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

WARNING: ignoring environment value of R_HOME

R Under development (unstable) (2025-07-04 r88383) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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> cargs <- commandArgs(trailingOnly=TRUE)
> if(length(cargs)==0){
+   ## before running interactively, make sure to start emacs/R with
+   ## environment defined in /scratch/...check_one.sh, particularly
+   ## R_LIBS_USER=/tmp/... otherwise we get error when installing
+   ## data.table.
+   base <- "/scratch/th798/data.table-revdeps/*"
+   cargs <- c(
+     Sys.glob(file.path(base,"deps.csv")),
+     "349",
+     Sys.glob(file.path(base, "data.table_release_*tar.gz")),
+     Sys.glob(file.path(base, "data.table_master_*tar.gz"))
+   )
+ }
> names(cargs) <- c("deps.csv", "task.str", "release", "master")
> dput(cargs)
c(deps.csv = "/scratch/th798/data.table-revdeps/2025-07-05/deps.csv", 
task.str = "1392", release = "/scratch/th798/data.table-revdeps/2025-07-05/data.table_release_1.17.6.tar.gz", 
master = "/scratch/th798/data.table-revdeps/2025-07-05/data.table_master_1.17.99.1e2e3badae6cc19a5270112c3ad11e64ce279174.tar.gz"
)
> (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers
[1] "/tmp/th798/18314188/R-devel/1392"
> if(requireNamespace("R.cache"))R.cache::getCachePath()
Loading required namespace: R.cache
[1] "/tmp/th798/18314188/R-devel/1392/R.cache"
> task.id <- as.integer(cargs[["task.str"]])
> deps.df <- read.csv(cargs[["deps.csv"]])
> (rev.dep <- deps.df$Package[task.id])
[1] "statgenGWAS"
> job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id)
> setwd(task.dir)
> .libPaths()
[1] "/tmp/th798/18314188/R-devel/1392/library"
[2] "/projects/genomic-ml/R/R-devel/library"  
> options(repos=c(#this should be in ~/.Rprofile too.
+   CRAN="http://cloud.r-project.org"))
> print(Sys.time())
[1] "2025-07-05 01:26:47 MST"
> install.time <- system.time({
+   install.packages(rev.dep, dep=TRUE)
+ })
Installing package into '/tmp/th798/18314188/R-devel/1392/library'
(as 'lib' is unspecified)
also installing the dependencies 'memuse', 'pinfsc50', 'LMMsolver', 'sommer', 'tinytest', 'vcfR'

trying URL 'http://cloud.r-project.org/src/contrib/memuse_4.2-3.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/pinfsc50_1.3.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/LMMsolver_1.0.10.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/sommer_4.4.2.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/tinytest_1.4.1.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/vcfR_1.15.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/statgenGWAS_1.0.12.tar.gz'
* installing *source* package 'memuse' ...
** this is package 'memuse' version '4.2-3'
** package 'memuse' successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... /packages/gcc/12.2.0-nnbserq/bin/gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc accepts -g... yes
checking for /packages/gcc/12.2.0-nnbserq/bin/gcc option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for features.h... yes
configure: creating ./config.status
config.status: creating src/meminfo/src/conf.h
** 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../inst/RNACI  -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 meminfo/src/cacheinfo.c -o meminfo/src/cacheinfo.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/RNACI  -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 meminfo/src/fileinfo.c -o meminfo/src/fileinfo.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/RNACI  -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 meminfo/src/platform.c -o meminfo/src/platform.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/RNACI  -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 meminfo/src/procinfo.c -o meminfo/src/procinfo.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/RNACI  -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 meminfo/src/raminfo.c -o meminfo/src/raminfo.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/RNACI  -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 meminfo/src/swapinfo.c -o meminfo/src/swapinfo.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/RNACI  -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 wrappers.c -o wrappers.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG -I../inst/RNACI  -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 memuse_native.c -o memuse_native.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 memuse.so meminfo/src/cacheinfo.o meminfo/src/fileinfo.o meminfo/src/platform.o meminfo/src/procinfo.o meminfo/src/raminfo.o meminfo/src/swapinfo.o wrappers.o memuse_native.o
installing to /tmp/th798/18314188/R-devel/1392/library/00LOCK-memuse/00new/memuse/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 (memuse)
* installing *source* package 'pinfsc50' ...
** this is package 'pinfsc50' version '1.3.0'
** package 'pinfsc50' 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 (pinfsc50)
* installing *source* package 'LMMsolver' ...
** this is package 'LMMsolver' version '1.0.10'
** package 'LMMsolver' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c ADcholesky.cpp -o ADcholesky.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c AuxFun.cpp -o AuxFun.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c SparseMatrix.cpp -o SparseMatrix.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c cholesky.cpp -o cholesky.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 LMMsolver.so ADcholesky.o AuxFun.o RcppExports.o SparseMatrix.o cholesky.o
installing to /tmp/th798/18314188/R-devel/1392/library/00LOCK-LMMsolver/00new/LMMsolver/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 (LMMsolver)
* installing *source* package 'sommer' ...
** this is package 'sommer' version '4.4.2'
** package 'sommer' 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 -DARMA_64BIT_WORD=1 -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c MNR.cpp -o MNR.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-devel/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/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 -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 sommer.so MNR.o RcppExports.o -fopenmp -L/home/th798/R/R-devel/lib -lRlapack -L/home/th798/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
installing to /tmp/th798/18314188/R-devel/1392/library/00LOCK-sommer/00new/sommer/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 (sommer)
* installing *source* package 'tinytest' ...
** this is package 'tinytest' version '1.4.1'
** package 'tinytest' 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
** 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 (tinytest)
* installing *source* package 'vcfR' ...
** this is package 'vcfR' version '1.15.0'
** package 'vcfR' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c NM2winNM.cpp -o NM2winNM.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c ad_frequency.cpp -o ad_frequency.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c deprecated_funcs.cpp -o deprecated_funcs.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c extract_gt.cpp -o extract_gt.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c freq_peak.cpp -o freq_peak.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c gt_to_popsum.cpp -o gt_to_popsum.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c is_het.cpp -o is_het.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c masplit.cpp -o masplit.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c pair_sort.cpp -o pair_sort.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c rank_variants.cpp -o rank_variants.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c read_vcfR.cpp -o read_vcfR.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c seq_to_rects.cpp -o seq_to_rects.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c var_window.cpp -o var_window.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c vcfRCommon.cpp -o vcfRCommon.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c write_vcfR.cpp -o write_vcfR.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 vcfR.so NM2winNM.o RcppExports.o ad_frequency.o deprecated_funcs.o extract_gt.o freq_peak.o gt_to_popsum.o is_het.o masplit.o pair_sort.o rank_variants.o read_vcfR.o seq_to_rects.o var_window.o vcfRCommon.o write_vcfR.o -lz
installing to /tmp/th798/18314188/R-devel/1392/library/00LOCK-vcfR/00new/vcfR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'rbind' from package 'base' in package 'vcfR'
Creating a generic function for 'nrow' from package 'base' in package 'vcfR'
** 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 (vcfR)
* installing *source* package 'statgenGWAS' ...
** this is package 'statgenGWAS' version '1.0.12'
** package 'statgenGWAS' successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 accepts -g... yes
checking for /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... /packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -E
checking for macOS... not found as on Linux
checking for OpenMP... R was not built as a library
missing
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DARMA_DONT_USE_OPENMP -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 EMMA.cpp -o EMMA.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DARMA_DONT_USE_OPENMP -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  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DARMA_DONT_USE_OPENMP -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 codeCharMarkers.cpp -o codeCharMarkers.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DARMA_DONT_USE_OPENMP -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 fastGLS.cpp -o fastGLS.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DARMA_DONT_USE_OPENMP -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 getThr.cpp -o getThr.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DARMA_DONT_USE_OPENMP -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 kinship.cpp -o kinship.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-devel/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-devel/library/Rcpp/include' -I'/projects/genomic-ml/R/R-devel/library/RcppArmadillo/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -DARMA_DONT_USE_OPENMP -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 statgenGWAS.so EMMA.o RcppExports.o codeCharMarkers.o fastGLS.o getThr.o kinship.o utils.o -DARMA_DONT_USE_OPENMP -L/home/th798/R/R-devel/lib -lRlapack -L/home/th798/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
installing to /tmp/th798/18314188/R-devel/1392/library/00LOCK-statgenGWAS/00new/statgenGWAS/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 (statgenGWAS)

The downloaded source packages are in
	'/tmp/th798/18314188/RtmpfaTTdb/downloaded_packages'
> cat("Time to install revdep:\n")
Time to install revdep:
> print(install.time)
   user  system elapsed 
161.902  19.559 203.816 
> print(Sys.time())
[1] "2025-07-05 01:30:11 MST"
> downloaded_packages <- file.path(
+   tempdir(),
+   "downloaded_packages")
> dl.glob <- file.path(
+   downloaded_packages,
+   paste0(rev.dep,"_*.tar.gz"))
> rev.dep.dl.row <- cbind(rev.dep, Sys.glob(dl.glob))
> colnames(rev.dep.dl.row) <- c("pkg","path")
> rev.dep.release.tar.gz <- normalizePath(rev.dep.dl.row[,"path"], mustWork=TRUE)
> pkg.Rcheck <- paste0(rev.dep, ".Rcheck")
> 
> proj.dir <- "~/genomic-ml/data.table-revdeps"
> source(file.path(proj.dir, "myStatus.R"))
> Rvers <- gsub("[()]", "", gsub(" ", "_", R.version[["version.string"]]))
> dir.create(Rvers, showWarnings=FALSE)
> Rcheck.list <- list()
> for(dt.version.short in c("release", "master")){
+   dt.tar.gz <- cargs[[dt.version.short]]
+   dt.version <- gsub(".tar.gz|/.*?_", "", dt.tar.gz)
+   print(Sys.time())
+   install.packages(dt.tar.gz, repos=NULL)
+   print(Sys.time())
+   check.cmd <- get_check_cmd(rev.dep.release.tar.gz)
+   system(check.cmd)
+   print(Sys.time())
+   dest.Rcheck <- file.path(
+     Rvers,
+     paste0(dt.version, ".Rcheck"))
+   unlink(dest.Rcheck, recursive=TRUE)
+   file.rename(pkg.Rcheck, dest.Rcheck)
+   Rcheck.list[[dt.version]] <- file.path(dest.Rcheck, "00check.log")
+ }
[1] "2025-07-05 01:30:11 MST"
Installing package into '/tmp/th798/18314188/R-devel/1392/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** this is package 'data.table' version '1.17.6'
** package 'data.table' successfully unpacked and MD5 sums checked
** using staged installation
zlib 1.2.13 is available ok
* checking if R installation supports OpenMP without any extra hints... yes
** libs
using C compiler: 'gcc (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c assign.c -o assign.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c between.c -o between.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c bmerge.c -o bmerge.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c chmatch.c -o chmatch.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c cj.c -o cj.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c coalesce.c -o coalesce.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c dogroups.c -o dogroups.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fastmean.c -o fastmean.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fcast.c -o fcast.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fifelse.c -o fifelse.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fmelt.c -o fmelt.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c forder.c -o forder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frank.c -o frank.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fread.c -o fread.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c freadR.c -o freadR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c froll.c -o froll.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frollR.c -o frollR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frolladaptive.c -o frolladaptive.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fsort.c -o fsort.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwrite.c -o fwrite.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwriteR.c -o fwriteR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c gsumm.c -o gsumm.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c idatetime.c -o idatetime.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ijoin.c -o ijoin.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c init.c -o init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c inrange.c -o inrange.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nafill.c -o nafill.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c negate.c -o negate.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nqrecreateindices.c -o nqrecreateindices.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c openmp-utils.c -o openmp-utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c programming.c -o programming.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c quickselect.c -o quickselect.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c rbindlist.c -o rbindlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c reorder.c -o reorder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c shift.c -o shift.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c snprintf.c -o snprintf.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c subset.c -o subset.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c transpose.c -o transpose.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c types.c -o types.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c uniqlist.c -o uniqlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c utils.c -o utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c vecseq.c -o vecseq.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c wrappers.c -o wrappers.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include
PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi
installing to /tmp/th798/18314188/R-devel/1392/library/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (data.table)
[1] "2025-07-05 01:30:40 MST"
* using log directory '/tmp/th798/18314188/R-devel/1392/statgenGWAS.Rcheck'
* using R Under development (unstable) (2025-07-04 r88383)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Spack GCC) 12.2.0
    GNU Fortran (Spack GCC) 12.2.0
* running under: Red Hat Enterprise Linux 8.10 (Ootpa)
* using session charset: ASCII
* checking for file 'statgenGWAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'statgenGWAS' version '1.0.12'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'statgenGWAS' can be installed ... OK
* used C++ compiler: 'g++ (Spack GCC) 12.2.0'
* checking installed package size ... INFO
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   1.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'tinytest.R'
 ERROR
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("statgenGWAS")
  + }
  
