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

WARNING: ignoring environment value of R_HOME

R Under development (unstable) (2025-03-26 r88060) -- "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/2025-03-27/deps.csv", 
task.str = "715", release = "/scratch/th798/data.table-revdeps/2025-03-27/data.table_release_1.17.0.tar.gz", 
master = "/scratch/th798/data.table-revdeps/2025-03-27/data.table_master_1.17.99.2cb03162a21328cc5f68a8c3b0e554f5edfcb5b9.tar.gz"
)
> (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers
[1] "/tmp/th798/16153372/R-devel/715"
> if(requireNamespace("R.cache"))R.cache::getCachePath()
Loading required namespace: R.cache
[1] "/tmp/th798/16153372/R-devel/715/R.cache"
> task.id <- as.integer(cargs[["task.str"]])
> deps.df <- read.csv(cargs[["deps.csv"]])
> (rev.dep <- deps.df$Package[task.id])
[1] "LabourMarketAreas"
> job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id)
> setwd(task.dir)
> .libPaths()
[1] "/tmp/th798/16153372/R-devel/715/library"
[2] "/projects/genomic-ml/R/R-devel/library" 
> options(repos=c(#this should be in ~/.Rprofile too.
+   CRAN="http://cloud.r-project.org"))
> print(Sys.time())
[1] "2025-03-27 00:52:54 MST"
> install.time <- system.time({
+   install.packages(rev.dep, dep=TRUE)
+ })
Installing package into '/tmp/th798/16153372/R-devel/715/library'
(as 'lib' is unspecified)
also installing the dependencies 'geometries', 'sfheaders', 'spacesXYZ', 'geojsonsf', 'jsonify', 'leaflet.providers', 'cols4all', 'leafem', 'leafgl', 'leaflegend', 'leaflet', 'leafsync', 'tmaptools', 'servr', 'tmap'

trying URL 'http://cloud.r-project.org/src/contrib/geometries_0.2.4.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/sfheaders_0.4.4.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/spacesXYZ_1.5-1.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/geojsonsf_2.0.3.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/jsonify_1.2.2.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/leaflet.providers_2.0.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/cols4all_0.8.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/leafem_0.2.3.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/leafgl_0.2.2.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/leaflegend_1.2.1.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/leaflet_2.2.2.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/leafsync_0.1.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/tmaptools_3.2.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/servr_0.32.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/tmap_4.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/LabourMarketAreas_3.4.tar.gz'
* installing *source* package 'geometries' ...
** this is package 'geometries' version '0.2.4'
** package 'geometries' 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 -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c bbox.cpp -o bbox.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c close.cpp -o close.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c columns.cpp -o columns.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c coordinates.cpp -o coordinates.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c geometries.cpp -o geometries.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c lines.cpp -o lines.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c lists.cpp -o lists.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c nest.cpp -o nest.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c shapes.cpp -o shapes.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c tests.cpp -o tests.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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.cpp -o utils.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 geometries.so RcppExports.o bbox.o close.o columns.o coordinates.o geometries.o lines.o lists.o nest.o shapes.o tests.o utils.o
installing to /tmp/th798/16153372/R-devel/715/library/00LOCK-geometries/00new/geometries/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 (geometries)
* installing *source* package 'spacesXYZ' ...
** this is package 'spacesXYZ' version '1.5-1'
** package 'spacesXYZ' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (spacesXYZ)
* installing *source* package 'jsonify' ...
** this is package 'jsonify' version '1.2.2'
** package 'jsonify' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
using C++11
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c from_json.cpp -o from_json.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c pretty.cpp -o pretty.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c read_json.cpp -o read_json.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c tests.cpp -o tests.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c to_json.cpp -o to_json.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-devel/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c validate.cpp -o validate.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o jsonify.so RcppExports.o from_json.o pretty.o read_json.o tests.o to_json.o validate.o
installing to /tmp/th798/16153372/R-devel/715/library/00LOCK-jsonify/00new/jsonify/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 (jsonify)
* installing *source* package 'leaflet.providers' ...
** this is package 'leaflet.providers' version '2.0.0'
** package 'leaflet.providers' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (leaflet.providers)
* installing *source* package 'tmaptools' ...
** this is package 'tmaptools' version '3.2'
** package 'tmaptools' 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 (tmaptools)
* installing *source* package 'servr' ...
** this is package 'servr' version '0.32'
** package 'servr' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (servr)
* installing *source* package 'sfheaders' ...
** this is package 'sfheaders' version '0.4.4'
** package 'sfheaders' 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 -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c bbox.cpp -o bbox.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c cast.cpp -o cast.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c lists.cpp -o lists.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c sfg_dimension.cpp -o sfg_dimension.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c shapes.cpp -o shapes.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c to_df.cpp -o to_df.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c to_sf.cpp -o to_sf.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c to_sfc.cpp -o to_sfc.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c to_sfg.cpp -o to_sfg.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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.cpp -o utils.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 sfheaders.so RcppExports.o bbox.o cast.o lists.o sfg_dimension.o shapes.o to_df.o to_sf.o to_sfc.o to_sfg.o utils.o
installing to /tmp/th798/16153372/R-devel/715/library/00LOCK-sfheaders/00new/sfheaders/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** 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 (sfheaders)
* installing *source* package 'cols4all' ...
** this is package 'cols4all' version '0.8'
** package 'cols4all' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cols4all)
* installing *source* package 'leaflet' ...
** this is package 'leaflet' version '2.2.2'
** package 'leaflet' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (leaflet)
* installing *source* package 'geojsonsf' ...
** this is package 'geojsonsf' version '2.0.3'
** package 'geojsonsf' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
using C++11
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/tmp/th798/16153372/R-devel/715/library/jsonify/include' -I'/projects/genomic-ml/R/R-devel/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/tmp/th798/16153372/R-devel/715/library/sfheaders/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/tmp/th798/16153372/R-devel/715/library/jsonify/include' -I'/projects/genomic-ml/R/R-devel/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/tmp/th798/16153372/R-devel/715/library/sfheaders/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c df_geojson.cpp -o df_geojson.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/tmp/th798/16153372/R-devel/715/library/jsonify/include' -I'/projects/genomic-ml/R/R-devel/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/tmp/th798/16153372/R-devel/715/library/sfheaders/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c geojson_to_sf.cpp -o geojson_to_sf.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/tmp/th798/16153372/R-devel/715/library/jsonify/include' -I'/projects/genomic-ml/R/R-devel/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/tmp/th798/16153372/R-devel/715/library/sfheaders/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c geojson_to_wkt.cpp -o geojson_to_wkt.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/tmp/th798/16153372/R-devel/715/library/jsonify/include' -I'/projects/genomic-ml/R/R-devel/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/tmp/th798/16153372/R-devel/715/library/sfheaders/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c geojson_wkt.cpp -o geojson_wkt.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/tmp/th798/16153372/R-devel/715/library/jsonify/include' -I'/projects/genomic-ml/R/R-devel/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/tmp/th798/16153372/R-devel/715/library/sfheaders/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c read_geojson.cpp -o read_geojson.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-devel/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-devel/715/library/geometries/include' -I'/tmp/th798/16153372/R-devel/715/library/jsonify/include' -I'/projects/genomic-ml/R/R-devel/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/tmp/th798/16153372/R-devel/715/library/sfheaders/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c sf_geojson.cpp -o sf_geojson.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o geojsonsf.so RcppExports.o df_geojson.o geojson_to_sf.o geojson_to_wkt.o geojson_wkt.o read_geojson.o sf_geojson.o
installing to /tmp/th798/16153372/R-devel/715/library/00LOCK-geojsonsf/00new/geojsonsf/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 (geojsonsf)
* installing *source* package 'leaflegend' ...
** this is package 'leaflegend' version '1.2.1'
** package 'leaflegend' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** 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 (leaflegend)
* installing *source* package 'leafsync' ...
** this is package 'leafsync' version '0.1.0'
** package 'leafsync' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** 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 (leafsync)
* installing *source* package 'leafem' ...
** this is package 'leafem' version '0.2.3'
** package 'leafem' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** 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 (leafem)
* installing *source* package 'leafgl' ...
** this is package 'leafgl' version '0.2.2'
** package 'leafgl' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** 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 (leafgl)
* installing *source* package 'tmap' ...
** this is package 'tmap' version '4.0'
** package 'tmap' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tmap)
* installing *source* package 'LabourMarketAreas' ...
** this is package 'LabourMarketAreas' version '3.4'
** package 'LabourMarketAreas' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (LabourMarketAreas)

