Install log for 'DEploid'

* installing *source* package ‘DEploid’ ...
** package ‘DEploid’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 19.1.3’
using C++ compiler: ‘clang version 19.1.3’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/DEploid/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c rvcf.cpp -o rvcf.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c dEploidr.cpp -o dEploidr.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c test_exports.cpp -o test_exports.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c RcppExports.cpp -o RcppExports.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c init.c -o init.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/dEploidIO.cpp -o DEploid/dEploidIO.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/ibd.cpp -o DEploid/ibd.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/mcmc.cpp -o DEploid/mcmc.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/panel.cpp -o DEploid/panel.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/txtReader.cpp -o DEploid/txtReader.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/updateHap.cpp -o DEploid/updateHap.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/utility.cpp -o DEploid/utility.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/variantIndex.cpp -o DEploid/variantIndex.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/vcfReader.cpp -o DEploid/vcfReader.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/gzstream/gzstream.cpp -o DEploid/gzstream/gzstream.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/random/fastfunc.cpp -o DEploid/random/fastfunc.o
DEploid/vcfReader.cpp:344:9: warning: variable 'field_index' set but not used [-Wunused-but-set-variable]
  344 |     int field_index = 0;
      |         ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/random/random_generator.cpp -o DEploid/random/random_generator.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/random/mersenne_twister.cpp -o DEploid/random/mersenne_twister.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/export/dEploidIOExportPosteriorProb.cpp -o DEploid/export/dEploidIOExportPosteriorProb.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/export/writeMcmcRelated.cpp -o DEploid/export/writeMcmcRelated.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/lasso/dEploidLasso.cpp -o DEploid/lasso/dEploidLasso.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/lasso/lasso.cpp -o DEploid/lasso/lasso.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/lasso/lassoDBG.cpp -o DEploid/lasso/lassoDBG.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/debug/vcfReaderDebug.cpp -o DEploid/debug/vcfReaderDebug.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include   -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c DEploid/debug/mcmcDebug.cpp -o DEploid/debug/mcmcDebug.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o DEploid.so rvcf.o dEploidr.o test_exports.o RcppExports.o init.o DEploid/dEploidIO.o DEploid/ibd.o DEploid/mcmc.o DEploid/panel.o DEploid/txtReader.o DEploid/updateHap.o DEploid/utility.o DEploid/variantIndex.o DEploid/vcfReader.o DEploid/gzstream/gzstream.o DEploid/random/fastfunc.o DEploid/random/random_generator.o DEploid/random/mersenne_twister.o DEploid/export/dEploidIOExportPosteriorProb.o DEploid/export/writeMcmcRelated.o DEploid/lasso/dEploidLasso.o DEploid/lasso/lasso.o DEploid/lasso/lassoDBG.o DEploid/debug/vcfReaderDebug.o DEploid/debug/mcmcDebug.o -lz
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/DEploid/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/DEploid/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/DEploid/src'
installing to /data/gannet/ripley/R/packages/tests-clang/DEploid.Rcheck/00LOCK-DEploid/00new/DEploid/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 (DEploid)