  test_GWAS.R...................    0 tests    
  test_GWAS.R...................    0 tests    
  test_GWAS.R...................    0 tests    
  test_GWAS.R...................    0 tests    
  test_GWAS.R...................    1 tests OK 
  test_GWAS.R...................    2 tests OK 
  test_GWAS.R...................    2 tests OK 
  test_GWAS.R...................    3 tests OK 
  test_GWAS.R...................    4 tests OK 
  test_GWAS.R...................    5 tests OK 
  test_GWAS.R...................    6 tests OK 
  test_GWAS.R...................    7 tests OK 
  test_GWAS.R...................    8 tests OK 
  test_GWAS.R...................    9 tests OK 
  test_GWAS.R...................   10 tests OK 
  test_GWAS.R...................   11 tests OK 
  test_GWAS.R...................   11 tests OK 
  test_GWAS.R...................   12 tests OK 
  test_GWAS.R...................   13 tests OK 
  test_GWAS.R...................   14 tests OK 
  test_GWAS.R...................   15 tests OK 
  test_GWAS.R...................   15 tests OK 
  test_GWAS.R...................   16 tests OK 
  test_GWAS.R...................   17 tests OK 0.4s
  
  test_STG.R....................    0 tests    
  test_STG.R....................    0 tests    
  test_STG.R....................    0 tests    
  test_STG.R....................    0 tests    
  test_STG.R....................    0 tests    
  test_STG.R....................    0 tests    
  test_STG.R....................    0 tests    
  test_STG.R....................    0 tests    
  test_STG.R....................    1 tests OK 
  test_STG.R....................    2 tests OK 
  test_STG.R....................    3 tests OK 
  test_STG.R....................    4 tests OK 
  test_STG.R....................    5 tests OK 
  test_STG.R....................    6 tests OK 
  test_STG.R....................    7 tests OK 
  test_STG.R....................    8 tests OK 
  test_STG.R....................    9 tests OK 
  test_STG.R....................   10 tests OK 
  test_STG.R....................   11 tests OK 
  test_STG.R....................   12 tests OK 
  test_STG.R....................   13 tests OK 
  test_STG.R....................   14 tests OK 
  test_STG.R....................   15 tests OK 
  test_STG.R....................   16 tests OK 
  test_STG.R....................   17 tests OK 
  test_STG.R....................   17 tests OK 
  test_STG.R....................   17 tests OK 
  test_STG.R....................   17 tests OK 
  test_STG.R....................   17 tests OK 
  test_STG.R....................   17 tests OK 
  test_STG.R....................   18 tests OK 
  test_STG.R....................   19 tests OK 
  test_STG.R....................   20 tests OK 
  test_STG.R....................   21 tests OK 
  test_STG.R....................   22 tests OK 
  test_STG.R....................   23 tests OK 
  test_STG.R....................   24 tests OK 
  test_STG.R....................   25 tests OK 
  test_STG.R....................   26 tests OK 
  test_STG.R....................   27 tests OK 
  test_STG.R....................   28 tests OK 
  test_STG.R....................   29 tests OK 
  test_STG.R....................   30 tests OK 
  test_STG.R....................   31 tests OK 
  test_STG.R....................   32 tests OK 
  test_STG.R....................   33 tests OK 
  test_STG.R....................   34 tests OK 
  test_STG.R....................   35 tests OK 
  test_STG.R....................   36 tests OK 
  test_STG.R....................   37 tests OK 1.2s
  
  test_STGHelper.R..............    0 tests    
  test_STGHelper.R..............    0 tests    
  test_STGHelper.R..............    0 tests    
  test_STGHelper.R..............    1 tests OK 
  test_STGHelper.R..............    2 tests OK 
  test_STGHelper.R..............    3 tests OK 
  test_STGHelper.R..............    3 tests OK 
  test_STGHelper.R..............    4 tests OK 
  test_STGHelper.R..............    5 tests OK 
  test_STGHelper.R..............    6 tests OK 
  test_STGHelper.R..............    7 tests OK 
  test_STGHelper.R..............    8 tests OK 
  test_STGHelper.R..............    9 tests OK 
  test_STGHelper.R..............   10 tests OK 
  test_STGHelper.R..............   11 tests OK 
  test_STGHelper.R..............   12 tests OK 
  test_STGHelper.R..............   13 tests OK 
  test_STGHelper.R..............   14 tests OK 
  test_STGHelper.R..............   14 tests OK 
  test_STGHelper.R..............   15 tests OK 
  test_STGHelper.R..............   16 tests OK 
  test_STGHelper.R..............   17 tests OK 
  test_STGHelper.R..............   18 tests OK 
  test_STGHelper.R..............   18 tests OK 
  test_STGHelper.R..............   19 tests OK 
  test_STGHelper.R..............   20 tests OK 
  test_STGHelper.R..............   20 tests OK 
  test_STGHelper.R..............   20 tests OK 
  test_STGHelper.R..............   21 tests OK 
  test_STGHelper.R..............   22 tests OK 
  test_STGHelper.R..............   23 tests OK 
  test_STGHelper.R..............   24 tests OK 
  test_STGHelper.R..............   25 tests OK 
  test_STGHelper.R..............   26 tests OK 
  test_STGHelper.R..............   27 tests OK 
  test_STGHelper.R..............   28 tests OK 
  test_STGHelper.R..............   29 tests OK 
  test_STGHelper.R..............   30 tests OK 
  test_STGHelper.R..............   31 tests OK 38ms
  
  test_STGoptions.R.............    0 tests    
  test_STGoptions.R.............    1 tests OK 
  test_STGoptions.R.............    1 tests OK 
  test_STGoptions.R.............    1 tests OK 
  test_STGoptions.R.............    2 tests OK 
  test_STGoptions.R.............    3 tests OK 
  test_STGoptions.R.............    4 tests OK 
  test_STGoptions.R.............    5 tests OK 
  test_STGoptions.R.............    6 tests OK 
  test_STGoptions.R.............    6 tests OK 
  test_STGoptions.R.............    6 tests OK 
  test_STGoptions.R.............    7 tests OK 
  test_STGoptions.R.............    8 tests OK 
  test_STGoptions.R.............    9 tests OK 
  test_STGoptions.R.............   10 tests OK 
  test_STGoptions.R.............   11 tests OK 
  test_STGoptions.R.............   11 tests OK 
  test_STGoptions.R.............   12 tests OK 
  test_STGoptions.R.............   13 tests OK 
  test_STGoptions.R.............   14 tests OK 
  test_STGoptions.R.............   14 tests OK 
  test_STGoptions.R.............   15 tests OK 
  test_STGoptions.R.............   16 tests OK 
  test_STGoptions.R.............   17 tests OK 
  test_STGoptions.R.............   18 tests OK 
  test_STGoptions.R.............   19 tests OK 
  test_STGoptions.R.............   19 tests OK 
  test_STGoptions.R.............   20 tests OK 
  test_STGoptions.R.............   21 tests OK 
  test_STGoptions.R.............   22 tests OK 
  test_STGoptions.R.............   22 tests OK 
  test_STGoptions.R.............   23 tests OK 
  test_STGoptions.R.............   24 tests OK 2.2s
  
  test_chkFuncs.R...............    0 tests    
  test_chkFuncs.R...............    1 tests OK 
  test_chkFuncs.R...............    2 tests OK 
  test_chkFuncs.R...............    3 tests OK 
  test_chkFuncs.R...............    3 tests OK 
  test_chkFuncs.R...............    3 tests OK 
  test_chkFuncs.R...............    4 tests OK 
  test_chkFuncs.R...............    5 tests OK 
  test_chkFuncs.R...............    6 tests OK 
  test_chkFuncs.R...............    7 tests OK 
  test_chkFuncs.R...............    8 tests OK 
  test_chkFuncs.R...............    9 tests OK 
  test_chkFuncs.R...............   10 tests OK 
  test_chkFuncs.R...............   11 tests OK 
  test_chkFuncs.R...............   12 tests OK 
  test_chkFuncs.R...............   13 tests OK 
  test_chkFuncs.R...............   14 tests OK 
  test_chkFuncs.R...............   15 tests OK 
  test_chkFuncs.R...............   16 tests OK 
  test_chkFuncs.R...............   17 tests OK 
  test_chkFuncs.R...............   18 tests OK 
  test_chkFuncs.R...............   19 tests OK 
  test_chkFuncs.R...............   20 tests OK 
  test_chkFuncs.R...............   21 tests OK 
  test_chkFuncs.R...............   22 tests OK 
  test_chkFuncs.R...............   23 tests OK 
  test_chkFuncs.R...............   24 tests OK 
  test_chkFuncs.R...............   25 tests OK 
  test_chkFuncs.R...............   26 tests OK 
  test_chkFuncs.R...............   27 tests OK 
  test_chkFuncs.R...............   28 tests OK 
  test_chkFuncs.R...............   29 tests OK 
  test_chkFuncs.R...............   30 tests OK 
  test_chkFuncs.R...............   30 tests OK 
  test_chkFuncs.R...............   31 tests OK 
  test_chkFuncs.R...............   31 tests OK 
  test_chkFuncs.R...............   32 tests OK 
  test_chkFuncs.R...............   33 tests OK 
  test_chkFuncs.R...............   34 tests OK 
  test_chkFuncs.R...............   35 tests OK 
  test_chkFuncs.R...............   36 tests OK 
  test_chkFuncs.R...............   37 tests OK 
  test_chkFuncs.R...............   38 tests OK 
  test_chkFuncs.R...............   39 tests OK 
  test_chkFuncs.R...............   40 tests OK 
  test_chkFuncs.R...............   41 tests OK 
  test_chkFuncs.R...............   42 tests OK 
  test_chkFuncs.R...............   43 tests OK 24ms
  
