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

WARNING: ignoring environment value of R_HOME

R Under development (unstable) (2025-07-04 r88383) -- "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/2025-07-05/deps.csv", 
task.str = "343", release = "/scratch/th798/data.table-revdeps/2025-07-05/data.table_release_1.17.6.tar.gz", 
master = "/scratch/th798/data.table-revdeps/2025-07-05/data.table_master_1.17.99.1e2e3badae6cc19a5270112c3ad11e64ce279174.tar.gz"
)
> (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers
[1] "/tmp/th798/18313058/R-devel/343"
> if(requireNamespace("R.cache"))R.cache::getCachePath()
Loading required namespace: R.cache
[1] "/tmp/th798/18313058/R-devel/343/R.cache"
> task.id <- as.integer(cargs[["task.str"]])
> deps.df <- read.csv(cargs[["deps.csv"]])
> (rev.dep <- deps.df$Package[task.id])
[1] "doblin"
> job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id)
> setwd(task.dir)
> .libPaths()
[1] "/tmp/th798/18313058/R-devel/343/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] "2025-07-05 00:42:46 MST"
> install.time <- system.time({
+   install.packages(rev.dep, dep=TRUE)
+ })
Installing package into '/tmp/th798/18313058/R-devel/343/library'
(as 'lib' is unspecified)
also installing the dependencies 'clv', 'stinepack', 'locpol', 'longitudinalData', 'pdc', 'TSclust', 'imputeTS', 'dtwclust', 'TSdist'

trying URL 'http://cloud.r-project.org/src/contrib/clv_0.3-2.4.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/stinepack_1.5.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/locpol_0.8.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/longitudinalData_2.4.7.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/pdc_1.0.3.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/TSclust_1.3.2.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/imputeTS_3.3.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/dtwclust_6.0.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/TSdist_3.7.1.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/doblin_0.1.1.tar.gz'
* installing *source* package 'clv' ...
** this is package 'clv' version '0.3-2.4'
** package 'clv' 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 SD_SDbw_indicies.c -o SD_SDbw_indicies.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 VCLDefines.c -o VCLDefines.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 cluster_scatter.c -o cluster_scatter.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 cluster_stability.c -o cluster_stability.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 connectivity.c -o connectivity.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 dot_product.c -o dot_product.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 matrix_scatter_measures.c -o matrix_scatter_measures.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 optimal_assignment.c -o optimal_assignment.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 standard_external_measures.c -o standard_external_measures.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 clv.so SD_SDbw_indicies.o VCLDefines.o cluster_scatter.o cluster_stability.o connectivity.o dot_product.o matrix_scatter_measures.o optimal_assignment.o standard_external_measures.o
installing to /tmp/th798/18313058/R-devel/343/library/00LOCK-clv/00new/clv/libs
** R
** demo
** 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 (clv)
* installing *source* package 'stinepack' ...
** this is package 'stinepack' version '1.5'
** package 'stinepack' 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 (stinepack)
* installing *source* package 'locpol' ...
** this is package 'locpol' version '0.8.0'
** package 'locpol' 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 locpol.c -o locpol.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 locpol.so init.o locpol.o
installing to /tmp/th798/18313058/R-devel/343/library/00LOCK-locpol/00new/locpol/libs
** 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
** 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 (locpol)
* installing *source* package 'pdc' ...
** this is package 'pdc' version '1.0.3'
** package 'pdc' 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 fast_codebook0.c -o fast_codebook0.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 fast_codebook2.c -o fast_codebook2.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 fast_codebook3.c -o fast_codebook3.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 fast_codebook4.c -o fast_codebook4.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 fast_codebook5.c -o fast_codebook5.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 fast_codebook6.c -o fast_codebook6.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 fast_codebook7.c -o fast_codebook7.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 pdc.so fast_codebook0.o fast_codebook2.o fast_codebook3.o fast_codebook4.o fast_codebook5.o fast_codebook6.o fast_codebook7.o
installing to /tmp/th798/18313058/R-devel/343/library/00LOCK-pdc/00new/pdc/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** 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 (pdc)
* installing *source* package 'dtwclust' ...
** this is package 'dtwclust' version '6.0.0'
** package 'dtwclust' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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/KahanSummer.cpp -o utils/KahanSummer.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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/utils.cpp -o utils/utils.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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/UndirectedGraph.cpp -o utils/UndirectedGraph.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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/ParallelWorker.cpp -o utils/ParallelWorker.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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/R-utils.cpp -o utils/R-utils.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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/envelope.cpp -o utils/envelope.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c tadpole/tadpole.cpp -o tadpole/tadpole.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c centroids/dba.cpp -o centroids/dba.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c centroids/sdtw-cent.cpp -o centroids/sdtw-cent.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distances/lbk.cpp -o distances/lbk.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distances/soft-dtw.cpp -o distances/soft-dtw.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distances/R-gateways.cpp -o distances/R-gateways.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distances/logGAK.cpp -o distances/logGAK.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distances/calculators.cpp -o distances/calculators.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distances/lbi.cpp -o distances/lbi.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distances/dtw-basic.cpp -o distances/dtw-basic.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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.cpp -o init.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distmat/distmat.cpp -o distmat/distmat.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distmat/dtw-lb.cpp -o distmat/dtw-lb.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distmat/fillers.cpp -o distmat/fillers.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/projects/genomic-ml/R/R-devel/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distmat/distmat-loop.cpp -o distmat/distmat-loop.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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 dtwclust.so ./utils/KahanSummer.o ./utils/utils.o ./utils/UndirectedGraph.o ./utils/ParallelWorker.o ./utils/R-utils.o ./utils/envelope.o ./tadpole/tadpole.o ./centroids/dba.o ./centroids/sdtw-cent.o ./distances/lbk.o ./distances/soft-dtw.o ./distances/R-gateways.o ./distances/logGAK.o ./distances/calculators.o ./distances/lbi.o ./distances/dtw-basic.o ./init.o ./distmat/distmat.o ./distmat/dtw-lb.o ./distmat/fillers.o ./distmat/distmat-loop.o -L/home/th798/R/R-devel/lib -lRlapack -L/home/th798/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
installing to /tmp/th798/18313058/R-devel/343/library/00LOCK-dtwclust/00new/dtwclust/libs
** 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
** 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 (dtwclust)
* installing *source* package 'longitudinalData' ...
** this is package 'longitudinalData' version '2.4.7'
** package 'longitudinalData' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading

