: -9.95792
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <420> LL/token: -9.9964
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <430> LL/token: -9.98962
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <440> LL/token: -9.96221
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.16972	positive troubled bothered optimism anxious disturbed troubled_bothered 
1	0.16597	joy smiling enjoyment peace love dog confined 
2	0.1525	life normal frustration hurt work demotivated worried 
3	0.18555	helpless agitated edgy unhappy_upset grumpy desperate tired_sad 
4	0.36033	happy content calm hopeful optimistic relaxed excited 
5	0.17238	yes worried_sad loneliness hopeless_tired question doubting_concerned cheerful_buoyant 
6	0.15447	elated_jolly antisocial coping hopeful_optimistic distracted sad_hopeless pleased 
7	0.18225	apathetic anxiety sorry laughter irritability bored average 
8	0.14653	na fear na_na na_na_na emotional critical despondent 
9	0.35795	lonely isolated hopeless worthless useless sad pointless 
10	0.19505	heavy anxiety happiness frustration alone_irrelevant_irriatble meaningful futility 
11	0.15417	fatigue upbeat tiredness well_coping_focused managing_active coping_focused_managing relaxing_optimistic_enthusiastic 
12	0.15623	scared despair heavy family balanced lonely_bored ok 
13	0.14816	dark struggling coping family content enthusiastic_bored irriatble_sad 
14	0.15219	self dejected relaxed_happy self_esteem esteem neutral broken 
15	0.62626	sad tired low worried upset lonely alone 
16	0.14744	trying self focused miserable teary content_optimistic overwhelmed 
17	0.16032	blue tired_lethargic cool hopeless_bleak sad_melancholy anger failure 
18	0.1659	sadness sad pain worry frozen tears failure 
19	0.14917	sadness energy abandoned blue surviving help grumpy_blue 

May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.1635] 
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <450> LL/token: -9.98591
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <460> LL/token: -9.92413
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <470> LL/token: -9.89601
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <480> LL/token: -9.92328
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <490> LL/token: -9.90131
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.15646	disturbed sadness dreariness lacking trouble isolation tearful 
1	0.15386	coping content_optimistic elated_jolly useful purposeful isolated_sad low_unhappy 
2	0.13439	stress steady positive quiet accepting gloomy loneliness 
3	0.16358	sad_numb helpless contemplative emotional peaceful gloomy worried 
4	0.37798	happy content calm relaxed optimistic hopeful excited 
5	0.15892	empty snappy teary heavy apathy stressed_moody low_devastated 
6	0.13957	tears life struggling weary loneliness_life happiness motivated_prepared 
7	0.16227	demotivated enthusiastic thought sad_low_unhappy unhappy_gloomy fear confused 
8	0.13394	na na_na na_na_na blue_tired despondent restless relaxation 
9	0.34009	nervous fear troubled anxiety neutral bothered tense 
10	0.16909	dark lively joyless heavy carefree tiredness afraid 
11	0.1366	random sleep flat average frustration miserable question_last_one 
12	0.14228	calm calm_cool painful desperate isolated worried bleak 
13	0.13707	sometimes change slow bright content_fulfilled love agitated_grumpy 
14	0.13694	fatigue suicidal distressed tiredness frustration joy_smiling normal_standard 
15	0.74647	sad tired lonely low anxious hopeless unhappy 
16	0.13906	agitated distracted drained critical_agitated agitated_grumpy_blue tired_cincerned anxious_pressurized_drained 
17	0.14131	pain tensed failure worry hopelessness tired_exhausted antisocial 
18	0.15671	sadness uninterested loss despair lazy fragile end 
19	0.13323	abandoned worthless_self restless miserable happy_tired_cincerned cincerned exercising 

May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.18319] 
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <500> LL/token: -9.89981
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <510> LL/token: -9.86441
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <520> LL/token: -9.8564
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <530> LL/token: -9.86544
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <540> LL/token: -9.88115
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.14248	tired_unmotivated critical isolated_angry gloomy nice happy_nice empty 
1	0.14105	smile anxious_stressed sad_lonely_isolated mindful_hopeful emotional cheerful question_last_one 
2	0.12685	steady sorrow sometimes joy miserable_sad meaningful_happy meaningful 
3	0.14766	suicidal crying quiet surviving help alone_irrelevant thoughtful_contemplative_considered 
4	0.37991	happy content calm hopeful relaxed optimistic excited 
5	0.14188	loneliness death sadness_loneliness smiling_enjoyment_bliss lethargic_lonely stressed_anxious_pressurized pressurized_drained 
6	0.1297	family heavy grey failure love worried pointless 
7	0.1432	sadness hopelessness despairing low_unhappy slightly enthusiastic darkness 
8	0.12473	scared na na_na agitated na_na_na locked lethargy 
9	0.29142	bothered jolly unmotivated_sad distracted busy emotional anger 
10	0.14851	joy insomnia love joy_happy grief laughter guilt 
11	0.12932	overwhelmed troubled family critical_agitated agitated_grumpy_blue agitated_grumpy focused_managing 
12	0.13033	stress broken insomnia happy_smiling abandoned welcome_satisfied welcome 
13	0.12327	tiredness bad emptiness stress normal unhappy_gloomy moody 
14	0.12696	miserable snappy light content irriatble_sad stressed_moody short_sweaty 
15	0.85654	sad tired lonely low hopeless worried anxious 
16	0.13203	unloved morose weary tired_motivated_prepared tired_motivated prepared bored_tired_motivated 
17	0.1338	fatigue doubtful shame_embarrassment_environment embarrassment_environment_achievement sadness_hopelessness_end hopelessness_end_confusion despair_sadness 
18	0.14846	sadness frozen tears antisocial desperate sad_empty eager 
19	0.12579	buoyant overwhelmed_tired trying lethargy_sad_energy doubting buoyant_doubting_concerned fine_normal_standard 