The downloaded source packages are in
	'/tmp/th798/16153372/RtmpnJ4CF8/downloaded_packages'
> cat("Time to install revdep:\n")
Time to install revdep:
> print(install.time)
   user  system elapsed 
208.769  23.685 308.420 
> print(Sys.time())
[1] "2025-03-27 00:58:03 MST"
> downloaded_packages <- file.path(
+   tempdir(),
+   "downloaded_packages")
> dl.glob <- file.path(
+   downloaded_packages,
+   paste0(rev.dep,"_*.tar.gz"))
> rev.dep.dl.row <- cbind(rev.dep, Sys.glob(dl.glob))
> colnames(rev.dep.dl.row) <- c("pkg","path")
> rev.dep.release.tar.gz <- normalizePath(rev.dep.dl.row[,"path"], mustWork=TRUE)
> pkg.Rcheck <- paste0(rev.dep, ".Rcheck")
> 
> proj.dir <- "~/genomic-ml/data.table-revdeps"
> source(file.path(proj.dir, "myStatus.R"))
> Rvers <- gsub("[()]", "", gsub(" ", "_", R.version[["version.string"]]))
> dir.create(Rvers, showWarnings=FALSE)
> Rcheck.list <- list()
> for(dt.version.short in c("release", "master")){
+   dt.tar.gz <- cargs[[dt.version.short]]
+   dt.version <- gsub(".tar.gz|/.*?_", "", dt.tar.gz)
+   print(Sys.time())
+   install.packages(dt.tar.gz, repos=NULL)
+   print(Sys.time())
+   check.cmd <- get_check_cmd(rev.dep.release.tar.gz)
+   system(check.cmd)
+   print(Sys.time())
+   dest.Rcheck <- file.path(
+     Rvers,
+     paste0(dt.version, ".Rcheck"))
+   unlink(dest.Rcheck, recursive=TRUE)
+   file.rename(pkg.Rcheck, dest.Rcheck)
+   Rcheck.list[[dt.version]] <- file.path(dest.Rcheck, "00check.log")
+ }
[1] "2025-03-27 00:58:03 MST"
Installing package into '/tmp/th798/16153372/R-devel/715/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** this is package 'data.table' version '1.17.0'
** package 'data.table' successfully unpacked and MD5 sums checked
** using staged installation
zlib 1.2.13 is available ok
* checking if R installation supports OpenMP without any extra hints... yes
** libs
using C compiler: 'gcc (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c assign.c -o assign.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c between.c -o between.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c bmerge.c -o bmerge.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c chmatch.c -o chmatch.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c cj.c -o cj.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c coalesce.c -o coalesce.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c dogroups.c -o dogroups.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fastmean.c -o fastmean.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fcast.c -o fcast.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fifelse.c -o fifelse.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fmelt.c -o fmelt.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c forder.c -o forder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frank.c -o frank.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fread.c -o fread.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c freadR.c -o freadR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c froll.c -o froll.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frollR.c -o frollR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frolladaptive.c -o frolladaptive.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fsort.c -o fsort.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwrite.c -o fwrite.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwriteR.c -o fwriteR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c gsumm.c -o gsumm.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c idatetime.c -o idatetime.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ijoin.c -o ijoin.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c init.c -o init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c inrange.c -o inrange.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nafill.c -o nafill.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c negate.c -o negate.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nqrecreateindices.c -o nqrecreateindices.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c openmp-utils.c -o openmp-utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c programming.c -o programming.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c quickselect.c -o quickselect.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c rbindlist.c -o rbindlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c reorder.c -o reorder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c shift.c -o shift.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c snprintf.c -o snprintf.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c subset.c -o subset.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c transpose.c -o transpose.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c types.c -o types.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c uniqlist.c -o uniqlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c utils.c -o utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c vecseq.c -o vecseq.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c wrappers.c -o wrappers.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include
PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi
installing to /tmp/th798/16153372/R-devel/715/library/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (data.table)
[1] "2025-03-27 00:58:26 MST"
* using log directory '/tmp/th798/16153372/R-devel/715/LabourMarketAreas.Rcheck'
* using R Under development (unstable) (2025-03-26 r88060)
* 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 'LabourMarketAreas/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LabourMarketAreas' version '3.4'
* 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 'LabourMarketAreas' 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 ... NOTE
checkRd: (-1) StatClusterData.Rd:34: Lost braces
    34 | \bold{LMA: }{ positive integer; labour market areas ID} 
       |             ^
checkRd: (-1) StatClusterData.Rd:36: Lost braces
    36 | \bold{EMP_live: }{numeric; number of commuters who live in the area} 
       |                  ^
checkRd: (-1) StatClusterData.Rd:38: Lost braces
    38 | \bold{EMP_work: }{numeric; number of commuters working in the area}
       |                  ^
checkRd: (-1) StatClusterData.Rd:40: Lost braces
    40 | \bold{validity: }{numeric; validity value computed with the current parameters}
       |                  ^
checkRd: (-1) StatClusterData.Rd:42: Lost braces
    42 | \bold{EMP_live_work: }{numeric; number of commuters living and working in the area}
       |                       ^
checkRd: (-1) StatClusterData.Rd:44: Lost braces
    44 | \bold{lma_commuter_percent: }{numeric; the quantity: (EMP_live-EMP_live_work)+(EMP_work-EMP_live_work)/(2*EMP_live_work) }
       |                              ^
checkRd: (-1) StatClusterData.Rd:46-48: Lost braces
    46 | \bold{Home_Work_Ratio: }{numeric; the quantity 
       |                         ^
checkRd: (-1) StatClusterData.Rd:50: Lost braces
    50 | \bold{SC_demand_side: }{numeric; demand side self-containment}
       |                        ^
checkRd: (-1) StatClusterData.Rd:52: Lost braces
    52 | \bold{SC_supply_side: }{numeric; supply side self-containment}
       |                        ^
checkRd: (-1) StatClusterData.Rd:54: Lost braces
    54 | \bold{N_com: }{integer; number of communities forming the LMA}
       |               ^
checkRd: (-1) StatClusterData.Rd:56-57: Lost braces
    56 | \bold{InternalCohesionLink: }{numeric; consistency of internal relationships. It is given by the ratio between number of links between communities inside LMA, excluding itself, and the maximum number of possible links, i.e. (N_com * (N_com-1)). See [1].
       |                              ^
checkRd: (-1) StatClusterData.Rd:59-60: Lost braces
    59 | \bold{InternalCohesionFlows: }{numeric; intensity of internal relationships. It is the percentage of internal flows (excluding flows having as origin and destination the same node) of the LMA between different communities w.r.t the total internal flows. See [3].
       |                               ^
checkRd: (-1) StatClusterData.Rd:62-63: Lost braces
    62 | \bold{NbCentralComm: }{integer; number of communities having a centrality index greater than 1 (for communities with more than 100 workers, the centrality index is the ratio between net incoming flows and net outgoing flows).
       |                       ^
checkRd: (-1) StatClusterData.Rd:65: Lost braces
    65 | \bold{N_links_in: }{integer; number of LMAs whose residents work in the current LMA (including itself) } 
       |                    ^
checkRd: (-1) StatClusterData.Rd:67: Lost braces
    67 | \bold{N_links_out: }{integer; number of LMAs where the residents of the current LMA work (including itself)}
       |                     ^