####################################################################
############################## Function ############################
####################################################################
### Functions accepting NA ###
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++ Fin Function ++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

### Constantes ###

####################################################################
########################## Class LongData ##########################
############################# Creation #############################
####################################################################
### Definition ###

###################################################################
########################## Class LongData #########################
########################### Constructeur ##########################
###################################################################

###################################################################
########################## Class LongData #########################
############################ Accesseurs ###########################
###################################################################
### Getteur ###

###################################################################
########################## Class LongData #########################
############################# Affichage ###########################
###################################################################
### Method: 'show' pour LongData ###
### Method: 'print' pour LongData ###

###################################################################
########################## Class LongData #########################
############################## Various ############################
###################################################################

-------------------------------------------------------------------
-------------------------- Class LongData -------------------------
------------------------------- Fin -------------------------------
-------------------------------------------------------------------

####################################################################
######################### Class LongData3d #########################
############################# Creation #############################
####################################################################
### Definition ###

###################################################################
########################## Class LongData #########################
########################### Constructeur ##########################
###################################################################

###################################################################
########################## Class LongData #########################
############################ Accesseurs ###########################
###################################################################
### Getteur ###

###################################################################
########################## Class LongData #########################
############################# Affichage ###########################
###################################################################
### Method: 'show' pour LongData3d ###
### Method: 'print' pour LongData3d ###

###################################################################
########################## Class LongData #########################
############################## Various ############################
###################################################################