  test_codeMarkers.R............    0 tests    
  test_codeMarkers.R............    0 tests    
  test_codeMarkers.R............    0 tests    
  test_codeMarkers.R............    0 tests    
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  test_codeMarkers.R............    0 tests    
  test_codeMarkers.R............    0 tests    
  test_codeMarkers.R............    0 tests    
  test_codeMarkers.R............    1 tests OK 
  test_codeMarkers.R............    2 tests OK 
  test_codeMarkers.R............    3 tests OK 
  test_codeMarkers.R............    4 tests OK 
  test_codeMarkers.R............    5 tests OK 
  test_codeMarkers.R............    6 tests OK 
  test_codeMarkers.R............    7 tests OK 
  test_codeMarkers.R............    8 tests OK 
  test_codeMarkers.R............    9 tests OK 
  test_codeMarkers.R............   10 tests OK 
  test_codeMarkers.R............   11 tests OK 
  test_codeMarkers.R............   12 tests OK 
  test_codeMarkers.R............   13 tests OK 
  test_codeMarkers.R............   14 tests OK 
  test_codeMarkers.R............   14 tests OK 
  test_codeMarkers.R............   15 tests OK 
  test_codeMarkers.R............   16 tests OK 
  test_codeMarkers.R............   17 tests OK 
  test_codeMarkers.R............   18 tests OK 
  test_codeMarkers.R............   19 tests OK 
  test_codeMarkers.R............   19 tests OK 
  test_codeMarkers.R............   19 tests OK 
  test_codeMarkers.R............   20 tests OK 
  test_codeMarkers.R............   21 tests OK 
  test_codeMarkers.R............   22 tests OK 
  test_codeMarkers.R............   23 tests OK 
  test_codeMarkers.R............   24 tests OK 
  test_codeMarkers.R............   25 tests OK 
  test_codeMarkers.R............   26 tests OK 
  test_codeMarkers.R............   27 tests OK 
  test_codeMarkers.R............   28 tests OK 
  test_codeMarkers.R............   29 tests OK 
  test_codeMarkers.R............   30 tests OK 
  test_codeMarkers.R............   31 tests OK 
  test_codeMarkers.R............   32 tests OK 
  test_codeMarkers.R............   33 tests OK 
  test_codeMarkers.R............   34 tests OK 
  test_codeMarkers.R............   35 tests OK 
  test_codeMarkers.R............   36 tests OK 
  test_codeMarkers.R............   37 tests OK 
  test_codeMarkers.R............   37 tests OK 
  test_codeMarkers.R............   37 tests OK 
  test_codeMarkers.R............   38 tests OK 
  test_codeMarkers.R............   38 tests OK 
  test_codeMarkers.R............   38 tests OK 
  test_codeMarkers.R............   39 tests OK 
  test_codeMarkers.R............   39 tests OK 
  test_codeMarkers.R............   40 tests OK 
  test_codeMarkers.R............   41 tests OK 
  test_codeMarkers.R............   42 tests OK 
  test_codeMarkers.R............   43 tests OK 
  test_codeMarkers.R............   44 tests OK 78ms
  
  test_gData.R..................    0 tests    
  test_gData.R..................    0 tests    
  test_gData.R..................    0 tests    
  test_gData.R..................    0 tests    
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  test_gData.R..................    0 tests    
  test_gData.R..................    1 tests OK 
  test_gData.R..................    2 tests OK 
  test_gData.R..................    3 tests OK 
  test_gData.R..................    4 tests OK 
  test_gData.R..................    4 tests OK 
  test_gData.R..................    4 tests OK 
  test_gData.R..................    5 tests OK 
  test_gData.R..................    6 tests OK 
  test_gData.R..................    6 tests OK 
  test_gData.R..................    6 tests OK 
  test_gData.R..................    7 tests OK 
  test_gData.R..................    8 tests OK 
  test_gData.R..................    9 tests OK 
  test_gData.R..................    9 tests OK 
  test_gData.R..................   10 tests OK 
  test_gData.R..................   11 tests OK 
  test_gData.R..................   12 tests OK 
  test_gData.R..................   13 tests OK 
  test_gData.R..................   14 tests OK 
  test_gData.R..................   15 tests OK 
  test_gData.R..................   16 tests OK 
  test_gData.R..................   16 tests OK 
  test_gData.R..................   17 tests OK 
  test_gData.R..................   17 tests OK 
  test_gData.R..................   17 tests OK 
  test_gData.R..................   18 tests OK 
  test_gData.R..................   19 tests OK 
  test_gData.R..................   19 tests OK 
  test_gData.R..................   19 tests OK 
  test_gData.R..................   20 tests OK 
  test_gData.R..................   21 tests OK 
  test_gData.R..................   22 tests OK 
  test_gData.R..................   23 tests OK 
  test_gData.R..................   23 tests OK 
  test_gData.R..................   24 tests OK 
  test_gData.R..................   25 tests OK 
  test_gData.R..................   25 tests OK 
  test_gData.R..................   25 tests OK 
  test_gData.R..................   26 tests OK 
  test_gData.R..................   27 tests OK 
  test_gData.R..................   28 tests OK 
  test_gData.R..................   29 tests OK 
  test_gData.R..................   30 tests OK 
  test_gData.R..................   30 tests OK 
  test_gData.R..................   30 tests OK 
  test_gData.R..................   31 tests OK 
  test_gData.R..................   32 tests OK 
  test_gData.R..................   33 tests OK 
  test_gData.R..................   34 tests OK 
  test_gData.R..................   35 tests OK 
  test_gData.R..................   36 tests OK 
  test_gData.R..................   37 tests OK 
  test_gData.R..................   38 tests OK 
  test_gData.R..................   39 tests OK 
  test_gData.R..................   40 tests OK 
  test_gData.R..................   41 tests OK 
  test_gData.R..................   42 tests OK 
  test_gData.R..................   43 tests OK 
  test_gData.R..................   43 tests OK 
  test_gData.R..................   43 tests OK 
  test_gData.R..................   44 tests OK 
  test_gData.R..................   45 tests OK 
  test_gData.R..................   46 tests OK 
  test_gData.R..................   47 tests OK 
  test_gData.R..................   47 tests OK 
  test_gData.R..................   48 tests OK 
  test_gData.R..................   49 tests OK 
  test_gData.R..................   50 tests OK 
  test_gData.R..................   51 tests OK 
  test_gData.R..................   51 tests OK 
  test_gData.R..................   51 tests OK 
  test_gData.R..................   52 tests OK 
  test_gData.R..................   53 tests OK 
  test_gData.R..................   54 tests OK 
  test_gData.R..................   55 tests OK 
  test_gData.R..................   56 tests OK 
  test_gData.R..................   57 tests OK 
  test_gData.R..................   58 tests OK 
  test_gData.R..................   59 tests OK 
  test_gData.R..................   60 tests OK 
  test_gData.R..................   60 tests OK 
  test_gData.R..................   60 tests OK 
  test_gData.R..................   61 tests OK 
  test_gData.R..................   61 tests OK 
  test_gData.R..................   62 tests OK 
  test_gData.R..................   62 tests OK 
  test_gData.R..................   63 tests OK 
  test_gData.R..................   64 tests OK 
  test_gData.R..................   65 tests OK 
  test_gData.R..................   65 tests OK Error: 'get_labs' is not an exported object from 'namespace:ggplot2'
  In addition: Warning messages:
  1: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
    conversion failure on '← 2@3' in 'mbcsToSbcs': dot substituted for <e2>
  2: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
    conversion failure on '← 2@3' in 'mbcsToSbcs': dot substituted for <86>
  3: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
    conversion failure on '← 2@3' in 'mbcsToSbcs': dot substituted for <90>
  Execution halted
* 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 ERROR
See
  '/tmp/th798/18314188/R-devel/1392/statgenGWAS.Rcheck/00check.log'
for details.

[1] "2025-07-05 01:34:40 MST"
[1] "2025-07-05 01:34:40 MST"
Installing package into '/tmp/th798/18314188/R-devel/1392/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** this is package 'data.table' version '1.17.99'
** using staged installation
zlib 1.2.13 is available ok
* checking if R installation supports OpenMP without any extra hints... yes
** libs
using C compiler: 'gcc (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c assign.c -o assign.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c between.c -o between.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c bmerge.c -o bmerge.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c chmatch.c -o chmatch.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c cj.c -o cj.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c coalesce.c -o coalesce.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c dogroups.c -o dogroups.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fastmean.c -o fastmean.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fcast.c -o fcast.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fifelse.c -o fifelse.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fmelt.c -o fmelt.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c forder.c -o forder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frank.c -o frank.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fread.c -o fread.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c freadR.c -o freadR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c froll.c -o froll.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frollR.c -o frollR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frolladaptive.c -o frolladaptive.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fsort.c -o fsort.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwrite.c -o fwrite.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwriteR.c -o fwriteR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c gsumm.c -o gsumm.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c idatetime.c -o idatetime.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ijoin.c -o ijoin.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c init.c -o init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c inrange.c -o inrange.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c mergelist.c -o mergelist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nafill.c -o nafill.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c negate.c -o negate.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nqrecreateindices.c -o nqrecreateindices.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c openmp-utils.c -o openmp-utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c programming.c -o programming.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c quickselect.c -o quickselect.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c rbindlist.c -o rbindlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c reorder.c -o reorder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c shift.c -o shift.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c snprintf.c -o snprintf.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c subset.c -o subset.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c transpose.c -o transpose.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c types.c -o types.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c uniqlist.c -o uniqlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c utils.c -o utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c vecseq.c -o vecseq.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-devel/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c wrappers.c -o wrappers.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include
PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi
installing to /tmp/th798/18314188/R-devel/1392/library/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (data.table)
[1] "2025-07-05 01:35:09 MST"
* using log directory '/tmp/th798/18314188/R-devel/1392/statgenGWAS.Rcheck'
* using R Under development (unstable) (2025-07-04 r88383)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Spack GCC) 12.2.0
    GNU Fortran (Spack GCC) 12.2.0
* running under: Red Hat Enterprise Linux 8.10 (Ootpa)
* using session charset: ASCII
* checking for file 'statgenGWAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'statgenGWAS' version '1.0.12'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'statgenGWAS' can be installed ... OK
* used C++ compiler: 'g++ (Spack GCC) 12.2.0'
* checking installed package size ... INFO
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   1.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'tinytest.R'
 ERROR
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   tinytest::test_package("statgenGWAS")
  + }
  
  test_GWAS.R...................    0 tests    
  test_GWAS.R...................    0 tests    
  test_GWAS.R...................    0 tests    
  test_GWAS.R...................    0 tests    
  test_GWAS.R...................    1 tests OK 
  test_GWAS.R...................    2 tests OK 
  test_GWAS.R...................    2 tests OK 
  test_GWAS.R...................    3 tests OK 
  test_GWAS.R...................    4 tests OK 
  test_GWAS.R...................    5 tests OK 
  test_GWAS.R...................    6 tests OK 
  test_GWAS.R...................    7 tests OK 
  test_GWAS.R...................    8 tests OK 
  test_GWAS.R...................    9 tests OK 
  test_GWAS.R...................   10 tests OK 
  test_GWAS.R...................   11 tests OK 
  test_GWAS.R...................   11 tests OK 
  test_GWAS.R...................   12 tests OK 
  test_GWAS.R...................   13 tests OK 
  test_GWAS.R...................   14 tests OK 
  test_GWAS.R...................   15 tests OK 
  test_GWAS.R...................   15 tests OK 
  test_GWAS.R...................   16 tests OK 
  test_GWAS.R...................   17 tests OK 0.4s
  