May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.19956] 
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <550> LL/token: -9.88062
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <560> LL/token: -9.81542
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <570> LL/token: -9.83269
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <580> LL/token: -9.7997
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <590> LL/token: -9.80976
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.1326	confident fluctuating uncertain optimistic_enthusiastic low_blue_anxious lethargy_futility heavy_dread_lethargy 
1	0.13188	dark hopeful fearful energised working amused buoyant_doubting_concerned 
2	0.11883	coping worthless_self afraid work fatigued empty fulfilled_inspired_creative 
3	0.13573	mindful inconsolable overwhelming_sad question_last_one question last resilient 
4	0.38464	happy content calm optimistic relaxed hopeful excited 
5	0.13254	sad_low_unhappy devastated trying fear happy sad_low_blue low_devastated_hopeless 
6	0.11916	fear edgy smiling_enjoyment_bliss relaxing exercising_contacting enthusiastic_exercising contacting 
7	0.13363	despair alive agitated grief troubled_bothered supported tears 
8	0.11428	na na_na na_na_na lifeless exhausted_lifeless uneasy trouble 
9	0.24404	emotional fatigue lethargic hungry pain joyless sad_numb 
10	0.13377	lacking light scared isolation sadness life tired_cincerned 
11	0.11857	sleepless tired_lethargic lonley busy capable frustration well 
12	0.12199	static family happy low_blue upset_low low_bad heavy_dread 
13	0.11738	lazy maybe shame sadness_loneliness lonely bored_tired_motivated irriatble_sad 
14	0.12105	strong doubtful contemplative downhearted darkness bored_tired troubled 
15	0.92781	sad tired lonely low hopeless worried anxious 
16	0.12174	snappy depressed_low calm_cool joy agitated_grumpy_blue joy_smiling_enjoyment one 
17	0.12577	gloomy sometimes death heavy optimism darkness sad_hopeless 
18	0.14711	frightened distressed bothered troubled frustrated hopelessness balanced 
19	0.11902	strong pointless worthless lethargic_lonely unstable_unhappy unhappy_sad_weak depressed_unstable 

May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.20209] 
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <600> LL/token: -9.85447
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <610> LL/token: -9.82284
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <620> LL/token: -9.84237
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <630> LL/token: -9.80204
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <640> LL/token: -9.80782
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.12662	meh repetitive help relaxing optimistic_enthusiastic exercising_contacting lonely_meh 
1	0.12458	na na_na na_na_na family agitated vulnerable work 
2	0.11488	snappy level guilt medication overthinking focused_managing_active question_last_one 
3	0.12679	tense_sad stable tired_anxious apathetic sometimes hopeless_worthless lonely_worthless 
4	0.38721	happy content relaxed calm hopeful optimistic excited 
5	0.12666	fear agitated_grumpy lethargy_sad_energy upset_low inspired_creative_happy inspired_creative fulfilled_inspired 
6	0.11081	ok great empty question_last fulfilled_inspired_creative creative_happy_calm creative 
7	0.12571	waiting broken_dejected dejected honest resilient_cheerful_buoyant resilient_cheerful low_devastated_hopeless 
8	0.10839	sad_tearful suicidal sad_distressed pathetic disturbed grumpy_blue critical_agitated_grumpy 
9	0.20542	worry sadness mindful loneliness trying tears darkness 
10	0.12766	grumpy downhearted maybe morose irritability family apathetic 
11	0.1125	sadness joyless coping desperate crying failure laziness 
12	0.11353	optimism strength sometimes angry well_coping_focused well_coping happy_tired_cincerned 
13	0.11266	dog grief laughter bored_tired_motivated cheerful_buoyant_doubting anxious_stressed_moody past_shame_embarrassment 
14	0.11209	lively random better tiredness doubting_concerned buoyant_doubting stress_occasional_tiredness 
15	0.97652	sad tired lonely low hopeless worried unhappy 
16	0.11637	driven stress coping hungry sleep cincerned doubful 
17	0.12479	coping recklessness lethargy demotivated pointless hopelessness lethargy_sad 
18	0.14183	bleak thinking elated_jolly elated self_esteem esteem doubtful 
19	0.11212	fear depressed_sad mixed overwhelmed_tired alert lonely_isolated love 