checkRd: (-1) StatClusterData.Rd:74: Lost braces
    74 | \bold{N_links: }{numeric; number of links between LMAs}
       |                 ^
checkRd: (-1) StatClusterData.Rd:76: Lost braces
    76 | \bold{PercNbLinksLessThreshold: }{numeric; percentage of links corresponding to flows below threshold}
       |                                  ^
checkRd: (-1) StatClusterData.Rd:78: Lost braces
    78 | \bold{summFlows: }{numeric vector; summary statistics on flows}
       |                   ^
checkRd: (-1) StatClusterData.Rd:80: Lost braces
    80 | \bold{summFlowsNoItself: }{numeric vector; summary statistics on flows, excluding the self-flows}
       |                           ^
checkRd: (-1) StatClusterData.Rd:82: Lost braces
    82 | \bold{summLinks_in: }{numeric vector; summary statistics on the number of incoming flows}
       |                      ^
checkRd: (-1) StatClusterData.Rd:84: Lost braces
    84 | \bold{summLinks_out: }{summary statistics on the number of outgoing flows}
       |                       ^
checkRd: (-1) StatClusterData.Rd:86: Lost braces
    86 | \bold{clusterMaxNlinks_in: }{positive integer; the LMA ID of the cluster reaching the maximum number of incoming flows}
       |                             ^
checkRd: (-1) StatClusterData.Rd:88: Lost braces
    88 | \bold{clusterMaxNlinks_out: }{positive integer; the LMA ID of the cluster reaching the maximum number of outgoing flows}
       |                              ^
checkRd: (-1) StatClusterData.Rd:90: Lost braces
    90 | \bold{clusterMinNlinks_in: }{positive integer; the LMA ID of the cluster reaching the minimum number of incoming flows}
       |                             ^
checkRd: (-1) StatClusterData.Rd:92: Lost braces
    92 | \bold{clusterMinNlinks_out: }{positive integer; the LMA ID of the cluster reaching the minimum number of outgoing flows}
       |                              ^
checkRd: (-1) StatClusterData.Rd:98: Lost braces
    98 | \bold{NbClusters: }{integer; number of clusters}
       |                    ^
checkRd: (-1) StatClusterData.Rd:100: Lost braces
   100 | \bold{NbClusterUniqueCom: }{integer; number of clusters with an unique community}
       |                            ^
checkRd: (-1) StatClusterData.Rd:102: Lost braces
   102 | \bold{NbClustersValidLess1: }{integer; number of clusters with validity smaller than 1}
       |                              ^
checkRd: (-1) StatClusterData.Rd:104: Lost braces
   104 | \bold{NbClustersNoCentralCom: }{integer; number of clusters with no communities having a centrality measure greater than 1 }
       |                                ^
checkRd: (-1) StatClusterData.Rd:106: Lost braces
   106 | \bold{Mean.SC_demand_side: }{numeric; mean of the demand side self-containment of the clusters in the partition  }
       |                             ^
checkRd: (-1) StatClusterData.Rd:108: Lost braces
   108 | \bold{Std.SC_demand_side: }{numeric; standard deviation of the demand side self-containment }
       |                            ^
checkRd: (-1) StatClusterData.Rd:110: Lost braces
   110 | \bold{Mean.SC_supply_side: }{numeric; mean of the supply side self-containment of the clusters in the partition }
       |                             ^
checkRd: (-1) StatClusterData.Rd:112: Lost braces
   112 | \bold{Std.SC_supply_side: }{numeric; standard deviation of the supply side self-containment   }
       |                            ^
checkRd: (-1) StatClusterData.Rd:114: Lost braces
   114 | \bold{Q1.InternalCohesionFlows: }{numeric; first quartile of the InternalCohesionFlows }
       |                                  ^
checkRd: (-1) StatClusterData.Rd:116: Lost braces
   116 | \bold{Q2.InternalCohesionFlows: }{numeric; median of the InternalCohesionFlows}
       |                                  ^
checkRd: (-1) StatClusterData.Rd:118: Lost braces
   118 | \bold{Q3.InternalCohesionFlows: }{numeric; third quartile of the InternalCohesionFlows }
       |                                  ^
checkRd: (-1) StatClusterData.Rd:120: Lost braces
   120 | \bold{Q1.InternalCohesionLink: }{numeric; first quartile of the InternalCohesionLink }
       |                                 ^
checkRd: (-1) StatClusterData.Rd:122: Lost braces
   122 | \bold{Q2.InternalCohesionLink: }{numeric; median of the InternalCohesionLink}
       |                                 ^
checkRd: (-1) StatClusterData.Rd:124: Lost braces
   124 | \bold{Q3.InternalCohesionLink: }{numeric; third quartile of the InternalCohesionLink }
       |                                 ^
checkRd: (-1) StatClusterData.Rd:126: Lost braces
   126 | \bold{Q1.EMP_live: }{numeric; first quartile of the residents }
       |                     ^
checkRd: (-1) StatClusterData.Rd:128: Lost braces
   128 | \bold{Q2.EMP_live: }{numeric; median of the residents}
       |                     ^
checkRd: (-1) StatClusterData.Rd:130: Lost braces
   130 | \bold{Q3.EMP_live: }{numeric; third quartile of the residents }
       |                     ^
checkRd: (-1) StatClusterData.Rd:132: Lost braces
   132 | \bold{Mean.EMP_live: }{numeric; mean value of the residents }
       |                       ^
checkRd: (-1) StatClusterData.Rd:134: Lost braces
   134 | \bold{Std.EMP_live: }{numeric; standard deviation of the residents }
       |                      ^
checkRd: (-1) StatClusterData.Rd:136: Lost braces
   136 | \bold{Min.EMP_live: }{numeric; minimum value of the residents }
       |                      ^
checkRd: (-1) StatClusterData.Rd:138: Lost braces
   138 | \bold{Max.EMP_live: }{numeric; maximum value of the residents }
       |                      ^
checkRd: (-1) StatClusterData.Rd:140: Lost braces
   140 | \bold{Q1.EMP_work: }{numeric; first quartile of the workers/jobs }
       |                     ^
checkRd: (-1) StatClusterData.Rd:142: Lost braces
   142 | \bold{Q2.EMP_work: }{numeric; median of the workers/jobs}
       |                     ^
checkRd: (-1) StatClusterData.Rd:144: Lost braces
   144 | \bold{Q3.EMP_work: }{numeric; third quartile of the workers/jobs }
       |                     ^
checkRd: (-1) StatClusterData.Rd:146: Lost braces
   146 | \bold{Mean.EMP_work: }{numeric; mean value of the workers }
       |                       ^
checkRd: (-1) StatClusterData.Rd:148: Lost braces
   148 | \bold{Std.EMP_work: }{numeric; standard deviation of the workers }
       |                      ^
checkRd: (-1) StatClusterData.Rd:150: Lost braces
   150 | \bold{Min.EMP_work: }{numeric; minimum value of the workers }
       |                      ^
checkRd: (-1) StatClusterData.Rd:152: Lost braces
   152 | \bold{Max.EMP_work: }{numeric; maximum value of the workers }
       |                      ^
checkRd: (-1) StatClusterData.Rd:154: Lost braces
   154 | \bold{Q1.EMP_live_work: }{numeric; first quartile of the commuters living and working in the same area}
       |                          ^
checkRd: (-1) StatClusterData.Rd:156: Lost braces
   156 | \bold{Q2.EMP_live_work: }{numeric; median of the commuters living and working in the same area}
       |                          ^
checkRd: (-1) StatClusterData.Rd:158: Lost braces
   158 | \bold{Q3.EMP_live_work: }{numeric; third quartile of the the commuters living and working in the same area }
       |                          ^
checkRd: (-1) StatClusterData.Rd:160: Lost braces
   160 | \bold{Min.EMP_live_work: }{numeric; minimum value of the commuters living and working in the same area }
       |                           ^
checkRd: (-1) StatClusterData.Rd:162: Lost braces
   162 | \bold{Max.EMP_live_work: }{numeric; maximum value of the commuters living and working in the same area }
       |                           ^
checkRd: (-1) StatClusterData.Rd:164: Lost braces
   164 | \bold{Mean.lma_commuter_percent: }{numeric; mean value of the quantity: (EMP_live-EMP_live_work)+(EMP_work-EMP_live_work)/(2*EMP_live_work) }
       |                                   ^
checkRd: (-1) StatClusterData.Rd:166: Lost braces
   166 | \bold{Std.lma_commuter_percent: }{numeric; standard deviation of the quantity (EMP_live-EMP_live_work)+(EMP_work-EMP_live_work)/(2*EMP_live_work) }
       |                                  ^
checkRd: (-1) StatClusterData.Rd:168-170: Lost braces
   168 | \bold{Mean.Home_Work_Ratio: }{numeric; mean value of the quantity 
       |                              ^
checkRd: (-1) StatClusterData.Rd:171-173: Lost braces
   171 |  \bold{Std.Home_Work_Ratio: }{numeric; standard deviation of the quantity 
       |                              ^
checkRd: (-1) StatClusterData.Rd:175: Lost braces
   175 | \bold{Q_modularity: }{numeric; Q_modularity index }
       |                      ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  '/tmp/th798/16153372/R-devel/715/LabourMarketAreas.Rcheck/00check.log'
for details.