  test_STG.R....................    0 tests    
  test_STG.R....................    0 tests    
  test_STG.R....................    0 tests    
  test_STG.R....................    0 tests    
  test_STG.R....................    0 tests    
  test_STG.R....................    0 tests    
  test_STG.R....................    0 tests    
  test_STG.R....................    0 tests    
  test_STG.R....................    1 tests OK 
  test_STG.R....................    2 tests OK 
  test_STG.R....................    3 tests OK 
  test_STG.R....................    4 tests OK 
  test_STG.R....................    5 tests OK 
  test_STG.R....................    6 tests OK 
  test_STG.R....................    7 tests OK 
  test_STG.R....................    8 tests OK 
  test_STG.R....................    9 tests OK 
  test_STG.R....................   10 tests OK 
  test_STG.R....................   11 tests OK 
  test_STG.R....................   12 tests OK 
  test_STG.R....................   13 tests OK 
  test_STG.R....................   14 tests OK 
  test_STG.R....................   15 tests OK 
  test_STG.R....................   16 tests OK 
  test_STG.R....................   17 tests OK 
  test_STG.R....................   17 tests OK 
  test_STG.R....................   17 tests OK 
  test_STG.R....................   17 tests OK 
  test_STG.R....................   17 tests OK 
  test_STG.R....................   17 tests OK 
  test_STG.R....................   18 tests OK 
  test_STG.R....................   19 tests OK 
  test_STG.R....................   20 tests OK 
  test_STG.R....................   21 tests OK 
  test_STG.R....................   22 tests OK 
  test_STG.R....................   23 tests OK 
  test_STG.R....................   24 tests OK 
  test_STG.R....................   25 tests OK 
  test_STG.R....................   26 tests OK 
  test_STG.R....................   27 tests OK 
  test_STG.R....................   28 tests OK 
  test_STG.R....................   29 tests OK 
  test_STG.R....................   30 tests OK 
  test_STG.R....................   31 tests OK 
  test_STG.R....................   32 tests OK 
  test_STG.R....................   33 tests OK 
  test_STG.R....................   34 tests OK 
  test_STG.R....................   35 tests OK 
  test_STG.R....................   36 tests OK 
  test_STG.R....................   37 tests OK 1.2s
  
  test_STGHelper.R..............    0 tests    
  test_STGHelper.R..............    0 tests    
  test_STGHelper.R..............    0 tests    
  test_STGHelper.R..............    1 tests OK 
  test_STGHelper.R..............    2 tests OK 
  test_STGHelper.R..............    3 tests OK 
  test_STGHelper.R..............    3 tests OK 
  test_STGHelper.R..............    4 tests OK 
  test_STGHelper.R..............    5 tests OK 
  test_STGHelper.R..............    6 tests OK 
  test_STGHelper.R..............    7 tests OK 
  test_STGHelper.R..............    8 tests OK 
  test_STGHelper.R..............    9 tests OK 
  test_STGHelper.R..............   10 tests OK 
  test_STGHelper.R..............   11 tests OK 
  test_STGHelper.R..............   12 tests OK 
  test_STGHelper.R..............   13 tests OK 
  test_STGHelper.R..............   14 tests OK 
  test_STGHelper.R..............   14 tests OK 
  test_STGHelper.R..............   15 tests OK 
  test_STGHelper.R..............   16 tests OK 
  test_STGHelper.R..............   17 tests OK 
  test_STGHelper.R..............   18 tests OK 
  test_STGHelper.R..............   18 tests OK 
  test_STGHelper.R..............   19 tests OK 
  test_STGHelper.R..............   20 tests OK 
  test_STGHelper.R..............   20 tests OK 
  test_STGHelper.R..............   20 tests OK 
  test_STGHelper.R..............   21 tests OK 
  test_STGHelper.R..............   22 tests OK 
  test_STGHelper.R..............   23 tests OK 
  test_STGHelper.R..............   24 tests OK 
  test_STGHelper.R..............   25 tests OK 
  test_STGHelper.R..............   26 tests OK 
  test_STGHelper.R..............   27 tests OK 
  test_STGHelper.R..............   28 tests OK 
  test_STGHelper.R..............   29 tests OK 
  test_STGHelper.R..............   30 tests OK 
  test_STGHelper.R..............   31 tests OK 39ms
  
  test_STGoptions.R.............    0 tests    
  test_STGoptions.R.............    1 tests OK 
  test_STGoptions.R.............    1 tests OK 
  test_STGoptions.R.............    1 tests OK 
  test_STGoptions.R.............    2 tests OK 
  test_STGoptions.R.............    3 tests OK 
  test_STGoptions.R.............    4 tests OK 
  test_STGoptions.R.............    5 tests OK 
  test_STGoptions.R.............    6 tests OK 
  test_STGoptions.R.............    6 tests OK 
  test_STGoptions.R.............    6 tests OK 
  test_STGoptions.R.............    7 tests OK 
  test_STGoptions.R.............    8 tests OK 
  test_STGoptions.R.............    9 tests OK 
  test_STGoptions.R.............   10 tests OK 
  test_STGoptions.R.............   11 tests OK 
  test_STGoptions.R.............   11 tests OK 
  test_STGoptions.R.............   12 tests OK 
  test_STGoptions.R.............   13 tests OK 
  test_STGoptions.R.............   14 tests OK 
  test_STGoptions.R.............   14 tests OK 
  test_STGoptions.R.............   15 tests OK 
  test_STGoptions.R.............   16 tests OK 
  test_STGoptions.R.............   17 tests OK 
  test_STGoptions.R.............   18 tests OK 
  test_STGoptions.R.............   19 tests OK 
  test_STGoptions.R.............   19 tests OK 
  test_STGoptions.R.............   20 tests OK 
  test_STGoptions.R.............   21 tests OK 
  test_STGoptions.R.............   22 tests OK 
  test_STGoptions.R.............   22 tests OK 
  test_STGoptions.R.............   23 tests OK 
  test_STGoptions.R.............   24 tests OK 2.2s
  
  test_chkFuncs.R...............    0 tests    
  test_chkFuncs.R...............    1 tests OK 
  test_chkFuncs.R...............    2 tests OK 
  test_chkFuncs.R...............    3 tests OK 
  test_chkFuncs.R...............    3 tests OK 
  test_chkFuncs.R...............    3 tests OK 
  test_chkFuncs.R...............    4 tests OK 
  test_chkFuncs.R...............    5 tests OK 
  test_chkFuncs.R...............    6 tests OK 
  test_chkFuncs.R...............    7 tests OK 
  test_chkFuncs.R...............    8 tests OK 
  test_chkFuncs.R...............    9 tests OK 
  test_chkFuncs.R...............   10 tests OK 
  test_chkFuncs.R...............   11 tests OK 
  test_chkFuncs.R...............   12 tests OK 
  test_chkFuncs.R...............   13 tests OK 
  test_chkFuncs.R...............   14 tests OK 
  test_chkFuncs.R...............   15 tests OK 
  test_chkFuncs.R...............   16 tests OK 
  test_chkFuncs.R...............   17 tests OK 
  test_chkFuncs.R...............   18 tests OK 
  test_chkFuncs.R...............   19 tests OK 
  test_chkFuncs.R...............   20 tests OK 
  test_chkFuncs.R...............   21 tests OK 
  test_chkFuncs.R...............   22 tests OK 
  test_chkFuncs.R...............   23 tests OK 
  test_chkFuncs.R...............   24 tests OK 
  test_chkFuncs.R...............   25 tests OK 
  test_chkFuncs.R...............   26 tests OK 
  test_chkFuncs.R...............   27 tests OK 
  test_chkFuncs.R...............   28 tests OK 
  test_chkFuncs.R...............   29 tests OK 
  test_chkFuncs.R...............   30 tests OK 
  test_chkFuncs.R...............   30 tests OK 
  test_chkFuncs.R...............   31 tests OK 
  test_chkFuncs.R...............   31 tests OK 
  test_chkFuncs.R...............   32 tests OK 
  test_chkFuncs.R...............   33 tests OK 
  test_chkFuncs.R...............   34 tests OK 
  test_chkFuncs.R...............   35 tests OK 
  test_chkFuncs.R...............   36 tests OK 
  test_chkFuncs.R...............   37 tests OK 
  test_chkFuncs.R...............   38 tests OK 
  test_chkFuncs.R...............   39 tests OK 
  test_chkFuncs.R...............   40 tests OK 
  test_chkFuncs.R...............   41 tests OK 
  test_chkFuncs.R...............   42 tests OK 
  test_chkFuncs.R...............   43 tests OK 22ms
  
  test_codeMarkers.R............    0 tests    
  test_codeMarkers.R............    0 tests    
  test_codeMarkers.R............    0 tests    
  test_codeMarkers.R............    0 tests    
  test_codeMarkers.R............    0 tests    
  test_codeMarkers.R............    0 tests    
  test_codeMarkers.R............    0 tests    
  test_codeMarkers.R............    0 tests    
  test_codeMarkers.R............    0 tests    
  test_codeMarkers.R............    1 tests OK 
  test_codeMarkers.R............    2 tests OK 
  test_codeMarkers.R............    3 tests OK 
  test_codeMarkers.R............    4 tests OK 
  test_codeMarkers.R............    5 tests OK 
  test_codeMarkers.R............    6 tests OK 
  test_codeMarkers.R............    7 tests OK 
  test_codeMarkers.R............    8 tests OK 
  test_codeMarkers.R............    9 tests OK 
  test_codeMarkers.R............   10 tests OK 
  test_codeMarkers.R............   11 tests OK 
  test_codeMarkers.R............   12 tests OK 
  test_codeMarkers.R............   13 tests OK 
  test_codeMarkers.R............   14 tests OK 
  test_codeMarkers.R............   14 tests OK 
  test_codeMarkers.R............   15 tests OK 
  test_codeMarkers.R............   16 tests OK 
  test_codeMarkers.R............   17 tests OK 
  test_codeMarkers.R............   18 tests OK 
  test_codeMarkers.R............   19 tests OK 
  test_codeMarkers.R............   19 tests OK 
  test_codeMarkers.R............   19 tests OK 
  test_codeMarkers.R............   20 tests OK 
  test_codeMarkers.R............   21 tests OK 
  test_codeMarkers.R............   22 tests OK 
  test_codeMarkers.R............   23 tests OK 
  test_codeMarkers.R............   24 tests OK 
  test_codeMarkers.R............   25 tests OK 
  test_codeMarkers.R............   26 tests OK 
  test_codeMarkers.R............   27 tests OK 
  test_codeMarkers.R............   28 tests OK 
  test_codeMarkers.R............   29 tests OK 
  test_codeMarkers.R............   30 tests OK 
  test_codeMarkers.R............   31 tests OK 
  test_codeMarkers.R............   32 tests OK 
  test_codeMarkers.R............   33 tests OK 
  test_codeMarkers.R............   34 tests OK 
  test_codeMarkers.R............   35 tests OK 
  test_codeMarkers.R............   36 tests OK 
  test_codeMarkers.R............   37 tests OK 
  test_codeMarkers.R............   37 tests OK 
  test_codeMarkers.R............   37 tests OK 
  test_codeMarkers.R............   38 tests OK 
  test_codeMarkers.R............   38 tests OK 
  test_codeMarkers.R............   38 tests OK 
  test_codeMarkers.R............   39 tests OK 
  test_codeMarkers.R............   39 tests OK 
  test_codeMarkers.R............   40 tests OK 
  test_codeMarkers.R............   41 tests OK 
  test_codeMarkers.R............   42 tests OK 
  test_codeMarkers.R............   43 tests OK 
  test_codeMarkers.R............   44 tests OK 74ms
  