May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.20541] 
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <650> LL/token: -9.79254
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <660> LL/token: -9.81146
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <670> LL/token: -9.76528
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <680> LL/token: -9.78481
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <690> LL/token: -9.77501
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.1226	sometimes loss stressed agitated_grumpy_blue managing_active managing coping_focused_managing 
1	0.11775	na na_na na_na_na melancholic tired_motivated_prepared enthusiastic_bored_tired enthusiastic_exercising 
2	0.11173	fine flat hatred worthless_self great sad_tired prepared 
3	0.11909	meh unmotivated_sad repetitive frustrated tearful worried bored_tired_motivated 
4	0.38262	happy content calm hopeful relaxed optimistic excited 
5	0.12091	fatigue unmotivated crying grumpy_blue stress_occasional_tiredness inspired sweaty_agitated_restless 
6	0.10976	upbeat emotionless low_tired loss life irrelevant_irriatble relaxing_optimistic 
7	0.12419	sadness despair confident stress tense tears isolation 
8	0.1064	distracted low_tired resilient crushing_heavy crushing unpredictable_doubtful exhausted_overwhelmed 
9	0.18219	heavy balanced painful overwhelmed uneasy sad_angry happy_tired_cincerned 
10	0.12066	driven distracted carefree strong_excited agitated_grumpy irriatble_sad stressed_moody_demotivated 
11	0.10943	purposeful sorrow trying pointless hopelessness well focused_managing_active 
12	0.10861	antisocial anxiety afraid crushing_heavy_dread gloomy_tense home dog_partner_job 
13	0.10723	family mindful lonely_isolated glad confusion lethargy_sad_energy welcome_satisfied 
14	0.10896	heavy lethargy frustration nervous motivated_prepared sad_energy_miserable irrelevant 
15	0.98008	sad tired lonely low hopeless anxious worried 
16	0.11163	loneliness fine hope downtrodden work worry last 
17	0.12005	ok calm_cool better hungry frustration tired bleak 
18	0.13392	sleep neutral grey somewhat darkness irritability worry 
19	0.10959	emotional uninterested lonely_tired lazy tired_exhausted unsettled triggered 

May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.20484] 
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <700> LL/token: -9.75143
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <710> LL/token: -9.77931
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <720> LL/token: -9.73048
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <730> LL/token: -9.76813
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <740> LL/token: -9.74105
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.11735	peace great unhappy_gloomy anger love anxiety sweaty_agitated 
1	0.11256	na na_na na_na_na hopeless_sad triggered fatigued happy 
2	0.10733	uncertain dreariness sad_loss fatigue sleep accepting critical_agitated 
3	0.11326	lively joyless death heavy tears fear fine 
4	0.3812	happy content calm hopeful relaxed optimistic excited 
5	0.11116	quiet restless bothered helpless emotional stressed_anxious_pressurized anxious_pressurized 
6	0.10956	sadness yes contacting optimistic_joy_honest welcome_satisfied environment_achievement embarrassment 
7	0.1184	bothered melancholy bored unwanted sadness frustrated amused 
8	0.10315	bored_listless joy cincerned lethargy_sad low_devastated_hopeless devastated_hopeless_numb fine_normal_standard 
9	0.15922	bleak talking smile free tiredness demotivated joyful_happy 
10	0.11894	family dejected guilt procrastination insomnia crying flat 
11	0.10674	elated_jolly okay relaxing_optimistic_enthusiastic exercising doubting_concerned carefree_fortunate sad_family_tired 
12	0.10272	balanced anger tense troubled blue numb hopeless_numb 
13	0.10629	dog sad_upset optimistic_joy stressed_moody anxious_stressed_moody sweaty_agitated_restless sweaty 
14	0.10093	smiling despondent happy_smiling bliss optimistic well_coping joy_smiling_enjoyment 
15	0.98447	sad tired lonely low hopeless worried anxious 
16	0.11025	disinterested static broken fragile irritable sad_lonely overthinking 
17	0.11369	mindful pointless stressed smiling_enjoyment tired_cincerned cincerned_normal meaningful 
18	0.12428	suicidal ok enjoyment_bliss tensed relaxation work dark 
19	0.10986	elated grey tense jolly unsociable enjoyment happy_joy 

May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.21118] 
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <750> LL/token: -9.78595
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <760> LL/token: -9.74117
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <770> LL/token: -9.75641
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <780> LL/token: -9.76302
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <790> LL/token: -9.74084
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.1114	upset_tired happy_balanced guilt lethargy shame sadness nice 
1	0.10773	na na_na irritable joy love na_na_na edgy 
2	0.10445	routine free reckless tired_lethargic_diet moody_sleep lethargic_diet_moody diet_moody_sleep 
3	0.11142	lazy dog emptiness maybe bright tiredness tired_motivated_prepared 
4	0.37381	happy content calm hopeful relaxed optimistic excited 
5	0.10619	sadness prepared motivated_prepared resilient_cheerful doubting_concerned low_devastated_hopeless depressed_low_devastated 
6	0.10343	sad_low_unhappy motivation fluctuating alone_sad smiling_enjoyment low_blue moody_demotivated 
7	0.1168	distracted somewhat despair lethargy_sad_energy irrelevant optimistic_joy_honest occasional 
8	0.10165	family fragile busy gloomy dejected life miserable 
9	0.14248	happy restless overwhelmed peace critical_agitated_grumpy agitated_grumpy_blue question 
10	0.11522	disturbed short grumpy lifeless heavy isolation agitated 
11	0.10406	ok bored_tired upset_low_bad fulfilled_inspired sitting_avoidance sitting low_quiet 
12	0.09999	level lonely_bored ok excited_happy tired_drained anxious_stressed_moody lethargic_lonely_meh 
13	0.10358	tired_bored struggling normal broken optimism stressed_anxious_pressurized pressurized 
14	0.09945	frozen darkness gloomy excited lonely_meh reckless_tired_worthless fearful_reckless_tired 
15	0.97518	sad tired lonely low hopeless anxious worried 
16	0.10771	dark distressed cheerful tiredness great frustration grumpy_blue 
17	0.10804	family relaxed well_coping_focused coping_focused_managing tired_cincerned_normal happy_tired_cincerned cincerned_normal 
18	0.12052	sadness joyless useful afraid sad_tired low_sad hopelessness 
19	0.10995	wonderful stress lacking well managing_active tiredness_stable stress_occasional 

