* installing *source* package ‘vcfppR’ ...
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 16.0.6 (15)’
using C++11
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Ihtslib-1.18 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c RcppExports.cpp -o RcppExports.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Ihtslib-1.18 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c vcfpp-filter.cpp -o vcfpp-filter.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Ihtslib-1.18 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c vcfpp-popgen.cpp -o vcfpp-popgen.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Ihtslib-1.18 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c vcfpp-read.cpp -o vcfpp-read.o
clang++-16  -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -Ihtslib-1.18 -I'/home/hornik/lib/R/Library/4.4/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O3 -Wall -pedantic -Wno-error=enum-constexpr-conversion -c vcfpp-stats.cpp -o vcfpp-stats.o
(cd htslib-1.18 && make libhts.a CXX="clang++-16  -std=gnu++11" CC="clang-16 " CPPFLAGS="-I/usr/local/include -fPIC " && cd ..)
make[1]: Entering directory '/srv/hornik/tmp/CRAN/vcfppR.Rcheck/00_pkg_src/vcfppR/src/htslib-1.18'
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o kfunc.o kfunc.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o kstring.o kstring.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o bcf_sr_sort.o bcf_sr_sort.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o bgzf.o bgzf.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o errmod.o errmod.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o faidx.o faidx.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o header.o header.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.18"' > version.h
printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \
'clang-16 ' \
'-I/usr/local/include -fPIC ' \
'-g -Wall -O2 -fvisibility=hidden' \
'-fvisibility=hidden' \
'-lz -lm -lbz2 -llzma -lcurl' > config_vars.h
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o hts.o hts.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o hts_expr.o hts_expr.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o hts_os.o hts_os.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o md5.o md5.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o multipart.o multipart.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o probaln.o probaln.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o realn.o realn.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o regidx.o regidx.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o region.o region.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o sam.o sam.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o sam_mods.o sam_mods.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o synced_bcf_reader.o synced_bcf_reader.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o vcf_sweep.o vcf_sweep.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o tbx.o tbx.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o textutils.o textutils.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o thread_pool.o thread_pool.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o vcf.o vcf.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o vcfutils.o vcfutils.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o cram/cram_codecs.o cram/cram_codecs.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o cram/cram_decode.o cram/cram_decode.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o cram/cram_encode.o cram/cram_encode.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o cram/cram_external.o cram/cram_external.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o cram/cram_index.o cram/cram_index.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o cram/cram_io.o cram/cram_io.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o cram/cram_stats.o cram/cram_stats.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o cram/mFILE.o cram/mFILE.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o cram/open_trace_file.o cram/open_trace_file.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o cram/string_alloc.o cram/string_alloc.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
clang-16  -g -Wall -O2 -fvisibility=hidden    -I. -I/usr/local/include -fPIC  -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
clang-16  -g -Wall -O2 -fvisibility=hidden  -I. -I/usr/local/include -fPIC  -c -o hfile_libcurl.o hfile_libcurl.c
ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o sam_mods.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o
ranlib libhts.a
make[1]: Leaving directory '/srv/hornik/tmp/CRAN/vcfppR.Rcheck/00_pkg_src/vcfppR/src/htslib-1.18'
clang++-16 -std=gnu++11 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o vcfppR.so RcppExports.o vcfpp-filter.o vcfpp-popgen.o vcfpp-read.o vcfpp-stats.o htslib-1.18/libhts.a -fPIC -lz -lbz2 -llzma -lcurl -L/home/hornik/tmp/R/lib -lR
installing to /srv/hornik/tmp/CRAN/vcfppR.Rcheck/00LOCK-vcfppR/00new/vcfppR/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 (vcfppR)