  test_gData.R..................    0 tests    
  test_gData.R..................    0 tests    
  test_gData.R..................    0 tests    
  test_gData.R..................    0 tests    
  test_gData.R..................    0 tests    
  test_gData.R..................    0 tests    
  test_gData.R..................    0 tests    
  test_gData.R..................    0 tests    
  test_gData.R..................    1 tests OK 
  test_gData.R..................    2 tests OK 
  test_gData.R..................    3 tests OK 
  test_gData.R..................    4 tests OK 
  test_gData.R..................    4 tests OK 
  test_gData.R..................    4 tests OK 
  test_gData.R..................    5 tests OK 
  test_gData.R..................    6 tests OK 
  test_gData.R..................    6 tests OK 
  test_gData.R..................    6 tests OK 
  test_gData.R..................    7 tests OK 
  test_gData.R..................    8 tests OK 
  test_gData.R..................    9 tests OK 
  test_gData.R..................    9 tests OK 
  test_gData.R..................   10 tests OK 
  test_gData.R..................   11 tests OK 
  test_gData.R..................   12 tests OK 
  test_gData.R..................   13 tests OK 
  test_gData.R..................   14 tests OK 
  test_gData.R..................   15 tests OK 
  test_gData.R..................   16 tests OK 
  test_gData.R..................   16 tests OK 
  test_gData.R..................   17 tests OK 
  test_gData.R..................   17 tests OK 
  test_gData.R..................   17 tests OK 
  test_gData.R..................   18 tests OK 
  test_gData.R..................   19 tests OK 
  test_gData.R..................   19 tests OK 
  test_gData.R..................   19 tests OK 
  test_gData.R..................   20 tests OK 
  test_gData.R..................   21 tests OK 
  test_gData.R..................   22 tests OK 
  test_gData.R..................   23 tests OK 
  test_gData.R..................   23 tests OK 
  test_gData.R..................   24 tests OK 
  test_gData.R..................   25 tests OK 
  test_gData.R..................   25 tests OK 
  test_gData.R..................   25 tests OK 
  test_gData.R..................   26 tests OK 
  test_gData.R..................   27 tests OK 
  test_gData.R..................   28 tests OK 
  test_gData.R..................   29 tests OK 
  test_gData.R..................   30 tests OK 
  test_gData.R..................   30 tests OK 
  test_gData.R..................   30 tests OK 
  test_gData.R..................   31 tests OK 
  test_gData.R..................   32 tests OK 
  test_gData.R..................   33 tests OK 
  test_gData.R..................   34 tests OK 
  test_gData.R..................   35 tests OK 
  test_gData.R..................   36 tests OK 
  test_gData.R..................   37 tests OK 
  test_gData.R..................   38 tests OK 
  test_gData.R..................   39 tests OK 
  test_gData.R..................   40 tests OK 
  test_gData.R..................   41 tests OK 
  test_gData.R..................   42 tests OK 
  test_gData.R..................   43 tests OK 
  test_gData.R..................   43 tests OK 
  test_gData.R..................   43 tests OK 
  test_gData.R..................   44 tests OK 
  test_gData.R..................   45 tests OK 
  test_gData.R..................   46 tests OK 
  test_gData.R..................   47 tests OK 
  test_gData.R..................   47 tests OK 
  test_gData.R..................   48 tests OK 
  test_gData.R..................   49 tests OK 
  test_gData.R..................   50 tests OK 
  test_gData.R..................   51 tests OK 
  test_gData.R..................   51 tests OK 
  test_gData.R..................   51 tests OK 
  test_gData.R..................   52 tests OK 
  test_gData.R..................   53 tests OK 
  test_gData.R..................   54 tests OK 
  test_gData.R..................   55 tests OK 
  test_gData.R..................   56 tests OK 
  test_gData.R..................   57 tests OK 
  test_gData.R..................   58 tests OK 
  test_gData.R..................   59 tests OK 
  test_gData.R..................   60 tests OK 
  test_gData.R..................   60 tests OK 
  test_gData.R..................   60 tests OK 
  test_gData.R..................   61 tests OK 
  test_gData.R..................   61 tests OK 
  test_gData.R..................   62 tests OK 
  test_gData.R..................   62 tests OK 
  test_gData.R..................   63 tests OK 
  test_gData.R..................   64 tests OK 
  test_gData.R..................   65 tests OK 
  test_gData.R..................   65 tests OK Error: 'get_labs' is not an exported object from 'namespace:ggplot2'
  In addition: Warning messages:
  1: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
    conversion failure on '← 2@3' in 'mbcsToSbcs': dot substituted for <e2>
  2: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
    conversion failure on '← 2@3' in 'mbcsToSbcs': dot substituted for <86>
  3: In grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
    conversion failure on '← 2@3' in 'mbcsToSbcs': dot substituted for <90>
  Execution halted
* 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 ERROR
See
  '/tmp/th798/18314188/R-devel/1392/statgenGWAS.Rcheck/00check.log'
for details.

[1] "2025-07-05 01:39:05 MST"
> system(paste(c("diff -u", Rcheck.list), collapse=" "))
--- R_Under_development_unstable_2025-07-04_r88383/release_1.17.6.Rcheck/00check.log	2025-07-05 01:34:40.861016223 -0700
+++ R_Under_development_unstable_2025-07-04_r88383/master_1.17.99.1e2e3badae6cc19a5270112c3ad11e64ce279174.Rcheck/00check.log	2025-07-05 01:39:05.712378494 -0700
@@ -192,7 +192,7 @@
   test_STGHelper.R..............   28 tests OK 
   test_STGHelper.R..............   29 tests OK 
   test_STGHelper.R..............   30 tests OK 
-  test_STGHelper.R..............   31 tests OK 38ms
+  test_STGHelper.R..............   31 tests OK 39ms
   
   test_STGoptions.R.............    0 tests    
   test_STGoptions.R.............    1 tests OK 
@@ -275,7 +275,7 @@
   test_chkFuncs.R...............   40 tests OK 
   test_chkFuncs.R...............   41 tests OK 
   test_chkFuncs.R...............   42 tests OK 
-  test_chkFuncs.R...............   43 tests OK 24ms
+  test_chkFuncs.R...............   43 tests OK 22ms
   
   test_codeMarkers.R............    0 tests    
   test_codeMarkers.R............    0 tests    
@@ -337,7 +337,7 @@
   test_codeMarkers.R............   41 tests OK 
   test_codeMarkers.R............   42 tests OK 
   test_codeMarkers.R............   43 tests OK 
-  test_codeMarkers.R............   44 tests OK 78ms
+  test_codeMarkers.R............   44 tests OK 74ms
   
   test_gData.R..................    0 tests    
   test_gData.R..................    0 tests    
> library(data.table, lib.loc=R.home("library"))
> (sig.diff.dt <- myDiff(Rvers))
Key: <checking>
Empty data.table (0 rows and 3 cols): checking,master,release
> 
> ## If there are significant differences, use git bisect to find when
> ## they started.
> if(nrow(sig.diff.dt)){
+   dt.git <- file.path(task.dir, "data.table.git")
+   system(paste("cd ~/R/data.table && git fetch --tags"))
+   system(paste("git clone ~/R/data.table", dt.git))
+   release.tag <- gsub(".tar.gz|.*_", "", cargs[["release"]])
+   rev.parse.cmd <- paste(
+     "cd", dt.git, "&& git rev-parse master")
+   master.sha <- system(rev.parse.cmd, intern=TRUE)
+   merge.base.cmd <- paste(
+     "cd", dt.git, "&& git merge-base master", release.tag)
+   merge.base.sha <- system(merge.base.cmd, intern=TRUE)
+   old.sha <- merge.base.sha
+   run_R <- file.path(proj.dir, "install_dt_then_check_dep.R")
+   sig.diff.dt[, first.bad.commit := NA_character_]
+   sig.diff.dt[, comments := NA_character_]
+   for(diff.i in 1:nrow(sig.diff.dt)){
+     sig.diff.row <- sig.diff.dt[diff.i]
+     bisect.cmd <- paste(
+       "cd", dt.git, "&&",
+       "git bisect start &&",
+       "git bisect old", old.sha, "&&",
+       "git bisect new master &&",
+       "git bisect run",
+       R.home('bin/Rscript'),
+       run_R,
+       shQuote(sig.diff.row$checking),
+       sig.diff.row$release,
+       rev.dep.release.tar.gz,
+       release.tag)
+     print(bisect.cmd)
+     bisect.out <- system(bisect.cmd, intern=TRUE)
+     cat(bisect.out,sep="\n")
+     if(is.null(attr(bisect.out,"status"))){
+       first.bad.sha <- nc::capture_all_str(
+         bisect.out,
+         sha="[0-9a-f]+",
+         " is the first new commit")$sha
+       parent.cmd <- paste(
+         "cd ~/R/data.table && git log --pretty=%P -n 1",
+         first.bad.sha)
+       parent.sha <- system(parent.cmd, intern=TRUE)
+       sig.diff.dt[diff.i, first.bad.commit := first.bad.sha]
+       parent.msg <- paste0("parent=", parent.sha)
+       this.comment <- if(parent.sha==old.sha){
+         paste(parent.msg, "same as git bisect old")
+       }else if(first.bad.sha==master.sha){
+         paste("same as git bisect new=master,", parent.msg)
+       }else{
+         parent.msg
+       }
+       sig.diff.dt[diff.i, comments := this.comment]
+     }
+   }
+   ## add CRAN column.
+   sig.diff.dt[, CRAN := {
+     flavor <- get_flavor(Rvers)
+     details <- data.table(flavor=unique(flavor))[, {
+       base <- "https://www.r-project.org/nosvn/R.check/"
+       u <- paste0(base, flavor, "/", rev.dep, "-00check.txt")
+       check.txt <- tempfile()
+       tryCatch({
+         download.file(u, check.txt, quiet=TRUE)
+       }, error=function(e){
+         NULL
+       })
+       check.lines <- if(file.exists(check.txt)){
+         readLines(check.txt,encoding="UTF-8")
+       }else{
+         ""
+       }
+       repl.lines <- gsub("[\u2018\u2019]", "'", check.lines)
+       ##gsub("[‘’]", "'", check.lines) does not work with LC_ALL=C.
+       myStatus(line.vec=repl.lines)
+     }, by=flavor]
+     select.dt <- data.table(flavor, checking)
+     details[select.dt, msg, on=.(flavor, checking)]
+   }]
+   dir.create(file.path(job.dir, Rvers))
+   diffs.csv <- file.path(job.dir, Rvers, "significant_differences.csv")
+   data.table::fwrite(sig.diff.dt, diffs.csv)
+   print(sig.diff.dt)
+ }
> 
WARNING: ignoring environment value of R_HOME