[1] "2025-03-27 01:03:44 MST"
[1] "2025-03-27 01:03:44 MST"
Installing package into '/tmp/th798/16153372/R-devel/715/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** this is package 'data.table' version '1.17.99'
** using staged installation
zlib 1.2.13 is available ok
* checking if R installation supports OpenMP without any extra hints... yes
** libs
using C compiler: 'gcc (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c assign.c -o assign.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c between.c -o between.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c bmerge.c -o bmerge.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c chmatch.c -o chmatch.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c cj.c -o cj.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c coalesce.c -o coalesce.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c dogroups.c -o dogroups.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fastmean.c -o fastmean.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fcast.c -o fcast.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fifelse.c -o fifelse.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fmelt.c -o fmelt.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c forder.c -o forder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frank.c -o frank.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fread.c -o fread.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c freadR.c -o freadR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c froll.c -o froll.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frollR.c -o frollR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frolladaptive.c -o frolladaptive.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fsort.c -o fsort.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwrite.c -o fwrite.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwriteR.c -o fwriteR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c gsumm.c -o gsumm.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c idatetime.c -o idatetime.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ijoin.c -o ijoin.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c init.c -o init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c inrange.c -o inrange.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nafill.c -o nafill.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c negate.c -o negate.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nqrecreateindices.c -o nqrecreateindices.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c openmp-utils.c -o openmp-utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c programming.c -o programming.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c quickselect.c -o quickselect.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c rbindlist.c -o rbindlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c reorder.c -o reorder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c shift.c -o shift.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c snprintf.c -o snprintf.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c subset.c -o subset.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c transpose.c -o transpose.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c types.c -o types.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c uniqlist.c -o uniqlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c utils.c -o utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c vecseq.c -o vecseq.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c wrappers.c -o wrappers.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include
PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi
installing to /tmp/th798/16153372/R-devel/715/library/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (data.table)
[1] "2025-03-27 01:04:07 MST"
* using log directory '/tmp/th798/16153372/R-devel/715/LabourMarketAreas.Rcheck'
* using R Under development (unstable) (2025-03-26 r88060)
* 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 'LabourMarketAreas/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LabourMarketAreas' version '3.4'
* 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 'LabourMarketAreas' 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 ... NOTE
checkRd: (-1) StatClusterData.Rd:34: Lost braces
    34 | \bold{LMA: }{ positive integer; labour market areas ID} 
       |             ^
checkRd: (-1) StatClusterData.Rd:36: Lost braces
    36 | \bold{EMP_live: }{numeric; number of commuters who live in the area} 
       |                  ^
checkRd: (-1) StatClusterData.Rd:38: Lost braces
    38 | \bold{EMP_work: }{numeric; number of commuters working in the area}
       |                  ^
checkRd: (-1) StatClusterData.Rd:40: Lost braces
    40 | \bold{validity: }{numeric; validity value computed with the current parameters}
       |                  ^
checkRd: (-1) StatClusterData.Rd:42: Lost braces
    42 | \bold{EMP_live_work: }{numeric; number of commuters living and working in the area}
       |                       ^
checkRd: (-1) StatClusterData.Rd:44: Lost braces
    44 | \bold{lma_commuter_percent: }{numeric; the quantity: (EMP_live-EMP_live_work)+(EMP_work-EMP_live_work)/(2*EMP_live_work) }
       |                              ^
checkRd: (-1) StatClusterData.Rd:46-48: Lost braces
    46 | \bold{Home_Work_Ratio: }{numeric; the quantity 
       |                         ^
checkRd: (-1) StatClusterData.Rd:50: Lost braces
    50 | \bold{SC_demand_side: }{numeric; demand side self-containment}
       |                        ^
checkRd: (-1) StatClusterData.Rd:52: Lost braces
    52 | \bold{SC_supply_side: }{numeric; supply side self-containment}
       |                        ^
checkRd: (-1) StatClusterData.Rd:54: Lost braces
    54 | \bold{N_com: }{integer; number of communities forming the LMA}
       |               ^
checkRd: (-1) StatClusterData.Rd:56-57: Lost braces
    56 | \bold{InternalCohesionLink: }{numeric; consistency of internal relationships. It is given by the ratio between number of links between communities inside LMA, excluding itself, and the maximum number of possible links, i.e. (N_com * (N_com-1)). See [1].
       |                              ^
checkRd: (-1) StatClusterData.Rd:59-60: Lost braces
    59 | \bold{InternalCohesionFlows: }{numeric; intensity of internal relationships. It is the percentage of internal flows (excluding flows having as origin and destination the same node) of the LMA between different communities w.r.t the total internal flows. See [3].
       |                               ^
checkRd: (-1) StatClusterData.Rd:62-63: Lost braces
    62 | \bold{NbCentralComm: }{integer; number of communities having a centrality index greater than 1 (for communities with more than 100 workers, the centrality index is the ratio between net incoming flows and net outgoing flows).
       |                       ^
checkRd: (-1) StatClusterData.Rd:65: Lost braces
    65 | \bold{N_links_in: }{integer; number of LMAs whose residents work in the current LMA (including itself) } 
       |                    ^
checkRd: (-1) StatClusterData.Rd:67: Lost braces
    67 | \bold{N_links_out: }{integer; number of LMAs where the residents of the current LMA work (including itself)}
       |                     ^
checkRd: (-1) StatClusterData.Rd:74: Lost braces
    74 | \bold{N_links: }{numeric; number of links between LMAs}
       |                 ^
checkRd: (-1) StatClusterData.Rd:76: Lost braces
    76 | \bold{PercNbLinksLessThreshold: }{numeric; percentage of links corresponding to flows below threshold}
       |                                  ^
checkRd: (-1) StatClusterData.Rd:78: Lost braces
    78 | \bold{summFlows: }{numeric vector; summary statistics on flows}
       |                   ^
checkRd: (-1) StatClusterData.Rd:80: Lost braces
    80 | \bold{summFlowsNoItself: }{numeric vector; summary statistics on flows, excluding the self-flows}
       |                           ^
checkRd: (-1) StatClusterData.Rd:82: Lost braces
    82 | \bold{summLinks_in: }{numeric vector; summary statistics on the number of incoming flows}
       |                      ^
checkRd: (-1) StatClusterData.Rd:84: Lost braces
    84 | \bold{summLinks_out: }{summary statistics on the number of outgoing flows}
       |                       ^
checkRd: (-1) StatClusterData.Rd:86: Lost braces
    86 | \bold{clusterMaxNlinks_in: }{positive integer; the LMA ID of the cluster reaching the maximum number of incoming flows}
       |                             ^
checkRd: (-1) StatClusterData.Rd:88: Lost braces
    88 | \bold{clusterMaxNlinks_out: }{positive integer; the LMA ID of the cluster reaching the maximum number of outgoing flows}
       |                              ^
checkRd: (-1) StatClusterData.Rd:90: Lost braces
    90 | \bold{clusterMinNlinks_in: }{positive integer; the LMA ID of the cluster reaching the minimum number of incoming flows}
       |                             ^
checkRd: (-1) StatClusterData.Rd:92: Lost braces
    92 | \bold{clusterMinNlinks_out: }{positive integer; the LMA ID of the cluster reaching the minimum number of outgoing flows}
       |                              ^
checkRd: (-1) StatClusterData.Rd:98: Lost braces
    98 | \bold{NbClusters: }{integer; number of clusters}
       |                    ^
checkRd: (-1) StatClusterData.Rd:100: Lost braces
   100 | \bold{NbClusterUniqueCom: }{integer; number of clusters with an unique community}
       |                            ^
checkRd: (-1) StatClusterData.Rd:102: Lost braces
   102 | \bold{NbClustersValidLess1: }{integer; number of clusters with validity smaller than 1}
       |                              ^
checkRd: (-1) StatClusterData.Rd:104: Lost braces
   104 | \bold{NbClustersNoCentralCom: }{integer; number of clusters with no communities having a centrality measure greater than 1 }
       |                                ^
checkRd: (-1) StatClusterData.Rd:106: Lost braces
   106 | \bold{Mean.SC_demand_side: }{numeric; mean of the demand side self-containment of the clusters in the partition  }
       |                             ^
checkRd: (-1) StatClusterData.Rd:108: Lost braces
   108 | \bold{Std.SC_demand_side: }{numeric; standard deviation of the demand side self-containment }
       |                            ^
checkRd: (-1) StatClusterData.Rd:110: Lost braces
   110 | \bold{Mean.SC_supply_side: }{numeric; mean of the supply side self-containment of the clusters in the partition }
       |                             ^
checkRd: (-1) StatClusterData.Rd:112: Lost braces
   112 | \bold{Std.SC_supply_side: }{numeric; standard deviation of the supply side self-containment   }
       |                            ^
checkRd: (-1) StatClusterData.Rd:114: Lost braces
   114 | \bold{Q1.InternalCohesionFlows: }{numeric; first quartile of the InternalCohesionFlows }
       |                                  ^
checkRd: (-1) StatClusterData.Rd:116: Lost braces
   116 | \bold{Q2.InternalCohesionFlows: }{numeric; median of the InternalCohesionFlows}
       |                                  ^
checkRd: (-1) StatClusterData.Rd:118: Lost braces
   118 | \bold{Q3.InternalCohesionFlows: }{numeric; third quartile of the InternalCohesionFlows }
       |                                  ^
checkRd: (-1) StatClusterData.Rd:120: Lost braces
   120 | \bold{Q1.InternalCohesionLink: }{numeric; first quartile of the InternalCohesionLink }
       |                                 ^
checkRd: (-1) StatClusterData.Rd:122: Lost braces
   122 | \bold{Q2.InternalCohesionLink: }{numeric; median of the InternalCohesionLink}
       |                                 ^
checkRd: (-1) StatClusterData.Rd:124: Lost braces
   124 | \bold{Q3.InternalCohesionLink: }{numeric; third quartile of the InternalCohesionLink }
       |                                 ^
checkRd: (-1) StatClusterData.Rd:126: Lost braces
   126 | \bold{Q1.EMP_live: }{numeric; first quartile of the residents }
       |                     ^
checkRd: (-1) StatClusterData.Rd:128: Lost braces
   128 | \bold{Q2.EMP_live: }{numeric; median of the residents}
       |                     ^
checkRd: (-1) StatClusterData.Rd:130: Lost braces
   130 | \bold{Q3.EMP_live: }{numeric; third quartile of the residents }
       |                     ^
checkRd: (-1) StatClusterData.Rd:132: Lost braces
   132 | \bold{Mean.EMP_live: }{numeric; mean value of the residents }
       |                       ^
checkRd: (-1) StatClusterData.Rd:134: Lost braces
   134 | \bold{Std.EMP_live: }{numeric; standard deviation of the residents }
       |                      ^
checkRd: (-1) StatClusterData.Rd:136: Lost braces
   136 | \bold{Min.EMP_live: }{numeric; minimum value of the residents }
       |                      ^
checkRd: (-1) StatClusterData.Rd:138: Lost braces
   138 | \bold{Max.EMP_live: }{numeric; maximum value of the residents }
       |                      ^
checkRd: (-1) StatClusterData.Rd:140: Lost braces
   140 | \bold{Q1.EMP_work: }{numeric; first quartile of the workers/jobs }
       |                     ^
checkRd: (-1) StatClusterData.Rd:142: Lost braces
   142 | \bold{Q2.EMP_work: }{numeric; median of the workers/jobs}
       |                     ^
checkRd: (-1) StatClusterData.Rd:144: Lost braces
   144 | \bold{Q3.EMP_work: }{numeric; third quartile of the workers/jobs }
       |                     ^
checkRd: (-1) StatClusterData.Rd:146: Lost braces
   146 | \bold{Mean.EMP_work: }{numeric; mean value of the workers }
       |                       ^
checkRd: (-1) StatClusterData.Rd:148: Lost braces
   148 | \bold{Std.EMP_work: }{numeric; standard deviation of the workers }
       |                      ^
checkRd: (-1) StatClusterData.Rd:150: Lost braces
   150 | \bold{Min.EMP_work: }{numeric; minimum value of the workers }
       |                      ^
checkRd: (-1) StatClusterData.Rd:152: Lost braces
   152 | \bold{Max.EMP_work: }{numeric; maximum value of the workers }
       |                      ^
checkRd: (-1) StatClusterData.Rd:154: Lost braces
   154 | \bold{Q1.EMP_live_work: }{numeric; first quartile of the commuters living and working in the same area}
       |                          ^
checkRd: (-1) StatClusterData.Rd:156: Lost braces
   156 | \bold{Q2.EMP_live_work: }{numeric; median of the commuters living and working in the same area}
       |                          ^
checkRd: (-1) StatClusterData.Rd:158: Lost braces
   158 | \bold{Q3.EMP_live_work: }{numeric; third quartile of the the commuters living and working in the same area }
       |                          ^
checkRd: (-1) StatClusterData.Rd:160: Lost braces
   160 | \bold{Min.EMP_live_work: }{numeric; minimum value of the commuters living and working in the same area }
       |                           ^
checkRd: (-1) StatClusterData.Rd:162: Lost braces
   162 | \bold{Max.EMP_live_work: }{numeric; maximum value of the commuters living and working in the same area }
       |                           ^
checkRd: (-1) StatClusterData.Rd:164: Lost braces
   164 | \bold{Mean.lma_commuter_percent: }{numeric; mean value of the quantity: (EMP_live-EMP_live_work)+(EMP_work-EMP_live_work)/(2*EMP_live_work) }
       |                                   ^
checkRd: (-1) StatClusterData.Rd:166: Lost braces
   166 | \bold{Std.lma_commuter_percent: }{numeric; standard deviation of the quantity (EMP_live-EMP_live_work)+(EMP_work-EMP_live_work)/(2*EMP_live_work) }
       |                                  ^
checkRd: (-1) StatClusterData.Rd:168-170: Lost braces
   168 | \bold{Mean.Home_Work_Ratio: }{numeric; mean value of the quantity 
       |                              ^
checkRd: (-1) StatClusterData.Rd:171-173: Lost braces
   171 |  \bold{Std.Home_Work_Ratio: }{numeric; standard deviation of the quantity 
       |                              ^
checkRd: (-1) StatClusterData.Rd:175: Lost braces
   175 | \bold{Q_modularity: }{numeric; Q_modularity index }
       |                      ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  '/tmp/th798/16153372/R-devel/715/LabourMarketAreas.Rcheck/00check.log'
for details.

