* installing *source* package ‘DEploid.utils’ ...
** package ‘DEploid.utils’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 19.1.6’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/DEploid.utils/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/ -Ivcf/ -Ivcf/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -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/ -Ivcf/ -Ivcf/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.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/ -Ivcf/ -Ivcf/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c vcf/txtReader.cpp -o vcf/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/ -Ivcf/ -Ivcf/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c vcf/variantIndex.cpp -o vcf/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/ -Ivcf/ -Ivcf/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c vcf/vcfReader.cpp -o vcf/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/ -Ivcf/ -Ivcf/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c vcf/gzstream/gzstream.cpp -o vcf/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/ -Ivcf/ -Ivcf/gzstream/ -DVERSION="\"R\"" -DRBUILD -DSTRICT_R_HEADERS -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -Wno-missing-template-arg-list-after-template-kw  -DR_NO_REMAP -c vcf/vcfReaderDebug.cpp -o vcf/vcfReaderDebug.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.
/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.utils.so rvcf.o RcppExports.o vcf/txtReader.o vcf/variantIndex.o vcf/vcfReader.o vcf/gzstream/gzstream.o vcf/vcfReaderDebug.o -lz
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/DEploid.utils/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/DEploid.utils/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/DEploid.utils/src'
installing to /data/gannet/ripley/R/packages/tests-clang/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)