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

> cargs <- commandArgs(trailingOnly=TRUE)
> if(length(cargs)==0){
+   ## before running interactively, make sure to start emacs/R with
+   ## environment defined in /scratch/...check_one.sh, particularly
+   ## R_LIBS_USER=/tmp/... otherwise we get error when installing
+   ## data.table.
+   base <- "/scratch/th798/data.table-revdeps/*"
+   cargs <- c(
+     Sys.glob(file.path(base,"deps.csv")),
+     "349",
+     Sys.glob(file.path(base, "data.table_release_*tar.gz")),
+     Sys.glob(file.path(base, "data.table_master_*tar.gz"))
+   )
+ }
> names(cargs) <- c("deps.csv", "task.str", "release", "master")
> dput(cargs)
c(deps.csv = "/scratch/th798/data.table-revdeps/2025-07-05/deps.csv", 
task.str = "1392", release = "/scratch/th798/data.table-revdeps/2025-07-05/data.table_release_1.17.6.tar.gz", 
master = "/scratch/th798/data.table-revdeps/2025-07-05/data.table_master_1.17.99.1e2e3badae6cc19a5270112c3ad11e64ce279174.tar.gz"
)
> (task.dir <- dirname(.libPaths()[1]))#should be /tmp/th798/slurmid/R-vers
[1] "/tmp/th798/18314188/R-release/1392"
> if(requireNamespace("R.cache"))R.cache::getCachePath()
Loading required namespace: R.cache
[1] "/tmp/th798/18314188/R-release/1392/R.cache"
> task.id <- as.integer(cargs[["task.str"]])
> deps.df <- read.csv(cargs[["deps.csv"]])
> (rev.dep <- deps.df$Package[task.id])
[1] "statgenGWAS"
> job.dir <- file.path(dirname(cargs[["deps.csv"]]), "tasks", task.id)
> setwd(task.dir)
> .libPaths()
[1] "/tmp/th798/18314188/R-release/1392/library"
[2] "/projects/genomic-ml/R/R-release/library"  
> options(repos=c(#this should be in ~/.Rprofile too.
+   CRAN="http://cloud.r-project.org"))
> print(Sys.time())
[1] "2025-07-05 01:39:12 MST"
> install.time <- system.time({
+   install.packages(rev.dep, dep=TRUE)
+ })
Installing package into '/tmp/th798/18314188/R-release/1392/library'
(as 'lib' is unspecified)
also installing the dependencies 'memuse', 'pinfsc50', 'LMMsolver', 'sommer', 'tinytest', 'vcfR'