[1] "2025-03-27 01:09:15 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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

> cargs <- commandArgs(trailingOnly=TRUE)
> if(length(cargs)==0){
+   ## before running interactively, make sure to start emacs/R with
+   ## environment defined in /scratch/...check_one.sh, particularly
+   ## R_LIBS_USER=/tmp/... otherwise we get error when installing
+   ## data.table.
+   base <- "/scratch/th798/data.table-revdeps/*"
+   cargs <- c(
+     Sys.glob(file.path(base,"deps.csv")),
+     "349",
+     Sys.glob(file.path(base, "data.table_release_*tar.gz")),
+     Sys.glob(file.path(base, "data.table_master_*tar.gz"))
+   )
+ }
> names(cargs) <- c("deps.csv", "task.str", "release", "master")
> dput(cargs)
c(deps.csv = "/scratch/th798/data.table-revdeps/2025-03-27/deps.csv", 
task.str = "715", release = "/scratch/th798/data.table-revdeps/2025-03-27/data.table_release_1.17.0.tar.gz", 
master = "/scratch/th798/data.table-revdeps/2025-03-27/data.table_master_1.17.99.2cb03162a21328cc5f68a8c3b0e554f5edfcb5b9.tar.gz"
)
> (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers
[1] "/tmp/th798/16153372/R-release/715"
> if(requireNamespace("R.cache"))R.cache::getCachePath()
Loading required namespace: R.cache
[1] "/tmp/th798/16153372/R-release/715/R.cache"
> task.id <- as.integer(cargs[["task.str"]])
> deps.df <- read.csv(cargs[["deps.csv"]])
> (rev.dep <- deps.df$Package[task.id])
[1] "LabourMarketAreas"
> job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id)
> setwd(task.dir)
> .libPaths()
[1] "/tmp/th798/16153372/R-release/715/library"
[2] "/projects/genomic-ml/R/R-release/library" 
> options(repos=c(#this should be in ~/.Rprofile too.
+   CRAN="http://cloud.r-project.org"))
> print(Sys.time())
[1] "2025-03-27 01:09:22 MST"
> install.time <- system.time({
+   install.packages(rev.dep, dep=TRUE)
+ })
Installing package into '/tmp/th798/16153372/R-release/715/library'
(as 'lib' is unspecified)
also installing the dependencies 'geometries', 'sfheaders', 'spacesXYZ', 'geojsonsf', 'jsonify', 'xfun', 'cols4all', 'leafem', 'leafgl', 'leaflegend', 'leafsync', 'tmaptools', 'servr', 'tmap'

trying URL 'http://cloud.r-project.org/src/contrib/geometries_0.2.4.tar.gz'
Content type 'application/x-gzip' length 53848 bytes (52 KB)
==================================================
downloaded 52 KB

trying URL 'http://cloud.r-project.org/src/contrib/sfheaders_0.4.4.tar.gz'
Content type 'application/x-gzip' length 84537 bytes (82 KB)
==================================================
downloaded 82 KB

trying URL 'http://cloud.r-project.org/src/contrib/spacesXYZ_1.5-1.tar.gz'
Content type 'application/x-gzip' length 310439 bytes (303 KB)
==================================================
downloaded 303 KB

trying URL 'http://cloud.r-project.org/src/contrib/geojsonsf_2.0.3.tar.gz'
Content type 'application/x-gzip' length 1483733 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'http://cloud.r-project.org/src/contrib/jsonify_1.2.2.tar.gz'
Content type 'application/x-gzip' length 471503 bytes (460 KB)
==================================================
downloaded 460 KB

trying URL 'http://cloud.r-project.org/src/contrib/xfun_0.51.tar.gz'
Content type 'application/x-gzip' length 175799 bytes (171 KB)
==================================================
downloaded 171 KB

trying URL 'http://cloud.r-project.org/src/contrib/cols4all_0.8.tar.gz'
Content type 'application/x-gzip' length 2333510 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

trying URL 'http://cloud.r-project.org/src/contrib/leafem_0.2.3.tar.gz'
Content type 'application/x-gzip' length 3435710 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

trying URL 'http://cloud.r-project.org/src/contrib/leafgl_0.2.2.tar.gz'
Content type 'application/x-gzip' length 1709933 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'http://cloud.r-project.org/src/contrib/leaflegend_1.2.1.tar.gz'
Content type 'application/x-gzip' length 1376125 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'http://cloud.r-project.org/src/contrib/leafsync_0.1.0.tar.gz'
Content type 'application/x-gzip' length 833532 bytes (813 KB)
==================================================
downloaded 813 KB

trying URL 'http://cloud.r-project.org/src/contrib/tmaptools_3.2.tar.gz'
Content type 'application/x-gzip' length 39300 bytes (38 KB)
==================================================
downloaded 38 KB

trying URL 'http://cloud.r-project.org/src/contrib/servr_0.32.tar.gz'
Content type 'application/x-gzip' length 25384 bytes (24 KB)
==================================================
downloaded 24 KB

trying URL 'http://cloud.r-project.org/src/contrib/tmap_4.0.tar.gz'
Content type 'application/x-gzip' length 1900038 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'http://cloud.r-project.org/src/contrib/LabourMarketAreas_3.4.tar.gz'
Content type 'application/x-gzip' length 1193301 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

* installing *source* package 'geometries' ...
** package 'geometries' 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 -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c bbox.cpp -o bbox.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c close.cpp -o close.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c columns.cpp -o columns.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c coordinates.cpp -o coordinates.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c geometries.cpp -o geometries.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c lines.cpp -o lines.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c lists.cpp -o lists.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c nest.cpp -o nest.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c shapes.cpp -o shapes.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c tests.cpp -o tests.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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.cpp -o utils.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 geometries.so RcppExports.o bbox.o close.o columns.o coordinates.o geometries.o lines.o lists.o nest.o shapes.o tests.o utils.o
installing to /tmp/th798/16153372/R-release/715/library/00LOCK-geometries/00new/geometries/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 (geometries)
* installing *source* package 'spacesXYZ' ...
** package 'spacesXYZ' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (spacesXYZ)
* installing *source* package 'jsonify' ...
** package 'jsonify' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
using C++11
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c from_json.cpp -o from_json.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c pretty.cpp -o pretty.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c read_json.cpp -o read_json.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c tests.cpp -o tests.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c to_json.cpp -o to_json.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/projects/genomic-ml/R/R-release/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c validate.cpp -o validate.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o jsonify.so RcppExports.o from_json.o pretty.o read_json.o tests.o to_json.o validate.o
installing to /tmp/th798/16153372/R-release/715/library/00LOCK-jsonify/00new/jsonify/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 (jsonify)
* installing *source* package 'xfun' ...
** package 'xfun' 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 base64.c -o base64.o
/packages/gcc/12.2.0-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 -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 xfun.so base64.o init.o
installing to /tmp/th798/16153372/R-release/715/library/00LOCK-xfun/00new/xfun/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 (xfun)
* installing *source* package 'leaflegend' ...
** package 'leaflegend' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** 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 (leaflegend)
* installing *source* package 'leafsync' ...
** package 'leafsync' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** 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 (leafsync)
* installing *source* package 'tmaptools' ...
** package 'tmaptools' 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 (tmaptools)
* installing *source* package 'sfheaders' ...
** package 'sfheaders' 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 -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c bbox.cpp -o bbox.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c cast.cpp -o cast.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c lists.cpp -o lists.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c sfg_dimension.cpp -o sfg_dimension.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c shapes.cpp -o shapes.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c to_df.cpp -o to_df.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c to_sf.cpp -o to_sf.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c to_sfc.cpp -o to_sfc.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c to_sfg.cpp -o to_sfg.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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.cpp -o utils.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 sfheaders.so RcppExports.o bbox.o cast.o lists.o sfg_dimension.o shapes.o to_df.o to_sf.o to_sfc.o to_sfg.o utils.o
installing to /tmp/th798/16153372/R-release/715/library/00LOCK-sfheaders/00new/sfheaders/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** 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 (sfheaders)
* installing *source* package 'cols4all' ...
** package 'cols4all' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cols4all)
* installing *source* package 'servr' ...
** package 'servr' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (servr)
* installing *source* package 'geojsonsf' ...
** package 'geojsonsf' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
using C++11
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/tmp/th798/16153372/R-release/715/library/jsonify/include' -I'/projects/genomic-ml/R/R-release/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/tmp/th798/16153372/R-release/715/library/sfheaders/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/tmp/th798/16153372/R-release/715/library/jsonify/include' -I'/projects/genomic-ml/R/R-release/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/tmp/th798/16153372/R-release/715/library/sfheaders/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c df_geojson.cpp -o df_geojson.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/tmp/th798/16153372/R-release/715/library/jsonify/include' -I'/projects/genomic-ml/R/R-release/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/tmp/th798/16153372/R-release/715/library/sfheaders/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c geojson_to_sf.cpp -o geojson_to_sf.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/tmp/th798/16153372/R-release/715/library/jsonify/include' -I'/projects/genomic-ml/R/R-release/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/tmp/th798/16153372/R-release/715/library/sfheaders/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c geojson_to_wkt.cpp -o geojson_to_wkt.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/tmp/th798/16153372/R-release/715/library/jsonify/include' -I'/projects/genomic-ml/R/R-release/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/tmp/th798/16153372/R-release/715/library/sfheaders/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c geojson_wkt.cpp -o geojson_wkt.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/tmp/th798/16153372/R-release/715/library/jsonify/include' -I'/projects/genomic-ml/R/R-release/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/tmp/th798/16153372/R-release/715/library/sfheaders/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c read_geojson.cpp -o read_geojson.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -I"/home/th798/R/R-release/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/tmp/th798/16153372/R-release/715/library/geometries/include' -I'/tmp/th798/16153372/R-release/715/library/jsonify/include' -I'/projects/genomic-ml/R/R-release/library/rapidjsonr/include' -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/tmp/th798/16153372/R-release/715/library/sfheaders/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -I../inst/include/ -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c sf_geojson.cpp -o sf_geojson.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++11 -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o geojsonsf.so RcppExports.o df_geojson.o geojson_to_sf.o geojson_to_wkt.o geojson_wkt.o read_geojson.o sf_geojson.o
installing to /tmp/th798/16153372/R-release/715/library/00LOCK-geojsonsf/00new/geojsonsf/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 (geojsonsf)
* installing *source* package 'leafem' ...
** package 'leafem' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** 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 (leafem)
* installing *source* package 'leafgl' ...
** package 'leafgl' successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** 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 (leafgl)
* installing *source* package 'tmap' ...
** package 'tmap' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (tmap)
* installing *source* package 'LabourMarketAreas' ...
** package 'LabourMarketAreas' successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (LabourMarketAreas)