-------------------------------------------------------------------
-------------------------- Class LongData -------------------------
------------------------------- Fin -------------------------------
-------------------------------------------------------------------
###################################################################
########################### class matrix ##########################
################### Imputations des manquantes ####################
###################################################################
###################################################################
########################### class matrix ##########################
################### Imputations des manquantes ####################
###################################################################
###################################################################
########################### class matrix ##########################
################### Imputations des manquantes ####################
###################################################################

###################################################################
########################## Class LongData #########################
############################ Imputation ###########################
###################################################################

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++ Class LongData +++++++++++++++++++++++++
++++++++++++++++++++++++++ Fin Imputation +++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

###################################################################
########################## Class Partition ########################
############################# Criterion ###########################
###################################################################
####################################################################
########################## Class Partition #########################
############################# Creation #############################
####################################################################
### Definition ###

####################################################################
########################## Class  Partition ########################
############################ Constructeur ##########################
####################################################################
### Method : 'show' for partition ###

####################################################################
########################## Class Partition #########################
############################# Accesseurs ###########################
####################################################################
### Getteur ###
### Setteur ###

####################################################################
########################## Class Partition #########################
############################### Autre ##############################
####################################################################

--------------------------------------------------------------------
------------------------ Fin Class Partition -----------------------
--------------------------------------------------------------------
####################################################################
######################## Class ListPartition ######################
############################## Creation ############################
####################################################################
### Definition ###
####################################################################
######################## Class ListPartition ######################
############################ Constructeur ##########################
####################################################################

####################################################################
######################## Test  ListPartition ######################
############################# Accesseurs ###########################
####################################################################
### Setteur ###
### Getteur ###
####################################################################
######################## Class ListPartition ######################
############################## Affichage ###########################
####################################################################
### Method : 'show' for yPartition ###

####################################################################
######################## Class ListPartition ######################
############################### Autres #############################
####################################################################
Creating a generic function for 'ordered' from package 'base' in package 'longitudinalData'
--------------------------------------------------------------------
------------------------ Class ListPartition ----------------------
------------------------------ Creation ----------------------------
--------------------------------------------------------------------

####################################################################
######################### Class parLongData ########################
############################# Creation #############################
####################################################################

###################################################################
######################## Class parLongData ########################
########################### Constructeur ##########################
###################################################################
### Method : 'show' for ParLongData ###
### Getteur ###
### Setteur ###

--------------------------------------------------------------------
----------------------- Fin Test ParLongData -----------------------
--------------------------------------------------------------------

####################################################################
######################### Class parWindows #########################
############################# Creation #############################
####################################################################

###################################################################
######################### Class parWindows ########################
########################### Constructeur ##########################
###################################################################
### Method : 'show' for ParWindows ###
### Getteur ###
### Setteur ###

--------------------------------------------------------------------
-------------------------- Fin ParWindows --------------------------
--------------------------------------------------------------------
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++ Class LongData +++++++++++++++++++++++++
+++++++++++++++++++++++++++++++ plot ++++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
### Method: 'plot' pour LongData et Partition, divers ###
### Method: 'plot' pour LongData3d sans Partition ###
###################################################################
########################## Class LongData #########################
############################## plot3d #############################
###################################################################
###################################################################
########################## Class LongData #########################
############################# plot3dPdf ###########################
###################################################################

-------------------------------------------------------------------
------------------------ Class LongData plot ----------------------
------------------------------- Fin -------------------------------
-------------------------------------------------------------------
** 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 (longitudinalData)
* installing *source* package 'imputeTS' ...
** this is package 'imputeTS' version '3.3'
** package 'imputeTS' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/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++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/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 locf.cpp -o locf.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/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 ma.cpp -o ma.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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 imputeTS.so RcppExports.o locf.o ma.o
installing to /tmp/th798/18313058/R-devel/343/library/00LOCK-imputeTS/00new/imputeTS/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 (imputeTS)
* installing *source* package 'TSclust' ...
** this is package 'TSclust' version '1.3.2'
** package 'TSclust' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TSclust)
* installing *source* package 'TSdist' ...
** this is package 'TSdist' version '3.7.1'
** package 'TSdist' 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 EDR.c -o EDR.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 EDRnw.c -o EDRnw.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 ERP.c -o ERP.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 ERPnw.c -o ERPnw.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 LCSS.c -o LCSS.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 LCSSnw.c -o LCSSnw.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 registerDynamicSymbol.c -o registerDynamicSymbol.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 TSdist.so EDR.o EDRnw.o ERP.o ERPnw.o LCSS.o LCSSnw.o registerDynamicSymbol.o
installing to /tmp/th798/18313058/R-devel/343/library/00LOCK-TSdist/00new/TSdist/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** 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 (TSdist)
* installing *source* package 'doblin' ...
** this is package 'doblin' version '0.1.1'
** package 'doblin' successfully unpacked and MD5 sums checked
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (doblin)

