* installing *source* package ‘DEploid.utils’ ...
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 19.1.4 (1)’
clang++-19  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -Ivcf/ -Ivcf/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -DR_NO_REMAP -c rvcf.cpp -o rvcf.o
clang++-19  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -Ivcf/ -Ivcf/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++-19  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -Ivcf/ -Ivcf/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -DR_NO_REMAP -c vcf/txtReader.cpp -o vcf/txtReader.o
clang++-19  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -Ivcf/ -Ivcf/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -DR_NO_REMAP -c vcf/variantIndex.cpp -o vcf/variantIndex.o
clang++-19  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -Ivcf/ -Ivcf/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -DR_NO_REMAP -c vcf/vcfReader.cpp -o vcf/vcfReader.o
vcf/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-d-clang-19/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -Ivcf/ -Ivcf/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -DR_NO_REMAP -c vcf/gzstream/gzstream.cpp -o vcf/gzstream/gzstream.o
clang++-19  -std=gnu++17 -I"/home/hornik/tmp/R-d-clang-19/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -I/usr/share/R/include/ -Ivcf/ -Ivcf/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -g -O3 -Wall -pedantic -DR_NO_REMAP -c vcf/vcfReaderDebug.cpp -o vcf/vcfReaderDebug.o
clang++-19 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-clang-19/lib -Wl,-O1 -o DEploid.utils.so rvcf.o RcppExports.o vcf/txtReader.o vcf/variantIndex.o vcf/vcfReader.o vcf/gzstream/gzstream.o vcf/vcfReaderDebug.o -lz -L/home/hornik/tmp/R-d-clang-19/lib -lR
installing to /srv/hornik/tmp/CRAN_pretest/DEploid.utils.Rcheck/00LOCK-DEploid.utils/00new/DEploid.utils/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DEploid.utils)