trying URL 'http://cloud.r-project.org/src/contrib/memuse_4.2-3.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/pinfsc50_1.3.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/LMMsolver_1.0.10.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/sommer_4.4.2.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/tinytest_1.4.1.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/vcfR_1.15.0.tar.gz'
trying URL 'http://cloud.r-project.org/src/contrib/statgenGWAS_1.0.12.tar.gz'
* installing *source* package 'memuse' ...
** this is package 'memuse' version '4.2-3'
** package 'memuse' successfully unpacked and MD5 sums checked
** using staged installation
checking for gcc... /packages/gcc/12.2.0-nnbserq/bin/gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether /packages/gcc/12.2.0-nnbserq/bin/gcc accepts -g... yes
checking for /packages/gcc/12.2.0-nnbserq/bin/gcc option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for features.h... yes
configure: creating ./config.status
config.status: creating src/meminfo/src/conf.h
** 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../inst/RNACI  -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 meminfo/src/cacheinfo.c -o meminfo/src/cacheinfo.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/RNACI  -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 meminfo/src/fileinfo.c -o meminfo/src/fileinfo.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/RNACI  -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 meminfo/src/platform.c -o meminfo/src/platform.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/RNACI  -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 meminfo/src/procinfo.c -o meminfo/src/procinfo.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/RNACI  -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 meminfo/src/raminfo.c -o meminfo/src/raminfo.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/RNACI  -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 meminfo/src/swapinfo.c -o meminfo/src/swapinfo.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/RNACI  -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 wrappers.c -o wrappers.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG -I../inst/RNACI  -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 memuse_native.c -o memuse_native.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 memuse.so meminfo/src/cacheinfo.o meminfo/src/fileinfo.o meminfo/src/platform.o meminfo/src/procinfo.o meminfo/src/raminfo.o meminfo/src/swapinfo.o wrappers.o memuse_native.o
installing to /tmp/th798/18314188/R-release/1392/library/00LOCK-memuse/00new/memuse/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 (memuse)
* installing *source* package 'pinfsc50' ...
** this is package 'pinfsc50' version '1.3.0'
** package 'pinfsc50' 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 (pinfsc50)
* installing *source* package 'LMMsolver' ...
** this is package 'LMMsolver' version '1.0.10'
** package 'LMMsolver' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c ADcholesky.cpp -o ADcholesky.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c AuxFun.cpp -o AuxFun.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c SparseMatrix.cpp -o SparseMatrix.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c cholesky.cpp -o cholesky.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 LMMsolver.so ADcholesky.o AuxFun.o RcppExports.o SparseMatrix.o cholesky.o
installing to /tmp/th798/18314188/R-release/1392/library/00LOCK-LMMsolver/00new/LMMsolver/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 (LMMsolver)
* installing *source* package 'sommer' ...
** this is package 'sommer' version '4.4.2'
** package 'sommer' 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 -DARMA_64BIT_WORD=1 -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I'/projects/genomic-ml/R/R-release/library/RcppArmadillo/include' -I'/projects/genomic-ml/R/R-release/library/RcppProgress/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c MNR.cpp -o MNR.o
In file included from /projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo:26,
                 from /projects/genomic-ml/R/R-release/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
                 from /projects/genomic-ml/R/R-release/library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from MNR.cpp:6:
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed'
  321 |   #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
      |                                                                                      ^
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead'
  326 |     #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
      |                                                                           ^
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: '#pragma message: INFO: see the documentation for details'
  329 |   #pragma message ("INFO: see the documentation for details")
      |                                                             ^
MNR.cpp: In function 'Rcpp::List ai_mme_sp(const arma::sp_mat&, const Rcpp::List&, const arma::vec&, const Rcpp::List&, const arma::sp_mat&, const Rcpp::List&, const Rcpp::List&, const arma::sp_mat&, const bool&, int, double, double, double, const Rcpp::List&, const Rcpp::List&, const arma::mat&, const arma::vec&, const arma::vec&, const arma::vec&, const bool&)':
MNR.cpp:1395:40: error: no matching function for call to 'stddev(const arma::sp_mat&)'
 1395 |   double stdy = arma::mean(arma::stddev(y0));
      |                            ~~~~~~~~~~~~^~~~
In file included from /projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo:503:
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/fn_stddev.hpp:33:1: note: candidate: 'template<class T1> typename arma::enable_if2<(arma::is_arma_type<T1>::value && arma::resolves_to_vector<T1>::yes), typename T1::pod_type>::result arma::stddev(const T1&, uword)'
   33 | stddev(const T1& X, const uword norm_type = 0)
      | ^~~~~~
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/fn_stddev.hpp:33:1: note:   template argument deduction/substitution failed:
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/fn_stddev.hpp: In substitution of 'template<class T1> typename arma::enable_if2<(arma::is_arma_type<T1>::value && arma::resolves_to_vector<T1>::yes), typename T1::pod_type>::result arma::stddev(const T1&, uword) [with T1 = arma::SpMat<double>]':
MNR.cpp:1395:40:   required from here
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/fn_stddev.hpp:33:1: error: no type named 'result' in 'struct arma::enable_if2<false, double>'
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/fn_stddev.hpp:51:1: note: candidate: 'template<class T1> typename arma::enable_if2<(arma::is_arma_type<T1>::value && arma::resolves_to_vector<T1>::no), const arma::mtOp<typename T1::pod_type, T1, arma::op_stddev> >::result arma::stddev(const T1&, uword)'
   51 | stddev(const T1& X, const uword norm_type = 0)
      | ^~~~~~
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/fn_stddev.hpp:51:1: note:   template argument deduction/substitution failed:
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/fn_stddev.hpp: In substitution of 'template<class T1> typename arma::enable_if2<(arma::is_arma_type<T1>::value && arma::resolves_to_vector<T1>::no), const arma::mtOp<typename T1::pod_type, T1, arma::op_stddev> >::result arma::stddev(const T1&, uword) [with T1 = arma::SpMat<double>]':
MNR.cpp:1395:40:   required from here
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/fn_stddev.hpp:51:1: error: no type named 'result' in 'struct arma::enable_if2<false, const arma::mtOp<double, arma::SpMat<double>, arma::op_stddev> >'
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/fn_stddev.hpp:69:1: note: candidate: 'template<class T1> typename arma::enable_if2<arma::is_arma_type<T1>::value, const arma::mtOp<typename T1::pod_type, T1, arma::op_stddev> >::result arma::stddev(const T1&, uword, uword)'
   69 | stddev(const T1& X, const uword norm_type, const uword dim)
      | ^~~~~~
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/fn_stddev.hpp:69:1: note:   template argument deduction/substitution failed:
MNR.cpp:1395:40: note:   candidate expects 3 arguments, 1 provided
 1395 |   double stdy = arma::mean(arma::stddev(y0));
      |                            ~~~~~~~~~~~~^~~~
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/fn_stddev.hpp:82:1: note: candidate: 'template<class T> typename arma::arma_scalar_only<T>::result arma::stddev(const T&)'
   82 | stddev(const T&)
      | ^~~~~~
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/fn_stddev.hpp:82:1: note:   template argument deduction/substitution failed:
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/fn_stddev.hpp: In substitution of 'template<class T> typename arma::arma_scalar_only<T>::result arma::stddev(const T&) [with T = arma::SpMat<double>]':
MNR.cpp:1395:40:   required from here
/projects/genomic-ml/R/R-release/library/RcppArmadillo/include/armadillo_bits/fn_stddev.hpp:82:1: error: no type named 'result' in 'struct arma::arma_scalar_only<arma::SpMat<double> >'
MNR.cpp:2133:28: error: no matching function for call to 'Rcpp::Vector<19>::create(Rcpp::traits::named_object<arma::Row<double> >, Rcpp::traits::named_object<arma::SpMat<double> >, Rcpp::traits::named_object<arma::Col<double> >, Rcpp::traits::named_object<arma::Col<double> >, Rcpp::traits::named_object<arma::Col<double> >, Rcpp::traits::named_object<arma::SpMat<double> >, Rcpp::traits::named_object<arma::field<arma::Mat<double> > >, Rcpp::traits::named_object<arma::Mat<double> >, Rcpp::traits::named_object<arma::Mat<double> >, Rcpp::traits::named_object<arma::Mat<double> >, Rcpp::traits::named_object<arma::field<arma::Mat<double> > >, Rcpp::traits::named_object<arma::field<arma::Mat<double> > >, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<double>, Rcpp::traits::named_object<bool>, Rcpp::traits::named_object<arma::field<arma::Mat<double> > >, Rcpp::traits::named_object<arma::Mat<double> >, Rcpp::traits::named_object<arma::Mat<double> >, Rcpp::traits::named_object<arma::Mat<double> >, Rcpp::traits::named_object<arma::Col<double> >, Rcpp::traits::named_object<arma::Mat<double> >)'
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
In file included from /projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/vector/Vector.h:1125,
                 from /projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/Vector.h:52,
                 from /projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp.h:40,
                 from /projects/genomic-ml/R/R-release/library/RcppArmadillo/include/RcppArmadillo.h:32:
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:70:23: note: candidate: 'template<class T1> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
   70 |         static Vector create(const T1& t1){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:70:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 1 argument, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:109:23: note: candidate: 'template<class T1, class T2> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&) [with T2 = T1; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
  109 |         static Vector create(const T1& t1, const T2& t2){                       // #nocov start
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:109:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 2 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:151:23: note: candidate: 'template<class T1, class T2, class T3> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&) [with T2 = T1; T3 = T2; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
  151 |         static Vector create(const T1& t1, const T2& t2, const T3& t3){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:151:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 3 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:196:23: note: candidate: 'template<class T1, class T2, class T3, class T4> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&) [with T2 = T1; T3 = T2; T4 = T3; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
  196 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:196:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 4 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:244:23: note: candidate: 'template<class T1, class T2, class T3, class T4, class T5> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&) [with T2 = T1; T3 = T2; T4 = T3; T5 = T4; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
  244 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4, const T5& t5){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:244:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 5 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:291:23: note: candidate: 'template<class T1, class T2, class T3, class T4, class T5, class T6> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&) [with T2 = T1; T3 = T2; T4 = T3; T5 = T4; T6 = T5; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
  291 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4, const T5& t5, const T6& t6){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:291:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 6 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:340:23: note: candidate: 'template<class T1, class T2, class T3, class T4, class T5, class T6, class T7> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&) [with T2 = T1; T3 = T2; T4 = T3; T5 = T4; T6 = T5; T7 = T6; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
  340 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4, const T5& t5, const T6& t6, const T7& t7){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:340:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 7 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:391:23: note: candidate: 'template<class T1, class T2, class T3, class T4, class T5, class T6, class T7, class T8> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&) [with T2 = T1; T3 = T2; T4 = T3; T5 = T4; T6 = T5; T7 = T6; T8 = T7; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
  391 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4, const T5& t5, const T6& t6, const T7& t7, const T8& t8){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:391:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 8 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:444:23: note: candidate: 'template<class T1, class T2, class T3, class T4, class T5, class T6, class T7, class T8, class T9> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&) [with T2 = T1; T3 = T2; T4 = T3; T5 = T4; T6 = T5; T7 = T6; T8 = T7; T9 = T8; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
  444 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4, const T5& t5, const T6& t6, const T7& t7, const T8& t8, const T9& t9){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:444:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 9 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:499:23: note: candidate: 'template<class T1, class T2, class T3, class T4, class T5, class T6, class T7, class T8, class T9, class T10> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&, const T10&) [with T2 = T1; T3 = T2; T4 = T3; T5 = T4; T6 = T5; T7 = T6; T8 = T7; T9 = T8; T10 = T9; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
  499 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4, const T5& t5, const T6& t6, const T7& t7, const T8& t8, const T9& t9, const T10& t10){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:499:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 10 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:556:23: note: candidate: 'template<class T1, class T2, class T3, class T4, class T5, class T6, class T7, class T8, class T9, class T10, class T11> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&, const T10&, const T11&) [with T2 = T1; T3 = T2; T4 = T3; T5 = T4; T6 = T5; T7 = T6; T8 = T7; T9 = T8; T10 = T9; T11 = T10; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
  556 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4, const T5& t5, const T6& t6, const T7& t7, const T8& t8, const T9& t9, const T10& t10, const T11& t11){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:556:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 11 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:615:23: note: candidate: 'template<class T1, class T2, class T3, class T4, class T5, class T6, class T7, class T8, class T9, class T10, class T11, class T12> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&, const T10&, const T11&, const T12&) [with T2 = T1; T3 = T2; T4 = T3; T5 = T4; T6 = T5; T7 = T6; T8 = T7; T9 = T8; T10 = T9; T11 = T10; T12 = T11; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
  615 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4, const T5& t5, const T6& t6, const T7& t7, const T8& t8, const T9& t9, const T10& t10, const T11& t11, const T12& t12){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:615:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 12 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:676:23: note: candidate: 'template<class T1, class T2, class T3, class T4, class T5, class T6, class T7, class T8, class T9, class T10, class T11, class T12, class T13> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&, const T10&, const T11&, const T12&, const T13&) [with T2 = T1; T3 = T2; T4 = T3; T5 = T4; T6 = T5; T7 = T6; T8 = T7; T9 = T8; T10 = T9; T11 = T10; T12 = T11; T13 = T12; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
  676 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4, const T5& t5, const T6& t6, const T7& t7, const T8& t8, const T9& t9, const T10& t10, const T11& t11, const T12& t12, const T13& t13){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:676:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 13 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:739:23: note: candidate: 'template<class T1, class T2, class T3, class T4, class T5, class T6, class T7, class T8, class T9, class T10, class T11, class T12, class T13, class T14> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&, const T10&, const T11&, const T12&, const T13&, const T14&) [with T2 = T1; T3 = T2; T4 = T3; T5 = T4; T6 = T5; T7 = T6; T8 = T7; T9 = T8; T10 = T9; T11 = T10; T12 = T11; T13 = T12; T14 = T13; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
  739 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4, const T5& t5, const T6& t6, const T7& t7, const T8& t8, const T9& t9, const T10& t10, const T11& t11, const T12& t12, const T13& t13, const T14& t14){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:739:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 14 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:804:23: note: candidate: 'template<class T1, class T2, class T3, class T4, class T5, class T6, class T7, class T8, class T9, class T10, class T11, class T12, class T13, class T14, class T15> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&, const T10&, const T11&, const T12&, const T13&, const T14&, const T15&) [with T2 = T1; T3 = T2; T4 = T3; T5 = T4; T6 = T5; T7 = T6; T8 = T7; T9 = T8; T10 = T9; T11 = T10; T12 = T11; T13 = T12; T14 = T13; T15 = T14; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
  804 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4, const T5& t5, const T6& t6, const T7& t7, const T8& t8, const T9& t9, const T10& t10, const T11& t11, const T12& t12, const T13& t13, const T14& t14, const T15& t15){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:804:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 15 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:871:23: note: candidate: 'template<class T1, class T2, class T3, class T4, class T5, class T6, class T7, class T8, class T9, class T10, class T11, class T12, class T13, class T14, class T15, class T16> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&, const T10&, const T11&, const T12&, const T13&, const T14&, const T15&, const T16&) [with T2 = T1; T3 = T2; T4 = T3; T5 = T4; T6 = T5; T7 = T6; T8 = T7; T9 = T8; T10 = T9; T11 = T10; T12 = T11; T13 = T12; T14 = T13; T15 = T14; T16 = T15; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
  871 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4, const T5& t5, const T6& t6, const T7& t7, const T8& t8, const T9& t9, const T10& t10, const T11& t11, const T12& t12, const T13& t13, const T14& t14, const T15& t15, const T16& t16){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:871:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 16 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:940:23: note: candidate: 'template<class T1, class T2, class T3, class T4, class T5, class T6, class T7, class T8, class T9, class T10, class T11, class T12, class T13, class T14, class T15, class T16, class T17> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&, const T10&, const T11&, const T12&, const T13&, const T14&, const T15&, const T16&, const T17&) [with T2 = T1; T3 = T2; T4 = T3; T5 = T4; T6 = T5; T7 = T6; T8 = T7; T9 = T8; T10 = T9; T11 = T10; T12 = T11; T13 = T12; T14 = T13; T15 = T14; T16 = T15; T17 = T16; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
  940 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4, const T5& t5, const T6& t6, const T7& t7, const T8& t8, const T9& t9, const T10& t10, const T11& t11, const T12& t12, const T13& t13, const T14& t14, const T15& t15, const T16& t16, const T17& t17){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:940:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 17 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:1011:23: note: candidate: 'template<class T1, class T2, class T3, class T4, class T5, class T6, class T7, class T8, class T9, class T10, class T11, class T12, class T13, class T14, class T15, class T16, class T17, class T18> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&, const T10&, const T11&, const T12&, const T13&, const T14&, const T15&, const T16&, const T17&, const T18&) [with T2 = T1; T3 = T2; T4 = T3; T5 = T4; T6 = T5; T7 = T6; T8 = T7; T9 = T8; T10 = T9; T11 = T10; T12 = T11; T13 = T12; T14 = T13; T15 = T14; T16 = T15; T17 = T16; T18 = T17; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
 1011 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4, const T5& t5, const T6& t6, const T7& t7, const T8& t8, const T9& t9, const T10& t10, const T11& t11, const T12& t12, const T13& t13, const T14& t14, const T15& t15, const T16& t16, const T17& t17, const T18& t18){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:1011:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 18 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:1084:23: note: candidate: 'template<class T1, class T2, class T3, class T4, class T5, class T6, class T7, class T8, class T9, class T10, class T11, class T12, class T13, class T14, class T15, class T16, class T17, class T18, class T19> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&, const T10&, const T11&, const T12&, const T13&, const T14&, const T15&, const T16&, const T17&, const T18&, const T19&) [with T2 = T1; T3 = T2; T4 = T3; T5 = T4; T6 = T5; T7 = T6; T8 = T7; T9 = T8; T10 = T9; T11 = T10; T12 = T11; T13 = T12; T14 = T13; T15 = T14; T16 = T15; T17 = T16; T18 = T17; T19 = T18; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
 1084 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4, const T5& t5, const T6& t6, const T7& t7, const T8& t8, const T9& t9, const T10& t10, const T11& t11, const T12& t12, const T13& t13, const T14& t14, const T15& t15, const T16& t16, const T17& t17, const T18& t18, const T19& t19){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:1084:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 19 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:1159:23: note: candidate: 'template<class T1, class T2, class T3, class T4, class T5, class T6, class T7, class T8, class T9, class T10, class T11, class T12, class T13, class T14, class T15, class T16, class T17, class T18, class T19, class T20> static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create(const T1&, const T2&, const T3&, const T4&, const T5&, const T6&, const T7&, const T8&, const T9&, const T10&, const T11&, const T12&, const T13&, const T14&, const T15&, const T16&, const T17&, const T18&, const T19&, const T20&) [with T2 = T1; T3 = T2; T4 = T3; T5 = T4; T6 = T5; T7 = T6; T8 = T7; T9 = T8; T10 = T9; T11 = T10; T12 = T11; T13 = T12; T14 = T13; T15 = T14; T16 = T15; T17 = T16; T18 = T17; T19 = T18; T20 = T19; int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
 1159 |         static Vector create(const T1& t1, const T2& t2, const T3& t3, const T4& t4, const T5& t5, const T6& t6, const T7& t7, const T8& t8, const T9& t9, const T10& t10, const T11& t11, const T12& t12, const T13& t13, const T14& t14, const T15& t15, const T16& t16, const T17& t17, const T18& t18, const T19& t19, const T20& t20){
      |                       ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/generated/Vector__create.h:1159:23: note:   template argument deduction/substitution failed:
MNR.cpp:2133:28: note:   candidate expects 20 arguments, 21 provided
 2133 |   return Rcpp::List::create(
      |          ~~~~~~~~~~~~~~~~~~^
 2134 |     Rcpp::Named("llik") = llik,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2135 |     // Rcpp::Named("M") = M,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~
 2136 |     Rcpp::Named("W") = W,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2137 |     Rcpp::Named("b") = b,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2138 |     Rcpp::Named("u") = u,
      |     ~~~~~~~~~~~~~~~~~~~~~   
 2139 |     Rcpp::Named("bu") = bu,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2140 |     Rcpp::Named("Ci") = Ci,
      |     ~~~~~~~~~~~~~~~~~~~~~~~ 
 2141 |     Rcpp::Named("theta") = theta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2142 |     Rcpp::Named("theta_se") = InfMatInv,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2143 |     Rcpp::Named("InfMat") = InfMat, //InfMat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2144 |     Rcpp::Named("monitor") = monitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2145 |     // Rcpp::Named("constraints") = thetaCUnlistedFinal,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2146 |     Rcpp::Named("uList") = uList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2147 |     Rcpp::Named("uPevList") = uPevList,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2148 |     Rcpp::Named("AIC") = AIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2149 |     Rcpp::Named("BIC") = BIC,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~
 2150 |     Rcpp::Named("convergence") = convergence,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2151 |     Rcpp::Named("partitions") = partitions,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2152 |     Rcpp::Named("percDelta") = percDelta,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2153 |     Rcpp::Named("normMonitor") = normMonitor,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2154 |     Rcpp::Named("toBoundary") = toBoundary,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2155 |     Rcpp::Named("dLu") = dLuOut,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2156 |     Rcpp::Named("Cchol") = Mchol_XZ
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2157 |     // Rcpp::Named("PMWu_mat") = PMWu_mat,
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2158 |     // Rcpp::Named("MWuchol") = MWuchol
      |     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 2159 |   );
      |   ~                         
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/vector/Vector.h:1121:19: note: candidate: 'static Rcpp::Vector<RTYPE, StoragePolicy> Rcpp::Vector<RTYPE, StoragePolicy>::create() [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]'
 1121 |     static Vector create(){
      |                   ^~~~~~
/projects/genomic-ml/R/R-release/library/Rcpp/include/Rcpp/vector/Vector.h:1121:19: note:   candidate expects 0 arguments, 21 provided
make: *** [/home/th798/R/R-release/etc/Makeconf:211: MNR.o] Error 1
ERROR: compilation failed for package 'sommer'
* removing '/tmp/th798/18314188/R-release/1392/library/sommer'
* installing *source* package 'tinytest' ...
** this is package 'tinytest' version '1.4.1'
** package 'tinytest' 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
** 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 (tinytest)
* installing *source* package 'vcfR' ...
** this is package 'vcfR' version '1.15.0'
** package 'vcfR' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++ (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c NM2winNM.cpp -o NM2winNM.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c RcppExports.cpp -o RcppExports.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c ad_frequency.cpp -o ad_frequency.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c deprecated_funcs.cpp -o deprecated_funcs.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c extract_gt.cpp -o extract_gt.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c freq_peak.cpp -o freq_peak.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c gt_to_popsum.cpp -o gt_to_popsum.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c is_het.cpp -o is_het.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c masplit.cpp -o masplit.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c pair_sort.cpp -o pair_sort.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c rank_variants.cpp -o rank_variants.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c read_vcfR.cpp -o read_vcfR.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c seq_to_rects.cpp -o seq_to_rects.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c var_window.cpp -o var_window.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c vcfRCommon.cpp -o vcfRCommon.o
/packages/gcc/12.2.0-nnbserq/bin/g++ -std=gnu++17 -I"/home/th798/R/R-release/include" -DNDEBUG  -I'/projects/genomic-ml/R/R-release/library/Rcpp/include' -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include    -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include   -c write_vcfR.cpp -o write_vcfR.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 vcfR.so NM2winNM.o RcppExports.o ad_frequency.o deprecated_funcs.o extract_gt.o freq_peak.o gt_to_popsum.o is_het.o masplit.o pair_sort.o rank_variants.o read_vcfR.o seq_to_rects.o var_window.o vcfRCommon.o write_vcfR.o -lz
installing to /tmp/th798/18314188/R-release/1392/library/00LOCK-vcfR/00new/vcfR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'rbind' from package 'base' in package 'vcfR'
Creating a generic function for 'nrow' from package 'base' in package 'vcfR'
** 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 (vcfR)
ERROR: dependency 'sommer' is not available for package 'statgenGWAS'
Perhaps try a variation of:
install.packages('sommer')
* removing '/tmp/th798/18314188/R-release/1392/library/statgenGWAS'