May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.221] 
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <800> LL/token: -9.74475
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <810> LL/token: -9.7748
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <820> LL/token: -9.73956
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <830> LL/token: -9.70987
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <840> LL/token: -9.74443
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.11048	overwhelmed quiet free thoughtful tired_motivated_prepared motivated_prepared enthusiastic_bored_tired 
1	0.10804	na na_na na_na_na fatigue happy_balanced yes somewhat 
2	0.10612	lazy exhausted_lifeless uninterested sometimes life despair tired_cincerned_normal 
3	0.1093	sadness contemplative headache smiling_enjoyment upset_low_bad upset_low contemplative_considered_appreciative 
4	0.36816	happy calm content relaxed optimistic excited active 
5	0.1007	sleepless overwhelmed insomnia morose darkness joy_honest resilient_cheerful_buoyant 
6	0.10174	sadness sluggish happy_joy_smiling question_last one last_one low_blue 
7	0.10741	heavy tense irritable despondent ok failure upset 
8	0.10611	suicidal poor trying uninterested worthless_self okay cheerful 
9	0.12982	flat lonely_sad repetitive laughter yes love fun 
10	0.11144	self upset lonely energy_miserable buoyant_doubting unpredictable_doubtful exhausted_overwhelmed 
11	0.10036	lively unhappy_gloomy strong coping_focused_managing question_last_one question low_devastated 
12	0.09827	heavy joyless sad_numb disinterested grey lethargy pointless 
13	0.10076	monotonous critical agitated loneliness sadness great uncertain 
14	0.09533	darkness content critical_agitated_grumpy partner_job home_dog_partner home_dog shame_embarrassment_environment 
15	0.95851	sad tired low lonely hopeless worried anxious 
16	0.10672	broken dejected edgy isolated_sad sorry guilt broken_dejected 
17	0.10217	neutral bothered weakness uncontrollable enthusiastic_exercising_contacting stressed_anxious drained_helpless 
18	0.11645	despair hopelessness pain sadness covid exhausted concern_stress_occasional 
19	0.10579	self_esteem supported lonely_crying frozen jolly quiet worried 

May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.21735] 
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <850> LL/token: -9.75613
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <860> LL/token: -9.73484
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <870> LL/token: -9.71793
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <880> LL/token: -9.70708
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <890> LL/token: -9.76688
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.10979	snappy resigned active sadness happy_sad happy_optimistic_joy resilient_cheerful_buoyant 
1	0.0985	na na_na na_na_na dejected sadness coping loneliness 
2	0.10182	failure peace great optimistic_enthusiastic_exercising low_blue_anxious moody_demotivated_unhappy anxious_stressed_moody 
3	0.10181	gloomy joy trapped smiling_enjoyment_bliss upset_low mobile itchy 
4	0.3646	happy content calm optimistic relaxed hopeful excited 
5	0.10155	tears dreariness antisocial frozen disturbed free resilient 
6	0.09853	glum inconsolable struggling grumpy moody inadequate weary 
7	0.09982	life stress tiredness grumpy_blue well managing_active focused_managing_active 
8	0.10177	locked lacking hopeless_bleak tense gloomy prepared motivated_prepared 
9	0.11942	sadness cool darkness listless apathetic alone_lonely lethargy_sad 
10	0.10372	hurt worthless_useless sleepless gloomy worthless agitated_grumpy sad_energy 
11	0.09876	worthless bored heavy self worthless_self weak alone_irrelevant 
12	0.10199	edgy neutral coping bad end sadness tiredness 
13	0.0978	normal fine despair fine_normal agitated tired_cincerned cincerned 
14	0.09645	emptiness thought strength bliss pathetic tired_motivated_prepared tired_motivated 
15	0.94344	sad tired lonely low hopeless worried anxious 
16	0.10604	overwhelmed grief bored_listless heavy uncertain nervous irriatble_sad 
17	0.09561	death alone_irrelevant_irriatble normal_standard calm_thoughtful gloomy_tense_sad tired_lethargic_diet energetic_active 
18	0.11284	anger useful self_esteem light agitated bored_tired_motivated question_last 
19	0.10323	work low_slow futile managing reckless_tired hopeful_energetic_active hopeful_energetic 

May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.22179] 
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <900> LL/token: -9.70502
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <910> LL/token: -9.70014
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <920> LL/token: -9.73723
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <930> LL/token: -9.71808
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <940> LL/token: -9.67047
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.10021	joyless distracted jumpy scared fine disturbed hope 
1	0.09667	na na_na na_na_na sleepless fatigue failure procrastination 
2	0.09775	disinterested grumpy_blue happy_joy_smiling doubting_concerned futility crushing_heavy guilty_emotional 
3	0.09542	anxiety doubtful isolated_angry vulnerable peace tired_motivated motivated_prepared 
4	0.35587	happy content calm hopeful relaxed optimistic excited 
5	0.09913	broken_dejected frozen scared embarrassment unmotivated_happy_sad unmotivated_happy unstable_unhappy_sad 
6	0.09893	sad_worried prepared irriatble irrelevant_irriatble_sad fortunate_happy distracted_unbothered fear_restless_emotional 
7	0.09799	suicidal fulfilled dejected optimistic_enthusiastic_exercising optimistic_enthusiastic exercising_contacting enthusiastic_exercising 
8	0.10097	hungry frightened routine accepting loneliness flat demotivated 
9	0.11325	missing uneasy pain useless tired cincerned_normal irrelevant_irriatble 
10	0.10345	lethargy irrelevant thoughtful_contemplative contemplative_considered calm_thoughtful unwillingness_gloomy_tense hopeless_miserable 
11	0.09791	purposeful happy_hopeful static work well_coping_focused lethargy_sad resilient_cheerful 
12	0.09786	headache sleep gloomy failure despair well_coping focused_managing_active 
13	0.09828	dreariness heavy managing_active managing sad_energy_miserable energy_miserable question 
14	0.09374	wonderful overwhelming_sad busy despair irriatble_sad sad_low_blue low_blue_anxious 
15	0.92698	sad tired lonely low hopeless worried anxious 
16	0.10602	neutral despondent crying sometimes peace relaxing tiredness_stable 
17	0.09514	tired_exhausted unsettled thinking irritated family weak tired 
18	0.11088	contemplative anxious tiredness frustration appreciative concern_stress_occasional concern_stress 
19	0.09599	dog covid optimism devastated_hopeless fulfilled_inspired sad_family_tired sad_family 