The downloaded source packages are in
	'/tmp/th798/16153372/RtmpprqJeZ/downloaded_packages'
> cat("Time to install revdep:\n")
Time to install revdep:
> print(install.time)
   user  system elapsed 
243.271  27.767 333.980 
> print(Sys.time())
[1] "2025-03-27 01:14:56 MST"
> downloaded_packages <- file.path(
+   tempdir(),
+   "downloaded_packages")
> dl.glob <- file.path(
+   downloaded_packages,
+   paste0(rev.dep,"_*.tar.gz"))
> rev.dep.dl.row <- cbind(rev.dep, Sys.glob(dl.glob))
> colnames(rev.dep.dl.row) <- c("pkg","path")
> rev.dep.release.tar.gz <- normalizePath(rev.dep.dl.row[,"path"], mustWork=TRUE)
> pkg.Rcheck <- paste0(rev.dep, ".Rcheck")
> 
> proj.dir <- "~/genomic-ml/data.table-revdeps"
> source(file.path(proj.dir, "myStatus.R"))
> Rvers <- gsub("[()]", "", gsub(" ", "_", R.version[["version.string"]]))
> dir.create(Rvers, showWarnings=FALSE)
> Rcheck.list <- list()
> for(dt.version.short in c("release", "master")){
+   dt.tar.gz <- cargs[[dt.version.short]]
+   dt.version <- gsub(".tar.gz|/.*?_", "", dt.tar.gz)
+   print(Sys.time())
+   install.packages(dt.tar.gz, repos=NULL)
+   print(Sys.time())
+   check.cmd <- get_check_cmd(rev.dep.release.tar.gz)
+   system(check.cmd)
+   print(Sys.time())
+   dest.Rcheck <- file.path(
+     Rvers,
+     paste0(dt.version, ".Rcheck"))
+   unlink(dest.Rcheck, recursive=TRUE)
+   file.rename(pkg.Rcheck, dest.Rcheck)
+   Rcheck.list[[dt.version]] <- file.path(dest.Rcheck, "00check.log")
+ }
[1] "2025-03-27 01:14:56 MST"
Installing package into '/tmp/th798/16153372/R-release/715/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** package 'data.table' successfully unpacked and MD5 sums checked
** using staged installation
zlib 1.2.13 is available ok
* checking if R installation supports OpenMP without any extra hints... yes
** libs
using C compiler: 'gcc (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c assign.c -o assign.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c between.c -o between.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c bmerge.c -o bmerge.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c chmatch.c -o chmatch.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c cj.c -o cj.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c coalesce.c -o coalesce.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c dogroups.c -o dogroups.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fastmean.c -o fastmean.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fcast.c -o fcast.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fifelse.c -o fifelse.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fmelt.c -o fmelt.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c forder.c -o forder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frank.c -o frank.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fread.c -o fread.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c freadR.c -o freadR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c froll.c -o froll.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frollR.c -o frollR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frolladaptive.c -o frolladaptive.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fsort.c -o fsort.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwrite.c -o fwrite.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwriteR.c -o fwriteR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c gsumm.c -o gsumm.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c idatetime.c -o idatetime.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ijoin.c -o ijoin.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c init.c -o init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c inrange.c -o inrange.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nafill.c -o nafill.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c negate.c -o negate.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nqrecreateindices.c -o nqrecreateindices.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c openmp-utils.c -o openmp-utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c programming.c -o programming.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c quickselect.c -o quickselect.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c rbindlist.c -o rbindlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c reorder.c -o reorder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c shift.c -o shift.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c snprintf.c -o snprintf.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c subset.c -o subset.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c transpose.c -o transpose.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c types.c -o types.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c uniqlist.c -o uniqlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c utils.c -o utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c vecseq.c -o vecseq.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c wrappers.c -o wrappers.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include
PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi
installing to /tmp/th798/16153372/R-release/715/library/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (data.table)
[1] "2025-03-27 01:15:18 MST"
* using log directory '/tmp/th798/16153372/R-release/715/LabourMarketAreas.Rcheck'
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Spack GCC) 12.2.0
    GNU Fortran (Spack GCC) 12.2.0
* running under: Red Hat Enterprise Linux 8.10 (Ootpa)
* using session charset: ASCII
* checking for file 'LabourMarketAreas/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LabourMarketAreas' version '3.4'
* 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 'LabourMarketAreas' 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 ... NOTE
checkRd: (-1) StatClusterData.Rd:34: Lost braces
    34 | \bold{LMA: }{ positive integer; labour market areas ID} 
       |             ^
checkRd: (-1) StatClusterData.Rd:36: Lost braces
    36 | \bold{EMP_live: }{numeric; number of commuters who live in the area} 
       |                  ^
checkRd: (-1) StatClusterData.Rd:38: Lost braces
    38 | \bold{EMP_work: }{numeric; number of commuters working in the area}
       |                  ^
checkRd: (-1) StatClusterData.Rd:40: Lost braces
    40 | \bold{validity: }{numeric; validity value computed with the current parameters}
       |                  ^
checkRd: (-1) StatClusterData.Rd:42: Lost braces
    42 | \bold{EMP_live_work: }{numeric; number of commuters living and working in the area}
       |                       ^
checkRd: (-1) StatClusterData.Rd:44: Lost braces
    44 | \bold{lma_commuter_percent: }{numeric; the quantity: (EMP_live-EMP_live_work)+(EMP_work-EMP_live_work)/(2*EMP_live_work) }
       |                              ^
checkRd: (-1) StatClusterData.Rd:46-48: Lost braces
    46 | \bold{Home_Work_Ratio: }{numeric; the quantity 
       |                         ^
checkRd: (-1) StatClusterData.Rd:50: Lost braces
    50 | \bold{SC_demand_side: }{numeric; demand side self-containment}
       |                        ^
checkRd: (-1) StatClusterData.Rd:52: Lost braces
    52 | \bold{SC_supply_side: }{numeric; supply side self-containment}
       |                        ^
checkRd: (-1) StatClusterData.Rd:54: Lost braces
    54 | \bold{N_com: }{integer; number of communities forming the LMA}
       |               ^
checkRd: (-1) StatClusterData.Rd:56-57: Lost braces
    56 | \bold{InternalCohesionLink: }{numeric; consistency of internal relationships. It is given by the ratio between number of links between communities inside LMA, excluding itself, and the maximum number of possible links, i.e. (N_com * (N_com-1)). See [1].
       |                              ^
checkRd: (-1) StatClusterData.Rd:59-60: Lost braces
    59 | \bold{InternalCohesionFlows: }{numeric; intensity of internal relationships. It is the percentage of internal flows (excluding flows having as origin and destination the same node) of the LMA between different communities w.r.t the total internal flows. See [3].
       |                               ^
checkRd: (-1) StatClusterData.Rd:62-63: Lost braces
    62 | \bold{NbCentralComm: }{integer; number of communities having a centrality index greater than 1 (for communities with more than 100 workers, the centrality index is the ratio between net incoming flows and net outgoing flows).
       |                       ^
checkRd: (-1) StatClusterData.Rd:65: Lost braces
    65 | \bold{N_links_in: }{integer; number of LMAs whose residents work in the current LMA (including itself) } 
       |                    ^
checkRd: (-1) StatClusterData.Rd:67: Lost braces
    67 | \bold{N_links_out: }{integer; number of LMAs where the residents of the current LMA work (including itself)}