The downloaded source packages are in
	'/tmp/th798/18314188/RtmptgFIzl/downloaded_packages'
Warning messages:
1: In install.packages(rev.dep, dep = TRUE) :
  installation of package 'sommer' had non-zero exit status
2: In install.packages(rev.dep, dep = TRUE) :
  installation of package 'statgenGWAS' had non-zero exit status
> cat("Time to install revdep:\n")
Time to install revdep:
> print(install.time)
   user  system elapsed 
119.658  12.898 141.809 
> print(Sys.time())
[1] "2025-07-05 01:41:34 MST"
> downloaded_packages <- file.path(
+   tempdir(),
+   "downloaded_packages")
> dl.glob <- file.path(
+   downloaded_packages,
+   paste0(rev.dep,"_*.tar.gz"))
> rev.dep.dl.row <- cbind(rev.dep, Sys.glob(dl.glob))
> colnames(rev.dep.dl.row) <- c("pkg","path")
> rev.dep.release.tar.gz <- normalizePath(rev.dep.dl.row[,"path"], mustWork=TRUE)
> pkg.Rcheck <- paste0(rev.dep, ".Rcheck")
> 
> proj.dir <- "~/genomic-ml/data.table-revdeps"
> source(file.path(proj.dir, "myStatus.R"))
> Rvers <- gsub("[()]", "", gsub(" ", "_", R.version[["version.string"]]))
> dir.create(Rvers, showWarnings=FALSE)
> Rcheck.list <- list()
> for(dt.version.short in c("release", "master")){
+   dt.tar.gz <- cargs[[dt.version.short]]
+   dt.version <- gsub(".tar.gz|/.*?_", "", dt.tar.gz)
+   print(Sys.time())
+   install.packages(dt.tar.gz, repos=NULL)
+   print(Sys.time())
+   check.cmd <- get_check_cmd(rev.dep.release.tar.gz)
+   system(check.cmd)
+   print(Sys.time())
+   dest.Rcheck <- file.path(
+     Rvers,
+     paste0(dt.version, ".Rcheck"))
+   unlink(dest.Rcheck, recursive=TRUE)
+   file.rename(pkg.Rcheck, dest.Rcheck)
+   Rcheck.list[[dt.version]] <- file.path(dest.Rcheck, "00check.log")
+ }
[1] "2025-07-05 01:41:34 MST"
Installing package into '/tmp/th798/18314188/R-release/1392/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** this is package 'data.table' version '1.17.6'
** package 'data.table' successfully unpacked and MD5 sums checked
** using staged installation
zlib 1.2.13 is available ok
* checking if R installation supports OpenMP without any extra hints... yes
** libs
using C compiler: 'gcc (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c assign.c -o assign.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c between.c -o between.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c bmerge.c -o bmerge.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c chmatch.c -o chmatch.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c cj.c -o cj.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c coalesce.c -o coalesce.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c dogroups.c -o dogroups.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fastmean.c -o fastmean.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fcast.c -o fcast.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fifelse.c -o fifelse.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fmelt.c -o fmelt.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c forder.c -o forder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frank.c -o frank.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fread.c -o fread.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c freadR.c -o freadR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c froll.c -o froll.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frollR.c -o frollR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frolladaptive.c -o frolladaptive.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fsort.c -o fsort.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwrite.c -o fwrite.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwriteR.c -o fwriteR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c gsumm.c -o gsumm.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c idatetime.c -o idatetime.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ijoin.c -o ijoin.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c init.c -o init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c inrange.c -o inrange.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nafill.c -o nafill.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c negate.c -o negate.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nqrecreateindices.c -o nqrecreateindices.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c openmp-utils.c -o openmp-utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c programming.c -o programming.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c quickselect.c -o quickselect.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c rbindlist.c -o rbindlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c reorder.c -o reorder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c shift.c -o shift.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c snprintf.c -o snprintf.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c subset.c -o subset.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c transpose.c -o transpose.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c types.c -o types.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c uniqlist.c -o uniqlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c utils.c -o utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c vecseq.c -o vecseq.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c wrappers.c -o wrappers.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include
PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi
installing to /tmp/th798/18314188/R-release/1392/library/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (data.table)
[1] "2025-07-05 01:42:03 MST"
* using log directory '/tmp/th798/18314188/R-release/1392/statgenGWAS.Rcheck'
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Spack GCC) 12.2.0
    GNU Fortran (Spack GCC) 12.2.0
* running under: Red Hat Enterprise Linux 8.10 (Ootpa)
* using session charset: ASCII
* checking for file 'statgenGWAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'statgenGWAS' version '1.0.12'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package required but not available: 'sommer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
* DONE

Status: 1 ERROR
See
  '/tmp/th798/18314188/R-release/1392/statgenGWAS.Rcheck/00check.log'
for details.

[1] "2025-07-05 01:42:08 MST"
[1] "2025-07-05 01:42:08 MST"
Installing package into '/tmp/th798/18314188/R-release/1392/library'
(as 'lib' is unspecified)
* installing *source* package 'data.table' ...
** this is package 'data.table' version '1.17.99'
** using staged installation
zlib 1.2.13 is available ok
* checking if R installation supports OpenMP without any extra hints... yes
** libs
using C compiler: 'gcc (Spack GCC) 12.2.0'
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c assign.c -o assign.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c between.c -o between.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c bmerge.c -o bmerge.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c chmatch.c -o chmatch.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c cj.c -o cj.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c coalesce.c -o coalesce.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c dogroups.c -o dogroups.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fastmean.c -o fastmean.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fcast.c -o fcast.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fifelse.c -o fifelse.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fmelt.c -o fmelt.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c forder.c -o forder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frank.c -o frank.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fread.c -o fread.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c freadR.c -o freadR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c froll.c -o froll.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frollR.c -o frollR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c frolladaptive.c -o frolladaptive.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fsort.c -o fsort.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwrite.c -o fwrite.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c fwriteR.c -o fwriteR.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c gsumm.c -o gsumm.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c idatetime.c -o idatetime.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c ijoin.c -o ijoin.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c init.c -o init.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c inrange.c -o inrange.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c mergelist.c -o mergelist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nafill.c -o nafill.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c negate.c -o negate.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c nqrecreateindices.c -o nqrecreateindices.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c openmp-utils.c -o openmp-utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c programming.c -o programming.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c quickselect.c -o quickselect.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c rbindlist.c -o rbindlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c reorder.c -o reorder.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c shift.c -o shift.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c snprintf.c -o snprintf.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c subset.c -o subset.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c transpose.c -o transpose.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c types.c -o types.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c uniqlist.c -o uniqlist.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c utils.c -o utils.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c vecseq.c -o vecseq.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -I"/home/th798/R/R-release/include" -DNDEBUG   -I/home/th798/.conda/envs/emacs1/include -I/home/th798/include   -fopenmp -I/home/th798/.conda/envs/emacs1/include -fpic  -I/packages/gcc/12.2.0-nnbserq/include -I/packages/zstd/1.5.2-cs5ansz/include -I/packages/zlib/1.2.13-po6bkge/include -I/packages/mpc/1.2.1-nnfoiwh/include -I/packages/mpfr/4.1.0-yfsqqka/include -I/packages/gmp/6.2.1-7ydtie6/include  -c wrappers.c -o wrappers.o
/packages/gcc/12.2.0-nnbserq/bin/gcc -shared -L/home/th798/.conda/envs/emacs1/lib -Wl,-rpath=/home/th798/.conda/envs/emacs1/lib -L/home/th798/lib -Wl,-rpath=/home/th798/lib -L/home/th798/lib64 -Wl,-rpath=/home/th798/lib64 -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o idatetime.o ijoin.o init.o inrange.o mergelist.o nafill.o negate.o nqrecreateindices.o openmp-utils.o programming.o quickselect.o rbindlist.o reorder.o shift.o snprintf.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
PKG_CFLAGS = -fopenmp -I/home/th798/.conda/envs/emacs1/include
PKG_LIBS = -fopenmp -L/home/th798/.conda/envs/emacs1/lib -lz
if [ "data.table.so" != "data_table.so" ]; then mv data.table.so data_table.so; fi
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id data_table.so data_table.so; fi
installing to /tmp/th798/18314188/R-release/1392/library/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (data.table)
[1] "2025-07-05 01:42:36 MST"
* using log directory '/tmp/th798/18314188/R-release/1392/statgenGWAS.Rcheck'
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Spack GCC) 12.2.0
    GNU Fortran (Spack GCC) 12.2.0
* running under: Red Hat Enterprise Linux 8.10 (Ootpa)
* using session charset: ASCII
* checking for file 'statgenGWAS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'statgenGWAS' version '1.0.12'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package required but not available: 'sommer'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
* DONE

Status: 1 ERROR
See
  '/tmp/th798/18314188/R-release/1392/statgenGWAS.Rcheck/00check.log'
for details.

[1] "2025-07-05 01:42:41 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)
+ }
>