May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.22087] 
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <950> LL/token: -9.71316
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <960> LL/token: -9.69979
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <970> LL/token: -9.70197
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <980> LL/token: -9.71049
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <990> LL/token: -9.71284
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
0	0.09835	happy_calm upset_emotional motivated insomnia_tired emotional sad_hopeless pain 
1	0.09272	nervous na_na overwhelmed okay sometimes contented_optimistic fine_normal_standard 
2	0.09983	normal family tired_cincerned_normal optimistic_joy_honest optimistic_joy joy_honest honest 
3	0.09613	calm_cool apathetic uncertain depressed happy_tired_cincerned irriatble_sad alone_irrelevant 
4	0.35625	happy content calm optimistic relaxed excited hopeful 
5	0.0992	pain lazy burden unhappy_gloomy withdrawn loss strong_excited 
6	0.09665	yes frozen weary disinterested upset_tired poor busy 
7	0.09523	disturbed mixed future agitated upset_low_bad short_sweaty agitated_restless 
8	0.09291	heavy fearful aggressive fatigue darkness emotional content_fulfilled 
9	0.1116	smile inactive antisocial lonely_lost despondent unhappy_weak good 
10	0.09627	despair end anxiety stressed_anxious_pressurized hopelessness_end_confusion hopelessness_end unmotivated_happy_sad 
11	0.09469	resigned alone joyful_happy question_last_one question_last happy_optimistic_joy stressed_moody_demotivated 
12	0.09514	worried_anxious ok sad_distressed agitated life optimistic_enthusiastic_exercising meaningful 
13	0.09497	locked fear failure critical_agitated feeling hopeful_energetic fulfilled_motivated 
14	0.08949	useful teary apathetic well_coping_focused well managing_active managing 
15	0.90789	sad tired lonely low hopeless worried anxious 
16	0.09825	thinking broken fear relaxed worry irrelevant_irriatble_sad alone_irrelevant_irriatble 
17	0.09343	tired_lethargic cool unloved fragile distressed isolated_hopeless average 
18	0.10642	na_na_na carefree unhappy_upset numb agitated_grumpy_blue exercising standard_average_flat 
19	0.09114	self hopeful confined random happy_balanced trapped sad_empty 

May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
INFO: [beta: 0.22529] 
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: <1000> LL/token: -9.7144
May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
INFO: 
Total time: 2 seconds

 *** caught segfault ***
address 0x1, cause 'memory not mapped'

Traceback:
 1: wordcloud_boxes(data_points = points_valid_first, boxes = boxes,     boxes_text = boxes_text, text_boxes = text_boxes, bigboxes = bigboxes,     boxes_masks = boxes_masks, boxes_mask = boxes_mask, mask_boxes = mask_boxes,     mask_group = mask_group, angle_group = angle_group, max_angle_group = x$data$max_angle_group[1],     xlim = range(x$limits$x), ylim = range(x$limits$y), eccentricity = x$eccentricity,     rstep = x$rstep, tstep = x$tstep, perc_step = x$perc_step,     max_steps = x$max_steps, rm_outside = x$rm_outside, shape = x$shape)
 2: makeContent.textwordcloudtree(x)
 3: makeContent(x)
 4: drawGTree(x)
 5: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
 6: grid.draw.gTree(x$children[[i]], recording = FALSE)
 7: grid.draw(x$children[[i]], recording = FALSE)
 8: drawGTree(x)
 9: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
10: grid.draw.gTree(x$children[[i]], recording = FALSE)
11: grid.draw(x$children[[i]], recording = FALSE)
12: drawGTree(x)
13: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
14: grid.draw.gTree(x$children[[i]], recording = FALSE)
15: grid.draw(x$children[[i]], recording = FALSE)
16: drawGTree(x)
17: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
18: grid.draw.gTree(gtable)
19: grid.draw(gtable)
20: print.ggplot(x)
21: (function (x, ...) UseMethod("print"))(x)
22: print.default(x)
23: print(x)
24: normal_print(x)
25: knit_print.default(x, ...)
26: knit_print(x, ...)
27: withVisible(knit_print(x, ...))
28: fun(x, options = options)
29: value_fun(ev$value, ev$visible)
30: withVisible(value_fun(ev$value, ev$visible))
31: withCallingHandlers(withVisible(value_fun(ev$value, ev$visible)),     warning = wHandler, error = eHandler, message = mHandler)
32: handle(pv <- withCallingHandlers(withVisible(value_fun(ev$value,     ev$visible)), warning = wHandler, error = eHandler, message = mHandler))
33: evaluate_call(expr, parsed$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)
34: evaluate::evaluate(...)
35: 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$render, options))
36: in_dir(input_dir(), expr)
37: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
38: eng_r(options)
39: block_exec(params)
40: call_block(x)
41: process_group(group)
42: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
43: 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)))})
44: 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)
45: process_file(text, output)
46: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
47: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
48: vweave_rmarkdown(...)
49: engine$weave(file, quiet = quiet, encoding = enc)
50: doTryCatch(return(expr), name, parentenv, handler)
51: tryCatchOne(expr, names, parentenv, handlers[[1L]])
52: tryCatchList(expr, classes, parentenv, handlers)
53: tryCatch({    engine$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)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
54: tools:::.buildOneVignette("topics.Rmd", "/tmp/th798/17369645/R-release/1488/topics.Rcheck/vign_test/topics",     TRUE, FALSE, "topics", "UTF-8", "/tmp/th798/17369645/RtmpQsjco6/filefe5c6f8e7ef3.rds")
An irrecoverable exception occurred. R is aborting now ...
SUMMARY: processing the following file failed:
  'topics.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  '/tmp/th798/17369645/R-release/1488/topics.Rcheck/00check.log'
for details.