The downloaded source packages are in
	'/tmp/th798/18313058/RtmpORVQtX/downloaded_packages'
> cat("Time to install revdep:\n")
Time to install revdep:
> print(install.time)
   user  system elapsed 
189.084  17.270 297.659 
> print(Sys.time())
[1] "2025-07-05 00:47:43 MST"
> downloaded_packages <- file.path(
+   tempdir(),
+   "downloaded_packages")
> dl.glob <- file.path(
+   downloaded_packages,
+   paste0(rev.dep,"_*.tar.gz"))
> rev.dep.dl.row <- cbind(rev.dep, Sys.glob(dl.glob))
> colnames(rev.dep.dl.row) <- c("pkg","path")
> rev.dep.release.tar.gz <- normalizePath(rev.dep.dl.row[,"path"], mustWork=TRUE)
> pkg.Rcheck <- paste0(rev.dep, ".Rcheck")
> 
> proj.dir <- "~/genomic-ml/data.table-revdeps"
> source(file.path(proj.dir, "myStatus.R"))
> Rvers <- gsub("[()]", "", gsub(" ", "_", R.version[["version.string"]]))
> dir.create(Rvers, showWarnings=FALSE)
> Rcheck.list <- list()
> for(dt.version.short in c("release", "master")){
+   dt.tar.gz <- cargs[[dt.version.short]]
+   dt.version <- gsub(".tar.gz|/.*?_", "", dt.tar.gz)
+   print(Sys.time())
+   install.packages(dt.tar.gz, repos=NULL)
+   print(Sys.time())
+   check.cmd <- get_check_cmd(rev.dep.release.tar.gz)
+   system(check.cmd)
+   print(Sys.time())
+   dest.Rcheck <- file.path(
+     Rvers,
+     paste0(dt.version, ".Rcheck"))
+   unlink(dest.Rcheck, recursive=TRUE)
+   file.rename(pkg.Rcheck, dest.Rcheck)
+   Rcheck.list[[dt.version]] <- file.path(dest.Rcheck, "00check.log")
+ }
[1] "2025-07-05 00:47:43 MST"
Installing package into '/tmp/th798/18313058/R-devel/343/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** this is package 'data.table' version '1.17.6'
** 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/th798/18313058/R-devel/343/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] "2025-07-05 00:48:17 MST"
* using log directory '/tmp/th798/18313058/R-devel/343/doblin.Rcheck'
* using R Under development (unstable) (2025-07-04 r88383)
* 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 'doblin/DESCRIPTION' ... OK
* this is package 'doblin' version '0.1.1'
* 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 'doblin' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under 'inst/doc' ... 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] "2025-07-05 00:50:33 MST"
[1] "2025-07-05 00:50:33 MST"
Installing package into '/tmp/th798/18313058/R-devel/343/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 mergelist.c -o mergelist.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 mergelist.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/th798/18313058/R-devel/343/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] "2025-07-05 00:51:06 MST"
* using log directory '/tmp/th798/18313058/R-devel/343/doblin.Rcheck'
* using R Under development (unstable) (2025-07-04 r88383)
* 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 'doblin/DESCRIPTION' ... OK
* this is package 'doblin' version '0.1.1'
* 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 'doblin' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under 'inst/doc' ... 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] "2025-07-05 00:53:26 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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> cargs <- commandArgs(trailingOnly=TRUE)
> if(length(cargs)==0){
+   ## before running interactively, make sure to start emacs/R with
+   ## environment defined in /scratch/...check_one.sh, particularly
+   ## R_LIBS_USER=/tmp/... otherwise we get error when installing
+   ## data.table.
+   base <- "/scratch/th798/data.table-revdeps/*"
+   cargs <- c(
+     Sys.glob(file.path(base,"deps.csv")),
+     "349",
+     Sys.glob(file.path(base, "data.table_release_*tar.gz")),
+     Sys.glob(file.path(base, "data.table_master_*tar.gz"))
+   )
+ }
> names(cargs) <- c("deps.csv", "task.str", "release", "master")
> dput(cargs)
c(deps.csv = "/scratch/th798/data.table-revdeps/2025-07-05/deps.csv", 
task.str = "343", release = "/scratch/th798/data.table-revdeps/2025-07-05/data.table_release_1.17.6.tar.gz", 
master = "/scratch/th798/data.table-revdeps/2025-07-05/data.table_master_1.17.99.1e2e3badae6cc19a5270112c3ad11e64ce279174.tar.gz"
)
> (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers
[1] "/tmp/th798/18313058/R-release/343"
> if(requireNamespace("R.cache"))R.cache::getCachePath()
Loading required namespace: R.cache
[1] "/tmp/th798/18313058/R-release/343/R.cache"
> task.id <- as.integer(cargs[["task.str"]])
> deps.df <- read.csv(cargs[["deps.csv"]])
> (rev.dep <- deps.df$Package[task.id])
[1] "doblin"
> job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id)
> setwd(task.dir)
> .libPaths()
[1] "/tmp/th798/18313058/R-release/343/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] "2025-07-05 00:53:33 MST"
> install.time <- system.time({
+   install.packages(rev.dep, dep=TRUE)
+ })
Installing package into '/tmp/th798/18313058/R-release/343/library'
(as 'lib' is unspecified)
also installing the dependencies 'clv', 'stinepack', 'RcppThread', 'locpol', 'longitudinalData', 'pdc', 'TSclust', 'imputeTS', 'dtwclust', 'TSdist'