       |                     ^
checkRd: (-1) StatClusterData.Rd:74: Lost braces
    74 | \bold{N_links: }{numeric; number of links between LMAs}
       |                 ^
checkRd: (-1) StatClusterData.Rd:76: Lost braces
    76 | \bold{PercNbLinksLessThreshold: }{numeric; percentage of links corresponding to flows below threshold}
       |                                  ^
checkRd: (-1) StatClusterData.Rd:78: Lost braces
    78 | \bold{summFlows: }{numeric vector; summary statistics on flows}
       |                   ^
checkRd: (-1) StatClusterData.Rd:80: Lost braces
    80 | \bold{summFlowsNoItself: }{numeric vector; summary statistics on flows, excluding the self-flows}
       |                           ^
checkRd: (-1) StatClusterData.Rd:82: Lost braces
    82 | \bold{summLinks_in: }{numeric vector; summary statistics on the number of incoming flows}
       |                      ^
checkRd: (-1) StatClusterData.Rd:84: Lost braces
    84 | \bold{summLinks_out: }{summary statistics on the number of outgoing flows}
       |                       ^
checkRd: (-1) StatClusterData.Rd:86: Lost braces
    86 | \bold{clusterMaxNlinks_in: }{positive integer; the LMA ID of the cluster reaching the maximum number of incoming flows}
       |                             ^
checkRd: (-1) StatClusterData.Rd:88: Lost braces
    88 | \bold{clusterMaxNlinks_out: }{positive integer; the LMA ID of the cluster reaching the maximum number of outgoing flows}
       |                              ^
checkRd: (-1) StatClusterData.Rd:90: Lost braces
    90 | \bold{clusterMinNlinks_in: }{positive integer; the LMA ID of the cluster reaching the minimum number of incoming flows}
       |                             ^
checkRd: (-1) StatClusterData.Rd:92: Lost braces
    92 | \bold{clusterMinNlinks_out: }{positive integer; the LMA ID of the cluster reaching the minimum number of outgoing flows}
       |                              ^
checkRd: (-1) StatClusterData.Rd:98: Lost braces
    98 | \bold{NbClusters: }{integer; number of clusters}
       |                    ^
checkRd: (-1) StatClusterData.Rd:100: Lost braces
   100 | \bold{NbClusterUniqueCom: }{integer; number of clusters with an unique community}
       |                            ^
checkRd: (-1) StatClusterData.Rd:102: Lost braces
   102 | \bold{NbClustersValidLess1: }{integer; number of clusters with validity smaller than 1}
       |                              ^
checkRd: (-1) StatClusterData.Rd:104: Lost braces
   104 | \bold{NbClustersNoCentralCom: }{integer; number of clusters with no communities having a centrality measure greater than 1 }
       |                                ^
checkRd: (-1) StatClusterData.Rd:106: Lost braces
   106 | \bold{Mean.SC_demand_side: }{numeric; mean of the demand side self-containment of the clusters in the partition  }
       |                             ^
checkRd: (-1) StatClusterData.Rd:108: Lost braces
   108 | \bold{Std.SC_demand_side: }{numeric; standard deviation of the demand side self-containment }
       |                            ^
checkRd: (-1) StatClusterData.Rd:110: Lost braces
   110 | \bold{Mean.SC_supply_side: }{numeric; mean of the supply side self-containment of the clusters in the partition }
       |                             ^
checkRd: (-1) StatClusterData.Rd:112: Lost braces
   112 | \bold{Std.SC_supply_side: }{numeric; standard deviation of the supply side self-containment   }
       |                            ^
checkRd: (-1) StatClusterData.Rd:114: Lost braces
   114 | \bold{Q1.InternalCohesionFlows: }{numeric; first quartile of the InternalCohesionFlows }
       |                                  ^
checkRd: (-1) StatClusterData.Rd:116: Lost braces
   116 | \bold{Q2.InternalCohesionFlows: }{numeric; median of the InternalCohesionFlows}
       |                                  ^
checkRd: (-1) StatClusterData.Rd:118: Lost braces
   118 | \bold{Q3.InternalCohesionFlows: }{numeric; third quartile of the InternalCohesionFlows }
       |                                  ^
checkRd: (-1) StatClusterData.Rd:120: Lost braces
   120 | \bold{Q1.InternalCohesionLink: }{numeric; first quartile of the InternalCohesionLink }
       |                                 ^
checkRd: (-1) StatClusterData.Rd:122: Lost braces
   122 | \bold{Q2.InternalCohesionLink: }{numeric; median of the InternalCohesionLink}
       |                                 ^
checkRd: (-1) StatClusterData.Rd:124: Lost braces
   124 | \bold{Q3.InternalCohesionLink: }{numeric; third quartile of the InternalCohesionLink }
       |                                 ^
checkRd: (-1) StatClusterData.Rd:126: Lost braces
   126 | \bold{Q1.EMP_live: }{numeric; first quartile of the residents }
       |                     ^
checkRd: (-1) StatClusterData.Rd:128: Lost braces
   128 | \bold{Q2.EMP_live: }{numeric; median of the residents}
       |                     ^
checkRd: (-1) StatClusterData.Rd:130: Lost braces
   130 | \bold{Q3.EMP_live: }{numeric; third quartile of the residents }
       |                     ^
checkRd: (-1) StatClusterData.Rd:132: Lost braces
   132 | \bold{Mean.EMP_live: }{numeric; mean value of the residents }
       |                       ^
checkRd: (-1) StatClusterData.Rd:134: Lost braces
   134 | \bold{Std.EMP_live: }{numeric; standard deviation of the residents }
       |                      ^
checkRd: (-1) StatClusterData.Rd:136: Lost braces
   136 | \bold{Min.EMP_live: }{numeric; minimum value of the residents }
       |                      ^
checkRd: (-1) StatClusterData.Rd:138: Lost braces
   138 | \bold{Max.EMP_live: }{numeric; maximum value of the residents }
       |                      ^
checkRd: (-1) StatClusterData.Rd:140: Lost braces
   140 | \bold{Q1.EMP_work: }{numeric; first quartile of the workers/jobs }
       |                     ^
checkRd: (-1) StatClusterData.Rd:142: Lost braces
   142 | \bold{Q2.EMP_work: }{numeric; median of the workers/jobs}
       |                     ^
checkRd: (-1) StatClusterData.Rd:144: Lost braces
   144 | \bold{Q3.EMP_work: }{numeric; third quartile of the workers/jobs }
       |                     ^
checkRd: (-1) StatClusterData.Rd:146: Lost braces
   146 | \bold{Mean.EMP_work: }{numeric; mean value of the workers }
       |                       ^
checkRd: (-1) StatClusterData.Rd:148: Lost braces
   148 | \bold{Std.EMP_work: }{numeric; standard deviation of the workers }
       |                      ^
checkRd: (-1) StatClusterData.Rd:150: Lost braces
   150 | \bold{Min.EMP_work: }{numeric; minimum value of the workers }
       |                      ^
checkRd: (-1) StatClusterData.Rd:152: Lost braces
   152 | \bold{Max.EMP_work: }{numeric; maximum value of the workers }
       |                      ^
checkRd: (-1) StatClusterData.Rd:154: Lost braces
   154 | \bold{Q1.EMP_live_work: }{numeric; first quartile of the commuters living and working in the same area}
       |                          ^
checkRd: (-1) StatClusterData.Rd:156: Lost braces
   156 | \bold{Q2.EMP_live_work: }{numeric; median of the commuters living and working in the same area}
       |                          ^
checkRd: (-1) StatClusterData.Rd:158: Lost braces
   158 | \bold{Q3.EMP_live_work: }{numeric; third quartile of the the commuters living and working in the same area }
       |                          ^
checkRd: (-1) StatClusterData.Rd:160: Lost braces
   160 | \bold{Min.EMP_live_work: }{numeric; minimum value of the commuters living and working in the same area }
       |                           ^
checkRd: (-1) StatClusterData.Rd:162: Lost braces
   162 | \bold{Max.EMP_live_work: }{numeric; maximum value of the commuters living and working in the same area }
       |                           ^
checkRd: (-1) StatClusterData.Rd:164: Lost braces
   164 | \bold{Mean.lma_commuter_percent: }{numeric; mean value of the quantity: (EMP_live-EMP_live_work)+(EMP_work-EMP_live_work)/(2*EMP_live_work) }
       |                                   ^
checkRd: (-1) StatClusterData.Rd:166: Lost braces
   166 | \bold{Std.lma_commuter_percent: }{numeric; standard deviation of the quantity (EMP_live-EMP_live_work)+(EMP_work-EMP_live_work)/(2*EMP_live_work) }
       |                                  ^
checkRd: (-1) StatClusterData.Rd:168-170: Lost braces
   168 | \bold{Mean.Home_Work_Ratio: }{numeric; mean value of the quantity 
       |                              ^
checkRd: (-1) StatClusterData.Rd:171-173: Lost braces
   171 |  \bold{Std.Home_Work_Ratio: }{numeric; standard deviation of the quantity 
       |                              ^
checkRd: (-1) StatClusterData.Rd:175: Lost braces
   175 | \bold{Q_modularity: }{numeric; Q_modularity index }
       |                      ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  '/tmp/th798/16153372/R-release/715/LabourMarketAreas.Rcheck/00check.log'
for details.