[1] "2025-05-19 00:52:44 MST"
> system(paste(c("diff -u", Rcheck.list), collapse=" "))
--- R_version_4.5.0_2025-04-11/release_1.17.2.Rcheck/00check.log	2025-05-19 00:50:07.995680302 -0700
+++ R_version_4.5.0_2025-04-11/master_1.17.99.c4ea09e099b1833fae0eacb50552bce6f051ed82.Rcheck/00check.log	2025-05-19 00:52:44.859069035 -0700
@@ -66,23 +66,23 @@
 --- re-building 'extended_installation_guide.Rmd' using rmarkdown
 --- finished re-building 'extended_installation_guide.Rmd'
 
-sh: line 1: 1036112 Segmentation fault      (core dumped) '/home/th798/R/R-release/bin/R' --vanilla --no-echo > '/tmp/th798/17369645/RtmppYoOtL/filefceb651f6a512' 2>&1 < '/tmp/th798/17369645/RtmppYoOtL/filefceb627bd8357'
+sh: line 1: 1042601 Segmentation fault      (core dumped) '/home/th798/R/R-release/bin/R' --vanilla --no-echo > '/tmp/th798/17369645/RtmpQsjco6/filefe5c6566df6a0' 2>&1 < '/tmp/th798/17369645/RtmpQsjco6/filefe5c644bb3cd9'
 --- re-building 'topics.Rmd' using rmarkdown
-May 19, 2025 12:49:56 AM cc.mallet.topics.ParallelTopicModel <init>
+May 19, 2025 12:52:33 AM cc.mallet.topics.ParallelTopicModel <init>
 INFO: Mallet LDA: 20 topics, 5 topic bits, 11111 topic mask
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel initializeHistograms
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel initializeHistograms
 INFO: max tokens: 18
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel initializeHistograms
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel initializeHistograms
 INFO: total tokens: 5789
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <10> LL/token: -10.54928
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <20> LL/token: -10.4368
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <30> LL/token: -10.46242
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <40> LL/token: -10.4171
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.25	worthless sad weak quiet melancholy lazy normal 
 1	0.25	sad alone isolated upset numb pessimistic critical 
@@ -105,17 +105,17 @@
 18	0.25	sad depressed alone exhausted crying troubled bothered 
 19	0.25	nervous positive unhappy fearful bleak tired irritable 
 
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <50> LL/token: -10.38957
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <60> LL/token: -10.42703
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <70> LL/token: -10.39149
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <80> LL/token: -10.39257
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <90> LL/token: -10.373
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.25	sad worthless hopeless melancholy ok suicidal pathetic 
 1	0.25	nervous helpless frozen distressed tears coping desperate 
@@ -138,17 +138,17 @@
 18	0.25	sad hopeful depressed troubled bothered frightened carefree 
 19	0.25	positive sad drained bleak yes fearful blue 
 
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <100> LL/token: -10.36726
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <110> LL/token: -10.37766
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <120> LL/token: -10.38785
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <130> LL/token: -10.35184
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <140> LL/token: -10.38075
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.25	useless worthless hopeless sad confident dull pathetic 
 1	0.25	nervous self family ok loss thinking self_esteem 
@@ -171,17 +171,17 @@
 18	0.25	sad angry troubled depressed bothered disturbed low 
 19	0.25	hopeful positive fearful flat mindful demotivated pointless 
 
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <150> LL/token: -10.39719
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <160> LL/token: -10.3788
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <170> LL/token: -10.36414
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <180> LL/token: -10.3433
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <190> LL/token: -10.36913
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.25	hopeless sad empty bleak flat pointless demotivated 
 1	0.25	nervous restless stress frozen sleepless contemplative pain 
@@ -204,17 +204,17 @@
 18	0.25	sad depressed anxiety angry tired anxious fearful 
 19	0.25	hopeful apathetic confused great life mindful trying 
 
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <200> LL/token: -10.33757
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <210> LL/token: -10.31999
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <220> LL/token: -10.35006
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <230> LL/token: -10.33597
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <240> LL/token: -10.33511
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.25	hopeless empty pain sad irritable flat lifeless 
 1	0.25	unhappy nervous bleak restless miserable hopelessness antisocial 
@@ -237,19 +237,19 @@
 18	0.25	sad depressed anxious fearful troubled bothered tense 
 19	0.25	hopeful mindful great confident stable hopeful_optimistic busy 
 