trying URL 'http://cloud.r-project.org/src/contrib/clv_0.3-2.4.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/stinepack_1.5.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/RcppThread_2.2.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/locpol_0.8.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/longitudinalData_2.4.7.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/pdc_1.0.3.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/TSclust_1.3.2.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/imputeTS_3.3.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/dtwclust_6.0.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/TSdist_3.7.1.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/doblin_0.1.1.tar.gz'
* installing *source* package 'clv' ...
** this is package 'clv' version '0.3-2.4'
** package 'clv' 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 SD_SDbw_indicies.c -o SD_SDbw_indicies.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 VCLDefines.c -o VCLDefines.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 cluster_scatter.c -o cluster_scatter.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 cluster_stability.c -o cluster_stability.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 connectivity.c -o connectivity.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 dot_product.c -o dot_product.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 matrix_scatter_measures.c -o matrix_scatter_measures.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 optimal_assignment.c -o optimal_assignment.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 standard_external_measures.c -o standard_external_measures.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 clv.so SD_SDbw_indicies.o VCLDefines.o cluster_scatter.o cluster_stability.o connectivity.o dot_product.o matrix_scatter_measures.o optimal_assignment.o standard_external_measures.o
installing to /tmp/th798/18313058/R-release/343/library/00LOCK-clv/00new/clv/libs
** R
** demo
** 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 (clv)
* installing *source* package 'stinepack' ...
** this is package 'stinepack' version '1.5'
** package 'stinepack' 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 (stinepack)
* installing *source* package 'RcppThread' ...
** this is package 'RcppThread' version '2.2.0'
** package 'RcppThread' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/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 detectCores.cpp -o detectCores.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/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 testGlobal.cpp -o testGlobal.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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 RcppThread.so detectCores.o testGlobal.o -latomic -lpthread
installing to /tmp/th798/18313058/R-release/343/library/00LOCK-RcppThread/00new/RcppThread/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 (RcppThread)
* installing *source* package 'locpol' ...
** this is package 'locpol' version '0.8.0'
** package 'locpol' 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 locpol.c -o locpol.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 locpol.so init.o locpol.o
installing to /tmp/th798/18313058/R-release/343/library/00LOCK-locpol/00new/locpol/libs
** 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
** 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 (locpol)
* installing *source* package 'pdc' ...
** this is package 'pdc' version '1.0.3'
** package 'pdc' 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 fast_codebook0.c -o fast_codebook0.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 fast_codebook2.c -o fast_codebook2.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 fast_codebook3.c -o fast_codebook3.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 fast_codebook4.c -o fast_codebook4.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 fast_codebook5.c -o fast_codebook5.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 fast_codebook6.c -o fast_codebook6.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 fast_codebook7.c -o fast_codebook7.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 pdc.so fast_codebook0.o fast_codebook2.o fast_codebook3.o fast_codebook4.o fast_codebook5.o fast_codebook6.o fast_codebook7.o
installing to /tmp/th798/18313058/R-release/343/library/00LOCK-pdc/00new/pdc/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** 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 (pdc)
* installing *source* package 'longitudinalData' ...
** this is package 'longitudinalData' version '2.4.7'
** package 'longitudinalData' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading

