Install log for 'DEploid'

* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘DEploid’ ...
** package ‘DEploid’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘Debian clang version 19.1.6 (1)’
using C++ compiler: ‘Debian clang version 19.1.6 (1)’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpyd86uV/R.INSTALL33b69964835b12/DEploid/src'
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c dEploidr.cpp -o dEploidr.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c test_exports.cpp -o test_exports.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang-19 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -c init.c -o init.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/dEploidIO.cpp -o DEploid/dEploidIO.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/ibd.cpp -o DEploid/ibd.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/mcmc.cpp -o DEploid/mcmc.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/panel.cpp -o DEploid/panel.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/updateHap.cpp -o DEploid/updateHap.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/utility.cpp -o DEploid/utility.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/vcf/src/txtReader.cpp -o DEploid/vcf/src/txtReader.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/vcf/src/variantIndex.cpp -o DEploid/vcf/src/variantIndex.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/vcf/src/vcfReader.cpp -o DEploid/vcf/src/vcfReader.o
DEploid/vcf/src/vcfReader.cpp:363:9: warning: variable 'field_index' set but not used [-Wunused-but-set-variable]
  363 |     int field_index = 0;
      |         ^
1 warning generated.
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/vcf/src/gzstream/gzstream.cpp -o DEploid/vcf/src/gzstream/gzstream.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/random/fastfunc.cpp -o DEploid/random/fastfunc.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/random/random_generator.cpp -o DEploid/random/random_generator.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/random/mersenne_twister.cpp -o DEploid/random/mersenne_twister.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/export/dEploidIOExportPosteriorProb.cpp -o DEploid/export/dEploidIOExportPosteriorProb.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/export/writeMcmcRelated.cpp -o DEploid/export/writeMcmcRelated.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/lasso/dEploidLasso.cpp -o DEploid/lasso/dEploidLasso.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/lasso/lasso.cpp -o DEploid/lasso/lasso.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/lasso/lassoDBG.cpp -o DEploid/lasso/lassoDBG.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/vcf/src/vcfReaderDebug.cpp -o DEploid/vcf/src/vcfReaderDebug.o
clang++-19 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/vcf/src/ -IDEploid/vcf/src/gzstream/ -IDEploid/lasso/  -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -Wno-missing-template-arg-list-after-template-kw -DR_NO_REMAP -c DEploid/debug/mcmcDebug.cpp -o DEploid/debug/mcmcDebug.o
clang++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o DEploid.so dEploidr.o test_exports.o RcppExports.o init.o DEploid/dEploidIO.o DEploid/ibd.o DEploid/mcmc.o DEploid/panel.o DEploid/updateHap.o DEploid/utility.o DEploid/vcf/src/txtReader.o DEploid/vcf/src/variantIndex.o DEploid/vcf/src/vcfReader.o DEploid/vcf/src/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/vcf/src/vcfReaderDebug.o DEploid/debug/mcmcDebug.o -lz -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpyd86uV/R.INSTALL33b69964835b12/DEploid/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpyd86uV/R.INSTALL33b69964835b12/DEploid/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpyd86uV/R.INSTALL33b69964835b12/DEploid/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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)