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
 INFO: [beta: 0.08028] 
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <250> LL/token: -9.91364
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <260> LL/token: -10.11753
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <270> LL/token: -10.09343
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:34 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <280> LL/token: -10.1188
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <290> LL/token: -10.11641
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.24601	alone hopeless sad tired numb distracted negative 
 1	0.22356	unhappy gloomy stressed moody agitated death happy_balanced 
@@ -272,19 +272,19 @@
 18	0.2374	sad bothered troubled tense anger frightened excited_happy 
 19	0.22696	dark blue_tired alert end ok irritable agitated 
 
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
 INFO: [beta: 0.11797] 
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <300> LL/token: -10.09088
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <310> LL/token: -10.12712
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <320> LL/token: -10.08908
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <330> LL/token: -10.11842
-May 19, 2025 12:49:57 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <340> LL/token: -10.08338
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.22589	bored drained listless bored_listless angry lonely_bored covid 
 1	0.20739	sad sadness broken dejected mixed snappy broken_dejected 
@@ -307,19 +307,19 @@
 18	0.21568	yes supported missing energy uninterested sad_distressed sleep 
 19	0.20147	blue lethargic trying emotionless despondent busy scared 
 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
 INFO: [beta: 0.1383] 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <350> LL/token: -10.09403
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <360> LL/token: -10.01065
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <370> LL/token: -10.05585
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <380> LL/token: -10.03154
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <390> LL/token: -10.04184
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.19463	stress family miserable happy headache alive fearful 
 1	0.18795	joy overwhelmed hopeful death blank insomnia family 
@@ -342,19 +342,19 @@
 18	0.1924	blue active carefree grey ok miserable grumpy_blue 
 19	0.17306	sluggish disinterested burden lethargic resilient_cheerful_buoyant doubting_concerned doubting 
 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
 INFO: [beta: 0.15331] 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <400> LL/token: -9.9999
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <410> LL/token: -9.95792
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <420> LL/token: -9.9964
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <430> LL/token: -9.98962
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <440> LL/token: -9.96221
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.16972	positive troubled bothered optimism anxious disturbed troubled_bothered 
 1	0.16597	joy smiling enjoyment peace love dog confined 
@@ -377,19 +377,19 @@
 18	0.1659	sadness sad pain worry frozen tears failure 
 19	0.14917	sadness energy abandoned blue surviving help grumpy_blue 
 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
 INFO: [beta: 0.1635] 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <450> LL/token: -9.98591
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <460> LL/token: -9.92413
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <470> LL/token: -9.89601
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <480> LL/token: -9.92328
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <490> LL/token: -9.90131
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.15646	disturbed sadness dreariness lacking trouble isolation tearful 
 1	0.15386	coping content_optimistic elated_jolly useful purposeful isolated_sad low_unhappy 
@@ -412,19 +412,19 @@
 18	0.15671	sadness uninterested loss despair lazy fragile end 
 19	0.13323	abandoned worthless_self restless miserable happy_tired_cincerned cincerned exercising 
 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
 INFO: [beta: 0.18319] 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <500> LL/token: -9.89981
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <510> LL/token: -9.86441
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <520> LL/token: -9.8564
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <530> LL/token: -9.86544
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <540> LL/token: -9.88115
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.14248	tired_unmotivated critical isolated_angry gloomy nice happy_nice empty 
 1	0.14105	smile anxious_stressed sad_lonely_isolated mindful_hopeful emotional cheerful question_last_one 
@@ -447,19 +447,19 @@
 18	0.14846	sadness frozen tears antisocial desperate sad_empty eager 
 19	0.12579	buoyant overwhelmed_tired trying lethargy_sad_energy doubting buoyant_doubting_concerned fine_normal_standard 
 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
 INFO: [beta: 0.19956] 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <550> LL/token: -9.88062
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <560> LL/token: -9.81542
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <570> LL/token: -9.83269
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <580> LL/token: -9.7997
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <590> LL/token: -9.80976
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.1326	confident fluctuating uncertain optimistic_enthusiastic low_blue_anxious lethargy_futility heavy_dread_lethargy 
 1	0.13188	dark hopeful fearful energised working amused buoyant_doubting_concerned 
@@ -482,19 +482,19 @@
 18	0.14711	frightened distressed bothered troubled frustrated hopelessness balanced 
 19	0.11902	strong pointless worthless lethargic_lonely unstable_unhappy unhappy_sad_weak depressed_unstable 
 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
 INFO: [beta: 0.20209] 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <600> LL/token: -9.85447
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <610> LL/token: -9.82284
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <620> LL/token: -9.84237
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <630> LL/token: -9.80204
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <640> LL/token: -9.80782
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.12662	meh repetitive help relaxing optimistic_enthusiastic exercising_contacting lonely_meh 
 1	0.12458	na na_na na_na_na family agitated vulnerable work 
@@ -517,19 +517,19 @@
 18	0.14183	bleak thinking elated_jolly elated self_esteem esteem doubtful 
 19	0.11212	fear depressed_sad mixed overwhelmed_tired alert lonely_isolated love 
 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
 INFO: [beta: 0.20541] 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <650> LL/token: -9.79254
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <660> LL/token: -9.81146