####################################################################
############################## Function ############################
####################################################################
### Functions accepting NA ###
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++++ Fin Function ++++++++++++++++++++++++++
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

### Constantes ###

####################################################################
########################## Class LongData ##########################
############################# Creation #############################
####################################################################
### Definition ###

###################################################################
########################## Class LongData #########################
########################### Constructeur ##########################
###################################################################

###################################################################
########################## Class LongData #########################
############################ Accesseurs ###########################
###################################################################
### Getteur ###

###################################################################
########################## Class LongData #########################
############################# Affichage ###########################
###################################################################
### Method: 'show' pour LongData ###
### Method: 'print' pour LongData ###

###################################################################
########################## Class LongData #########################
############################## Various ############################
###################################################################

-------------------------------------------------------------------
-------------------------- Class LongData -------------------------
------------------------------- Fin -------------------------------
-------------------------------------------------------------------

####################################################################
######################### Class LongData3d #########################
############################# Creation #############################
####################################################################
### Definition ###

###################################################################
########################## Class LongData #########################
########################### Constructeur ##########################
###################################################################

###################################################################
########################## Class LongData #########################
############################ Accesseurs ###########################
###################################################################
### Getteur ###

###################################################################
########################## Class LongData #########################
############################# Affichage ###########################
###################################################################
### Method: 'show' pour LongData3d ###
### Method: 'print' pour LongData3d ###

###################################################################
########################## Class LongData #########################
############################## Various ############################
###################################################################

-------------------------------------------------------------------
-------------------------- Class LongData -------------------------
------------------------------- Fin -------------------------------
-------------------------------------------------------------------
###################################################################
########################### class matrix ##########################
################### Imputations des manquantes ####################
###################################################################
###################################################################
########################### class matrix ##########################
################### Imputations des manquantes ####################
###################################################################
###################################################################
########################### class matrix ##########################
################### Imputations des manquantes ####################
###################################################################

###################################################################
########################## Class LongData #########################
############################ Imputation ###########################
###################################################################

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++ Class LongData +++++++++++++++++++++++++
++++++++++++++++++++++++++ Fin Imputation +++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

###################################################################
########################## Class Partition ########################
############################# Criterion ###########################
###################################################################
####################################################################
########################## Class Partition #########################
############################# Creation #############################
####################################################################
### Definition ###

####################################################################
########################## Class  Partition ########################
############################ Constructeur ##########################
####################################################################
### Method : 'show' for partition ###

####################################################################
########################## Class Partition #########################
############################# Accesseurs ###########################
####################################################################
### Getteur ###
### Setteur ###

####################################################################
########################## Class Partition #########################
############################### Autre ##############################
####################################################################