[1] "2025-03-27 01:20:13 MST"
[1] "2025-03-27 01:20:13 MST"
Installing package into '/tmp/th798/16153372/R-release/715/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** using staged installation
zlib 1.2.13 is available ok
* checking if R installation supports OpenMP without any extra hints... yes
** libs
using C compiler: 'gcc (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c assign.c -o assign.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c between.c -o between.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c bmerge.c -o bmerge.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c chmatch.c -o chmatch.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c cj.c -o cj.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c coalesce.c -o coalesce.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c dogroups.c -o dogroups.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fastmean.c -o fastmean.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fcast.c -o fcast.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fifelse.c -o fifelse.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fmelt.c -o fmelt.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c forder.c -o forder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frank.c -o frank.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fread.c -o fread.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c freadR.c -o freadR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c froll.c -o froll.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frollR.c -o frollR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frolladaptive.c -o frolladaptive.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fsort.c -o fsort.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwrite.c -o fwrite.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwriteR.c -o fwriteR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c gsumm.c -o gsumm.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c idatetime.c -o idatetime.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ijoin.c -o ijoin.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c init.c -o init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c inrange.c -o inrange.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nafill.c -o nafill.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c negate.c -o negate.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nqrecreateindices.c -o nqrecreateindices.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c openmp-utils.c -o openmp-utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c programming.c -o programming.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c quickselect.c -o quickselect.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c rbindlist.c -o rbindlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c reorder.c -o reorder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c shift.c -o shift.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c snprintf.c -o snprintf.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c subset.c -o subset.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c transpose.c -o transpose.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c types.c -o types.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c uniqlist.c -o uniqlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c utils.c -o utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c vecseq.c -o vecseq.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c wrappers.c -o wrappers.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include
PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi
installing to /tmp/th798/16153372/R-release/715/library/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (data.table)
[1] "2025-03-27 01:20:35 MST"
* using log directory '/tmp/th798/16153372/R-release/715/LabourMarketAreas.Rcheck'
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Spack GCC) 12.2.0
    GNU Fortran (Spack GCC) 12.2.0
* running under: Red Hat Enterprise Linux 8.10 (Ootpa)
* using session charset: ASCII
* checking for file 'LabourMarketAreas/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'LabourMarketAreas' version '3.4'
* 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 'LabourMarketAreas' 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 ... NOTE
checkRd: (-1) StatClusterData.Rd:34: Lost braces
    34 | \bold{LMA: }{ positive integer; labour market areas ID} 
       |             ^
checkRd: (-1) StatClusterData.Rd:36: Lost braces
    36 | \bold{EMP_live: }{numeric; number of commuters who live in the area} 
       |                  ^
checkRd: (-1) StatClusterData.Rd:38: Lost braces
    38 | \bold{EMP_work: }{numeric; number of commuters working in the area}
       |                  ^
checkRd: (-1) StatClusterData.Rd:40: Lost braces
    40 | \bold{validity: }{numeric; validity value computed with the current parameters}
       |                  ^
checkRd: (-1) StatClusterData.Rd:42: Lost braces
    42 | \bold{EMP_live_work: }{numeric; number of commuters living and working in the area}
       |                       ^
checkRd: (-1) StatClusterData.Rd:44: Lost braces
    44 | \bold{lma_commuter_percent: }{numeric; the quantity: (EMP_live-EMP_live_work)+(EMP_work-EMP_live_work)/(2*EMP_live_work) }
       |                              ^
checkRd: (-1) StatClusterData.Rd:46-48: Lost braces
    46 | \bold{Home_Work_Ratio: }{numeric; the quantity 
       |                         ^
checkRd: (-1) StatClusterData.Rd:50: Lost braces
    50 | \bold{SC_demand_side: }{numeric; demand side self-containment}
       |                        ^
checkRd: (-1) StatClusterData.Rd:52: Lost braces
    52 | \bold{SC_supply_side: }{numeric; supply side self-containment}
       |                        ^
checkRd: (-1) StatClusterData.Rd:54: Lost braces
    54 | \bold{N_com: }{integer; number of communities forming the LMA}
       |               ^
checkRd: (-1) StatClusterData.Rd:56-57: Lost braces
    56 | \bold{InternalCohesionLink: }{numeric; consistency of internal relationships. It is given by the ratio between number of links between communities inside LMA, excluding itself, and the maximum number of possible links, i.e. (N_com * (N_com-1)). See [1].
       |                              ^
checkRd: (-1) StatClusterData.Rd:59-60: Lost braces
    59 | \bold{InternalCohesionFlows: }{numeric; intensity of internal relationships. It is the percentage of internal flows (excluding flows having as origin and destination the same node) of the LMA between different communities w.r.t the total internal flows. See [3].
       |                               ^
checkRd: (-1) StatClusterData.Rd:62-63: Lost braces
    62 | \bold{NbCentralComm: }{integer; number of communities having a centrality index greater than 1 (for communities with more than 100 workers, the centrality index is the ratio between net incoming flows and net outgoing flows).
       |                       ^
checkRd: (-1) StatClusterData.Rd:65: Lost braces
    65 | \bold{N_links_in: }{integer; number of LMAs whose residents work in the current LMA (including itself) } 
       |                    ^
checkRd: (-1) StatClusterData.Rd:67: Lost braces
    67 | \bold{N_links_out: }{integer; number of LMAs where the residents of the current LMA work (including itself)}
       |                     ^
checkRd: (-1) StatClusterData.Rd:74: Lost braces
    74 | \bold{N_links: }{numeric; number of links between LMAs}
       |                 ^
checkRd: (-1) StatClusterData.Rd:76: Lost braces
    76 | \bold{PercNbLinksLessThreshold: }{numeric; percentage of links corresponding to flows below threshold}
       |                                  ^
checkRd: (-1) StatClusterData.Rd:78: Lost braces
    78 | \bold{summFlows: }{numeric vector; summary statistics on flows}
       |                   ^
checkRd: (-1) StatClusterData.Rd:80: Lost braces
    80 | \bold{summFlowsNoItself: }{numeric vector; summary statistics on flows, excluding the self-flows}
       |                           ^
checkRd: (-1) StatClusterData.Rd:82: Lost braces
    82 | \bold{summLinks_in: }{numeric vector; summary statistics on the number of incoming flows}
       |                      ^
checkRd: (-1) StatClusterData.Rd:84: Lost braces
    84 | \bold{summLinks_out: }{summary statistics on the number of outgoing flows}
       |                       ^
checkRd: (-1) StatClusterData.Rd:86: Lost braces
    86 | \bold{clusterMaxNlinks_in: }{positive integer; the LMA ID of the cluster reaching the maximum number of incoming flows}
       |                             ^
checkRd: (-1) StatClusterData.Rd:88: Lost braces
    88 | \bold{clusterMaxNlinks_out: }{positive integer; the LMA ID of the cluster reaching the maximum number of outgoing flows}
       |                              ^
checkRd: (-1) StatClusterData.Rd:90: Lost braces
    90 | \bold{clusterMinNlinks_in: }{positive integer; the LMA ID of the cluster reaching the minimum number of incoming flows}
       |                             ^
checkRd: (-1) StatClusterData.Rd:92: Lost braces
    92 | \bold{clusterMinNlinks_out: }{positive integer; the LMA ID of the cluster reaching the minimum number of outgoing flows}
       |                              ^
checkRd: (-1) StatClusterData.Rd:98: Lost braces
    98 | \bold{NbClusters: }{integer; number of clusters}
       |                    ^
checkRd: (-1) StatClusterData.Rd:100: Lost braces
   100 | \bold{NbClusterUniqueCom: }{integer; number of clusters with an unique community}
       |                            ^
checkRd: (-1) StatClusterData.Rd:102: Lost braces
   102 | \bold{NbClustersValidLess1: }{integer; number of clusters with validity smaller than 1}
       |                              ^
checkRd: (-1) StatClusterData.Rd:104: Lost braces
   104 | \bold{NbClustersNoCentralCom: }{integer; number of clusters with no communities having a centrality measure greater than 1 }
       |                                ^
checkRd: (-1) StatClusterData.Rd:106: Lost braces
   106 | \bold{Mean.SC_demand_side: }{numeric; mean of the demand side self-containment of the clusters in the partition  }
       |                             ^
checkRd: (-1) StatClusterData.Rd:108: Lost braces
   108 | \bold{Std.SC_demand_side: }{numeric; standard deviation of the demand side self-containment }
       |                            ^
checkRd: (-1) StatClusterData.Rd:110: Lost braces
   110 | \bold{Mean.SC_supply_side: }{numeric; mean of the supply side self-containment of the clusters in the partition }
       |                             ^
checkRd: (-1) StatClusterData.Rd:112: Lost braces
   112 | \bold{Std.SC_supply_side: }{numeric; standard deviation of the supply side self-containment   }
       |                            ^
checkRd: (-1) StatClusterData.Rd:114: Lost braces
   114 | \bold{Q1.InternalCohesionFlows: }{numeric; first quartile of the InternalCohesionFlows }
       |                                  ^
checkRd: (-1) StatClusterData.Rd:116: Lost braces
   116 | \bold{Q2.InternalCohesionFlows: }{numeric; median of the InternalCohesionFlows}
       |                                  ^
checkRd: (-1) StatClusterData.Rd:118: Lost braces
   118 | \bold{Q3.InternalCohesionFlows: }{numeric; third quartile of the InternalCohesionFlows }
       |                                  ^
checkRd: (-1) StatClusterData.Rd:120: Lost braces
   120 | \bold{Q1.InternalCohesionLink: }{numeric; first quartile of the InternalCohesionLink }
       |                                 ^
checkRd: (-1) StatClusterData.Rd:122: Lost braces
   122 | \bold{Q2.InternalCohesionLink: }{numeric; median of the InternalCohesionLink}
       |                                 ^
checkRd: (-1) StatClusterData.Rd:124: Lost braces
   124 | \bold{Q3.InternalCohesionLink: }{numeric; third quartile of the InternalCohesionLink }
       |                                 ^
checkRd: (-1) StatClusterData.Rd:126: Lost braces
   126 | \bold{Q1.EMP_live: }{numeric; first quartile of the residents }
       |                     ^
checkRd: (-1) StatClusterData.Rd:128: Lost braces
   128 | \bold{Q2.EMP_live: }{numeric; median of the residents}
       |                     ^
checkRd: (-1) StatClusterData.Rd:130: Lost braces
   130 | \bold{Q3.EMP_live: }{numeric; third quartile of the residents }
       |                     ^
checkRd: (-1) StatClusterData.Rd:132: Lost braces
   132 | \bold{Mean.EMP_live: }{numeric; mean value of the residents }
       |                       ^
checkRd: (-1) StatClusterData.Rd:134: Lost braces
   134 | \bold{Std.EMP_live: }{numeric; standard deviation of the residents }
       |                      ^
checkRd: (-1) StatClusterData.Rd:136: Lost braces
   136 | \bold{Min.EMP_live: }{numeric; minimum value of the residents }
       |                      ^
checkRd: (-1) StatClusterData.Rd:138: Lost braces
   138 | \bold{Max.EMP_live: }{numeric; maximum value of the residents }
       |                      ^
checkRd: (-1) StatClusterData.Rd:140: Lost braces
   140 | \bold{Q1.EMP_work: }{numeric; first quartile of the workers/jobs }
       |                     ^
checkRd: (-1) StatClusterData.Rd:142: Lost braces
   142 | \bold{Q2.EMP_work: }{numeric; median of the workers/jobs}
       |                     ^
checkRd: (-1) StatClusterData.Rd:144: Lost braces
   144 | \bold{Q3.EMP_work: }{numeric; third quartile of the workers/jobs }
       |                     ^
checkRd: (-1) StatClusterData.Rd:146: Lost braces
   146 | \bold{Mean.EMP_work: }{numeric; mean value of the workers }
       |                       ^
checkRd: (-1) StatClusterData.Rd:148: Lost braces
   148 | \bold{Std.EMP_work: }{numeric; standard deviation of the workers }
       |                      ^
checkRd: (-1) StatClusterData.Rd:150: Lost braces
   150 | \bold{Min.EMP_work: }{numeric; minimum value of the workers }
       |                      ^
checkRd: (-1) StatClusterData.Rd:152: Lost braces
   152 | \bold{Max.EMP_work: }{numeric; maximum value of the workers }
       |                      ^
checkRd: (-1) StatClusterData.Rd:154: Lost braces
   154 | \bold{Q1.EMP_live_work: }{numeric; first quartile of the commuters living and working in the same area}
       |                          ^
checkRd: (-1) StatClusterData.Rd:156: Lost braces
   156 | \bold{Q2.EMP_live_work: }{numeric; median of the commuters living and working in the same area}
       |                          ^
checkRd: (-1) StatClusterData.Rd:158: Lost braces
   158 | \bold{Q3.EMP_live_work: }{numeric; third quartile of the the commuters living and working in the same area }
       |                          ^
checkRd: (-1) StatClusterData.Rd:160: Lost braces
   160 | \bold{Min.EMP_live_work: }{numeric; minimum value of the commuters living and working in the same area }
       |                           ^
checkRd: (-1) StatClusterData.Rd:162: Lost braces
   162 | \bold{Max.EMP_live_work: }{numeric; maximum value of the commuters living and working in the same area }
       |                           ^
checkRd: (-1) StatClusterData.Rd:164: Lost braces
   164 | \bold{Mean.lma_commuter_percent: }{numeric; mean value of the quantity: (EMP_live-EMP_live_work)+(EMP_work-EMP_live_work)/(2*EMP_live_work) }
       |                                   ^
checkRd: (-1) StatClusterData.Rd:166: Lost braces
   166 | \bold{Std.lma_commuter_percent: }{numeric; standard deviation of the quantity (EMP_live-EMP_live_work)+(EMP_work-EMP_live_work)/(2*EMP_live_work) }
       |                                  ^
checkRd: (-1) StatClusterData.Rd:168-170: Lost braces
   168 | \bold{Mean.Home_Work_Ratio: }{numeric; mean value of the quantity 
       |                              ^
checkRd: (-1) StatClusterData.Rd:171-173: Lost braces
   171 |  \bold{Std.Home_Work_Ratio: }{numeric; standard deviation of the quantity 
       |                              ^
checkRd: (-1) StatClusterData.Rd:175: Lost braces
   175 | \bold{Q_modularity: }{numeric; Q_modularity index }
       |                      ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  '/tmp/th798/16153372/R-release/715/LabourMarketAreas.Rcheck/00check.log'
for details.

[1] "2025-03-27 01:25:28 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)
+ }
>