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <670> LL/token: -9.76528
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <680> LL/token: -9.78481
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <690> LL/token: -9.77501
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.1226	sometimes loss stressed agitated_grumpy_blue managing_active managing coping_focused_managing 
 1	0.11775	na na_na na_na_na melancholic tired_motivated_prepared enthusiastic_bored_tired enthusiastic_exercising 
@@ -552,19 +552,19 @@
 18	0.13392	sleep neutral grey somewhat darkness irritability worry 
 19	0.10959	emotional uninterested lonely_tired lazy tired_exhausted unsettled triggered 
 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
 INFO: [beta: 0.20484] 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <700> LL/token: -9.75143
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <710> LL/token: -9.77931
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <720> LL/token: -9.73048
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <730> LL/token: -9.76813
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <740> LL/token: -9.74105
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.11735	peace great unhappy_gloomy anger love anxiety sweaty_agitated 
 1	0.11256	na na_na na_na_na hopeless_sad triggered fatigued happy 
@@ -587,19 +587,19 @@
 18	0.12428	suicidal ok enjoyment_bliss tensed relaxation work dark 
 19	0.10986	elated grey tense jolly unsociable enjoyment happy_joy 
 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
 INFO: [beta: 0.21118] 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <750> LL/token: -9.78595
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <760> LL/token: -9.74117
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <770> LL/token: -9.75641
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <780> LL/token: -9.76302
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <790> LL/token: -9.74084
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.1114	upset_tired happy_balanced guilt lethargy shame sadness nice 
 1	0.10773	na na_na irritable joy love na_na_na edgy 
@@ -622,19 +622,19 @@
 18	0.12052	sadness joyless useful afraid sad_tired low_sad hopelessness 
 19	0.10995	wonderful stress lacking well managing_active tiredness_stable stress_occasional 
 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
 INFO: [beta: 0.221] 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <800> LL/token: -9.74475
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <810> LL/token: -9.7748
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <820> LL/token: -9.73956
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <830> LL/token: -9.70987
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <840> LL/token: -9.74443
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.11048	overwhelmed quiet free thoughtful tired_motivated_prepared motivated_prepared enthusiastic_bored_tired 
 1	0.10804	na na_na na_na_na fatigue happy_balanced yes somewhat 
@@ -657,19 +657,19 @@
 18	0.11645	despair hopelessness pain sadness covid exhausted concern_stress_occasional 
 19	0.10579	self_esteem supported lonely_crying frozen jolly quiet worried 
 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
 INFO: [beta: 0.21735] 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <850> LL/token: -9.75613
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <860> LL/token: -9.73484
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <870> LL/token: -9.71793
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <880> LL/token: -9.70708
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <890> LL/token: -9.76688
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.10979	snappy resigned active sadness happy_sad happy_optimistic_joy resilient_cheerful_buoyant 
 1	0.0985	na na_na na_na_na dejected sadness coping loneliness 
@@ -692,19 +692,19 @@
 18	0.11284	anger useful self_esteem light agitated bored_tired_motivated question_last 
 19	0.10323	work low_slow futile managing reckless_tired hopeful_energetic_active hopeful_energetic 
 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
 INFO: [beta: 0.22179] 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <900> LL/token: -9.70502
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <910> LL/token: -9.70014
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <920> LL/token: -9.73723
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <930> LL/token: -9.71808
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <940> LL/token: -9.67047
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.10021	joyless distracted jumpy scared fine disturbed hope 
 1	0.09667	na na_na na_na_na sleepless fatigue failure procrastination 
@@ -727,19 +727,19 @@
 18	0.11088	contemplative anxious tiredness frustration appreciative concern_stress_occasional concern_stress 
 19	0.09599	dog covid optimism devastated_hopeless fulfilled_inspired sad_family_tired sad_family 
 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
 INFO: [beta: 0.22087] 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <950> LL/token: -9.71316
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <960> LL/token: -9.69979
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <970> LL/token: -9.70197
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <980> LL/token: -9.71049
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <990> LL/token: -9.71284
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 0	0.09835	happy_calm upset_emotional motivated insomnia_tired emotional sad_hopeless pain 
 1	0.09272	nervous na_na overwhelmed okay sometimes contented_optimistic fine_normal_standard 
@@ -762,11 +762,11 @@
 18	0.10642	na_na_na carefree unhappy_upset numb agitated_grumpy_blue exercising standard_average_flat 
 19	0.09114	self hopeful confined random happy_balanced trapped sad_empty 
 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel optimizeBeta
 INFO: [beta: 0.22529] 
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: <1000> LL/token: -9.7144
-May 19, 2025 12:49:58 AM cc.mallet.topics.ParallelTopicModel estimate
+May 19, 2025 12:52:35 AM cc.mallet.topics.ParallelTopicModel estimate
 INFO: 
 Total time: 2 seconds
 
@@ -827,7 +827,7 @@
 51: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 52: tryCatchList(expr, classes, parentenv, handlers)
 53: 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)    }}, error = function(e) {    OK <<- FALSE    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)))})
-54: tools:::.buildOneVignette("topics.Rmd", "/tmp/th798/17369645/R-release/1488/topics.Rcheck/vign_test/topics",     TRUE, FALSE, "topics", "UTF-8", "/tmp/th798/17369645/RtmppYoOtL/filefceb62414a207.rds")
+54: tools:::.buildOneVignette("topics.Rmd", "/tmp/th798/17369645/R-release/1488/topics.Rcheck/vign_test/topics",     TRUE, FALSE, "topics", "UTF-8", "/tmp/th798/17369645/RtmpQsjco6/filefe5c6f8e7ef3.rds")
 An irrecoverable exception occurred. R is aborting now ...
 SUMMARY: processing the following file failed:
   'topics.Rmd'
> library(data.table, lib.loc=R.home("library"))
> (sig.diff.dt <- myDiff(Rvers))
Key: <checking>
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)
+ }
>