--------------------------------------------------------------------
------------------------ Fin Class Partition -----------------------
--------------------------------------------------------------------
####################################################################
######################## Class ListPartition ######################
############################## Creation ############################
####################################################################
### Definition ###
####################################################################
######################## Class ListPartition ######################
############################ Constructeur ##########################
####################################################################

####################################################################
######################## Test  ListPartition ######################
############################# Accesseurs ###########################
####################################################################
### Setteur ###
### Getteur ###
####################################################################
######################## Class ListPartition ######################
############################## Affichage ###########################
####################################################################
### Method : 'show' for yPartition ###

####################################################################
######################## Class ListPartition ######################
############################### Autres #############################
####################################################################
Creating a generic function for 'ordered' from package 'base' in package 'longitudinalData'
--------------------------------------------------------------------
------------------------ Class ListPartition ----------------------
------------------------------ Creation ----------------------------
--------------------------------------------------------------------

####################################################################
######################### Class parLongData ########################
############################# Creation #############################
####################################################################

###################################################################
######################## Class parLongData ########################
########################### Constructeur ##########################
###################################################################
### Method : 'show' for ParLongData ###
### Getteur ###
### Setteur ###

--------------------------------------------------------------------
----------------------- Fin Test ParLongData -----------------------
--------------------------------------------------------------------

####################################################################
######################### Class parWindows #########################
############################# Creation #############################
####################################################################

###################################################################
######################### Class parWindows ########################
########################### Constructeur ##########################
###################################################################
### Method : 'show' for ParWindows ###
### Getteur ###
### Setteur ###

--------------------------------------------------------------------
-------------------------- Fin ParWindows --------------------------
--------------------------------------------------------------------
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++++++++++++++++++ Class LongData +++++++++++++++++++++++++
+++++++++++++++++++++++++++++++ plot ++++++++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
### Method: 'plot' pour LongData et Partition, divers ###
### Method: 'plot' pour LongData3d sans Partition ###
###################################################################
########################## Class LongData #########################
############################## plot3d #############################
###################################################################
###################################################################
########################## Class LongData #########################
############################# plot3dPdf ###########################
###################################################################

