* installing *source* package ‘vcfppR’ ...
** package ‘vcfppR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 18.1.4’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/vcfppR/src'
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'htslib-1.19.1' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'htslib-1.19.1' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c vcf-popgen.cpp -o vcf-popgen.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'htslib-1.19.1' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c vcf-reader.cpp -o vcf-reader.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'htslib-1.19.1' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c vcf-stats.cpp -o vcf-stats.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'htslib-1.19.1' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c vcf-table.cpp -o vcf-table.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I. -I'htslib-1.19.1' -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c vcf-writer.cpp -o vcf-writer.o
(cd 'htslib-1.19.1' && make -f Makefile.vcfppR libhts.a && cd ..)
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/vcfppR/src/htslib-1.19.1'
echo '/* Default config.h generated by Makefile */' > config.h
echo '#ifndef _XOPEN_SOURCE' >> config.h
echo '#define _XOPEN_SOURCE 600' >> config.h
echo '#endif' >> config.h
echo '#define HAVE_LIBBZ2 1' >> config.h
echo '#define HAVE_LIBLZMA 1' >> config.h
echo '#ifndef __APPLE__' >> config.h
echo '#define HAVE_LZMA_H 1' >> config.h
echo '#endif' >> config.h
echo '#define HAVE_DRAND48 1' >> config.h
echo '#define HAVE_LIBCURL 1' >> config.h
if [ "x" != "x" ]; then \
echo '#if defined(HTS_ALLOW_UNALIGNED) && HTS_ALLOW_UNALIGNED == 0' >> config.h ; \
echo '#define UBSAN 1' >> config.h ; \
echo '#endif' >> config.h ; \
fi
if [ "x" != "x" ] ; then \
echo '#define HAVE_AVX2 1' >> config.h ; \
fi
if [ "x" != "x" ] ; then \
echo '#define HAVE_AVX512 1' >> config.h ; \
fi
echo '#define HTS_VERSION_TEXT "1.19.1"' > 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' \
'/usr/local/clang18/bin/clang' \
'' \
'-O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes' \
'-L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -fvisibility=hidden' \
'-lz -lm -lbz2 -llzma -lcurl' > config_vars.h
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o hts_expr.o hts_expr.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o hts_os.o hts_os.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o md5.o md5.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o multipart.o multipart.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o probaln.o probaln.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o realn.o realn.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o regidx.o regidx.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o region.o region.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o sam.o sam.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o sam_mods.o sam_mods.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o vcf_sweep.o vcf_sweep.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o tbx.o tbx.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o textutils.o textutils.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o thread_pool.o thread_pool.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o vcf.o vcf.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o vcfutils.o vcfutils.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/cram_decode.o cram/cram_decode.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/cram_encode.o cram/cram_encode.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/cram_external.o cram/cram_external.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/cram_index.o cram/cram_index.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/cram_io.o cram/cram_io.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/cram_stats.o cram/cram_stats.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/mFILE.o cram/mFILE.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/string_alloc.o cram/string_alloc.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
htscodecs/htscodecs/fqzcomp_qual.c:274:13: warning: unused function 'dump_params' [-Wunused-function]
274 | static void dump_params(fqz_gparams *gp) {
| ^~~~~~~~~~~
1 warning generated.
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
htscodecs/htscodecs/rANS_static4x16pr.c:929:13: warning: variable 'use_gather' set but not used [-Wunused-but-set-variable]
929 | int use_gather;
| ^
htscodecs/htscodecs/rANS_static4x16pr.c:899:9: warning: variable 'have_e_sse4_1' set but not used [-Wunused-but-set-variable]
899 | int have_e_sse4_1 = have_sse4_1;
| ^
htscodecs/htscodecs/rANS_static4x16pr.c:901:9: warning: variable 'have_e_avx512f' set but not used [-Wunused-but-set-variable]
901 | int have_e_avx512f = have_avx512f;
| ^
htscodecs/htscodecs/rANS_static4x16pr.c:973:9: warning: variable 'have_d_sse4_1' set but not used [-Wunused-but-set-variable]
973 | int have_d_sse4_1 = have_sse4_1;
| ^
htscodecs/htscodecs/rANS_static4x16pr.c:974:9: warning: variable 'have_d_avx2' set but not used [-Wunused-but-set-variable]
974 | int have_d_avx2 = have_avx2;
| ^
htscodecs/htscodecs/rANS_static4x16pr.c:975:9: warning: variable 'have_d_avx512f' set but not used [-Wunused-but-set-variable]
975 | int have_d_avx512f = have_avx512f;
| ^
6 warnings generated.
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o hfile_libcurl.o hfile_libcurl.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o kfunc.o kfunc.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o kstring.o kstring.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o bcf_sr_sort.o bcf_sr_sort.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o bgzf.o bgzf.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o errmod.o errmod.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o faidx.o faidx.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o header.o header.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o hfile.o hfile.c
/usr/local/clang18/bin/clang -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o hts.o hts.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[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/vcfppR/src/htslib-1.19.1'
/usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o vcfppR.so RcppExports.o vcf-popgen.o vcf-reader.o vcf-stats.o vcf-table.o vcf-writer.o htslib-1.19.1/libhts.a -fPIC -lz -lm -lbz2 -llzma -lcurl
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/vcfppR/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/vcfppR/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/vcfppR/src'
installing to /data/gannet/ripley/R/packages/tests-clang/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)