* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’ * installing *source* package ‘vcfppR’ ... ** package ‘vcfppR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘Debian clang version 18.1.4 (1)’ make[1]: Entering directory '/tmp/RtmpJTFsTq/R.INSTALL94a891b90857a/vcfppR/src' clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'htslib-1.19.1' -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 RcppExports.cpp -o RcppExports.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'htslib-1.19.1' -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 vcf-popgen.cpp -o vcf-popgen.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'htslib-1.19.1' -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 vcf-reader.cpp -o vcf-reader.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'htslib-1.19.1' -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 vcf-stats.cpp -o vcf-stats.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'htslib-1.19.1' -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 vcf-table.cpp -o vcf-table.o clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I. -I'htslib-1.19.1' -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 vcf-writer.cpp -o vcf-writer.o (cd 'htslib-1.19.1' && make -f Makefile.vcfppR libhts.a && cd ..) make[2]: Entering directory '/tmp/RtmpJTFsTq/R.INSTALL94a891b90857a/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 clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o kfunc.o kfunc.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o kstring.o kstring.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o bcf_sr_sort.o bcf_sr_sort.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o bgzf.o bgzf.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o errmod.o errmod.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o faidx.o faidx.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o header.o header.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o hfile.o hfile.c 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' \ 'clang-18' \ '' \ '-g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes' \ '-Wl,-O1 -fvisibility=hidden' \ '-lz -lm -lbz2 -llzma -lcurl' > config_vars.h clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o hts.o hts.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o hts_expr.o hts_expr.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o hts_os.o hts_os.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o md5.o md5.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o multipart.o multipart.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o probaln.o probaln.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o realn.o realn.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o regidx.o regidx.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o region.o region.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o sam.o sam.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o sam_mods.o sam_mods.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o synced_bcf_reader.o synced_bcf_reader.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o vcf_sweep.o vcf_sweep.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o tbx.o tbx.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o textutils.o textutils.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o thread_pool.o thread_pool.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o vcf.o vcf.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o vcfutils.o vcfutils.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/cram_codecs.o cram/cram_codecs.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/cram_decode.o cram/cram_decode.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/cram_encode.o cram/cram_encode.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/cram_external.o cram/cram_external.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/cram_index.o cram/cram_index.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/cram_io.o cram/cram_io.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/cram_stats.o cram/cram_stats.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/mFILE.o cram/mFILE.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/open_trace_file.o cram/open_trace_file.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o cram/string_alloc.o cram/string_alloc.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c clang-18 -g -O3 -Wall -pedantic -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. clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c clang-18 -g -O3 -Wall -pedantic -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. clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c clang-18 -g -O3 -Wall -pedantic -fpic -fvisibility=hidden -Wstrict-prototypes -I. -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[2]: Leaving directory '/tmp/RtmpJTFsTq/R.INSTALL94a891b90857a/vcfppR/src/htslib-1.19.1' clang++-18 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -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 -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR make[1]: Leaving directory '/tmp/RtmpJTFsTq/R.INSTALL94a891b90857a/vcfppR/src' make[1]: Entering directory '/tmp/RtmpJTFsTq/R.INSTALL94a891b90857a/vcfppR/src' make[1]: Leaving directory '/tmp/RtmpJTFsTq/R.INSTALL94a891b90857a/vcfppR/src' installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/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)