-------------------------------------------------------------------
------------------------ Class LongData plot ----------------------
------------------------------- Fin -------------------------------
-------------------------------------------------------------------
** 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 (longitudinalData)
* installing *source* package 'imputeTS' ...
** this is package 'imputeTS' version '3.3'
** package 'imputeTS' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/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++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/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 locf.cpp -o locf.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/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 ma.cpp -o ma.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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 imputeTS.so RcppExports.o locf.o ma.o
installing to /tmp/th798/18313058/R-release/343/library/00LOCK-imputeTS/00new/imputeTS/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 (imputeTS)
* installing *source* package 'dtwclust' ...
** this is package 'dtwclust' version '6.0.0'
** package 'dtwclust' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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/KahanSummer.cpp -o utils/KahanSummer.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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/utils.cpp -o utils/utils.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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/UndirectedGraph.cpp -o utils/UndirectedGraph.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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/ParallelWorker.cpp -o utils/ParallelWorker.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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/R-utils.cpp -o utils/R-utils.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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/envelope.cpp -o utils/envelope.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c tadpole/tadpole.cpp -o tadpole/tadpole.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c centroids/dba.cpp -o centroids/dba.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c centroids/sdtw-cent.cpp -o centroids/sdtw-cent.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distances/lbk.cpp -o distances/lbk.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distances/soft-dtw.cpp -o distances/soft-dtw.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distances/R-gateways.cpp -o distances/R-gateways.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distances/logGAK.cpp -o distances/logGAK.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distances/calculators.cpp -o distances/calculators.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distances/lbi.cpp -o distances/lbi.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distances/dtw-basic.cpp -o distances/dtw-basic.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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.cpp -o init.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distmat/distmat.cpp -o distmat/distmat.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distmat/dtw-lb.cpp -o distmat/dtw-lb.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distmat/fillers.cpp -o distmat/fillers.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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/RcppParallel/include' -I'/tmp/th798/18313058/R-release/343/library/RcppThread/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DRCPP_USE_UNWIND_PROTECT  -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c distmat/distmat-loop.cpp -o distmat/distmat-loop.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -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 dtwclust.so ./utils/KahanSummer.o ./utils/utils.o ./utils/UndirectedGraph.o ./utils/ParallelWorker.o ./utils/R-utils.o ./utils/envelope.o ./tadpole/tadpole.o ./centroids/dba.o ./centroids/sdtw-cent.o ./distances/lbk.o ./distances/soft-dtw.o ./distances/R-gateways.o ./distances/logGAK.o ./distances/calculators.o ./distances/lbi.o ./distances/dtw-basic.o ./init.o ./distmat/distmat.o ./distmat/dtw-lb.o ./distmat/fillers.o ./distmat/distmat-loop.o -L/home/th798/R/R-release/lib -lRlapack -L/home/th798/R/R-release/lib -lRblas -lgfortran -lm -lquadmath
installing to /tmp/th798/18313058/R-release/343/library/00LOCK-dtwclust/00new/dtwclust/libs
** 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
** 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 (dtwclust)
* installing *source* package 'TSclust' ...
** this is package 'TSclust' version '1.3.2'
** package 'TSclust' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (TSclust)
* installing *source* package 'TSdist' ...
** this is package 'TSdist' version '3.7.1'
** package 'TSdist' 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 EDR.c -o EDR.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 EDRnw.c -o EDRnw.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 ERP.c -o ERP.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 ERPnw.c -o ERPnw.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 LCSS.c -o LCSS.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 LCSSnw.c -o LCSSnw.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 registerDynamicSymbol.c -o registerDynamicSymbol.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 TSdist.so EDR.o EDRnw.o ERP.o ERPnw.o LCSS.o LCSSnw.o registerDynamicSymbol.o
installing to /tmp/th798/18313058/R-release/343/library/00LOCK-TSdist/00new/TSdist/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** 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 (TSdist)
* installing *source* package 'doblin' ...
** this is package 'doblin' version '0.1.1'
** package 'doblin' successfully unpacked and MD5 sums checked
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (doblin)

The downloaded source packages are in
	'/tmp/th798/18313058/RtmpnoAetY/downloaded_packages'
> cat("Time to install revdep:\n")
Time to install revdep:
> print(install.time)
   user  system elapsed 
224.243  18.967 332.318 
> print(Sys.time())
[1] "2025-07-05 00:59:06 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] "2025-07-05 00:59:06 MST"
Installing package into '/tmp/th798/18313058/R-release/343/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** this is package 'data.table' version '1.17.6'
** 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/th798/18313058/R-release/343/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] "2025-07-05 00:59:35 MST"
* using log directory '/tmp/th798/18313058/R-release/343/doblin.Rcheck'
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Spack GCC) 12.2.0
    GNU Fortran (Spack GCC) 12.2.0
* running under: Red Hat Enterprise Linux 8.10 (Ootpa)
* using session charset: ASCII
* checking for file 'doblin/DESCRIPTION' ... OK
* this is package 'doblin' version '0.1.1'
* 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 'doblin' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under 'inst/doc' ... 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] "2025-07-05 01:02:30 MST"
[1] "2025-07-05 01:02:30 MST"
Installing package into '/tmp/th798/18313058/R-release/343/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 mergelist.c -o mergelist.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 mergelist.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/th798/18313058/R-release/343/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] "2025-07-05 01:03:05 MST"
* using log directory '/tmp/th798/18313058/R-release/343/doblin.Rcheck'
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Spack GCC) 12.2.0
    GNU Fortran (Spack GCC) 12.2.0
* running under: Red Hat Enterprise Linux 8.10 (Ootpa)
* using session charset: ASCII
* checking for file 'doblin/DESCRIPTION' ... OK
* this is package 'doblin' version '0.1.1'
* 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 'doblin' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under 'inst/doc' ... 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] "2025-07-05 01:06:04 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)
+ }
>