* installing *source* package 'vcfppR' ...
** package 'vcfppR' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: 'g++.exe (GCC) 13.3.0'
make[1]: Entering directory '/d/temp/2024_12_08_01_50_01_8405/RtmpMjuKrR/R.INSTALL2cb343dbf8a9/vcfppR/src'
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -Ihtslib-1.18 -I../inst/include -D_FILE_OFFSET_BITS=64 -ID:/rtools44/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -DPSL_STATIC -DCURL_STATICLIB -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -Ihtslib-1.18 -I../inst/include -D_FILE_OFFSET_BITS=64 -ID:/rtools44/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -DPSL_STATIC -DCURL_STATICLIB -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vcf-popgen.cpp -o vcf-popgen.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -Ihtslib-1.18 -I../inst/include -D_FILE_OFFSET_BITS=64 -ID:/rtools44/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -DPSL_STATIC -DCURL_STATICLIB -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vcf-reader.cpp -o vcf-reader.o
vcf-reader.cpp: In member function 'double vcfreader::infoFloat(std::string)':
vcf-reader.cpp:176:28: warning: 'f' may be used uninitialized [-Wmaybe-uninitialized]
176 | return (double)f;
| ^
vcf-reader.cpp:174:15: note: 'f' was declared here
174 | float f;
| ^
vcf-reader.cpp: In member function 'int vcfreader::infoInt(std::string)':
vcf-reader.cpp:168:20: warning: 'i' may be used uninitialized [-Wmaybe-uninitialized]
168 | return i;
| ^
vcf-reader.cpp:166:13: note: 'i' was declared here
166 | int i;
| ^
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -Ihtslib-1.18 -I../inst/include -D_FILE_OFFSET_BITS=64 -ID:/rtools44/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -DPSL_STATIC -DCURL_STATICLIB -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vcf-stats.cpp -o vcf-stats.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -Ihtslib-1.18 -I../inst/include -D_FILE_OFFSET_BITS=64 -ID:/rtools44/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -DPSL_STATIC -DCURL_STATICLIB -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vcf-table.cpp -o vcf-table.o
g++ -std=gnu++17 -I"D:/RCompile/recent/R-4.4.2/include" -DNDEBUG -Ihtslib-1.18 -I../inst/include -D_FILE_OFFSET_BITS=64 -ID:/rtools44/x86_64-w64-mingw32.static.posix/include -DCURL_STATICLIB -DPSL_STATIC -DCURL_STATICLIB -I'D:/RCompile/CRANpkg/lib/4.4/Rcpp/include' -I"d:/rtools44/x86_64-w64-mingw32.static.posix/include" -pedantic -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vcf-writer.cpp -o vcf-writer.o
cd htslib-1.18 && make -f Makefile.win libhts.a && cd ..
make[2]: Entering directory '/d/temp/2024_12_08_01_50_01_8405/RtmpMjuKrR/R.INSTALL2cb343dbf8a9/vcfppR/src/htslib-1.18'
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_LIBCURL 1' >> config.h
if [ "x" != "x" ] && \
[ "x" != "x" ] && \
[ "x" != "x" ]; then \
echo '#define HAVE_POPCNT 1' >> config.h ; \
echo '#define HAVE_SSE4_1 1' >> config.h ; \
echo '#define HAVE_SSSE3 1' >> config.h ; \
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
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o kfunc.o kfunc.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o kstring.o kstring.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o bgzf.o bgzf.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o errmod.o errmod.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o faidx.o faidx.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o header.o header.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -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' \
'gcc' \
'-D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB' \
'-pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes ' \
'-fvisibility=hidden' \
'-lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex' > config_vars.h
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts.o hts.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts_expr.o hts_expr.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts_os.o hts_os.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o md5.o md5.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o multipart.o multipart.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o probaln.o probaln.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o realn.o realn.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o regidx.o regidx.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o region.o region.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o sam.o sam.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o sam_mods.o sam_mods.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcf_sweep.o vcf_sweep.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o tbx.o tbx.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o textutils.o textutils.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o thread_pool.o thread_pool.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcf.o vcf.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcfutils.o vcfutils.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_decode.o cram/cram_decode.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_encode.o cram/cram_encode.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_external.o cram/cram_external.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_index.o cram/cram_index.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_io.o cram/cram_io.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_stats.o cram/cram_stats.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/mFILE.o cram/mFILE.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/string_alloc.o cram/string_alloc.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
htscodecs/htscodecs/fqzcomp_qual.c:274:13: warning: 'dump_params' defined but not used [-Wunused-function]
274 | static void dump_params(fqz_gparams *gp) {
| ^~~~~~~~~~~
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
gcc -pedantic -Wstrict-prototypes -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden -Wstrict-prototypes -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -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 '/d/temp/2024_12_08_01_50_01_8405/RtmpMjuKrR/R.INSTALL2cb343dbf8a9/vcfppR/src/htslib-1.18'
D:\rtools44\x86_64-w64-mingw32.static.posix\bin\nm.exe: 'HTSLIB': No such file
g++ -std=gnu++17 -shared -s -static-libgcc -o vcfppR.dll tmp.def RcppExports.o vcf-popgen.o vcf-reader.o vcf-stats.o vcf-table.o vcf-writer.o htslib-1.18/libhts.a -llzma -lbz2 -lregex -LD:/rtools44/x86_64-w64-mingw32.static.posix/lib -lcurl -lssh2 -lgcrypt -lgpg-error -lbcrypt -ladvapi32 -lssl -lcrypto -lcrypt32 -lgdi32 -lwldap32 -lzstd -lz -lpsl -lws2_32 -lidn2 -lunistring -liconv -lcharset -lbrotlidec -lbrotlicommon -lpthread -lidn2 -lunistring -liconv -lcharset -lssh2 -lgcrypt -lgpg-error -lws2_32 -lgcrypt -lgpg-error -lws2_32 -lws2_32 -lz -lpsl -lunistring -lws2_32 -lidn2 -lunistring -liconv -lcharset -lbcrypt -ladvapi32 -lcrypt32 -lssl -lcrypto -lz -lws2_32 -lgdi32 -lcrypt32 -lcrypto -lz -lws2_32 -lgdi32 -lcrypt32 -lgdi32 -lwldap32 -lbrotlidec -lbrotlidec -lbrotlicommon -lunistring -lws2_32 -lunistring -liconv -lcharset -lbrotlicommon -lpthread -liconv -lcharset -lz -LD:/rtools44/x86_64-w64-mingw32.static.posix/lib -lbrotlicommon -LD:/rtools44/x86_64-w64-mingw32.static.posix -LD:/rtools44/x86_64-w64-mingw32.static.posix -lz -lws2_32 -lgdi32 -lcrypt32 -lcrypto -lz -lgdi32 -lcrypt32 -lunistring -lidn2 -lunistring -liconv -lcharset -lgcrypt -lgpg-error -lws2_32 -LD:/rtools44/x86_64-w64-mingw32.static.posix/lib -lgcrypt -lgpg-error -lws2_32 -LD:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/rtools44/x86_64-w64-mingw32.static.posix/lib -lws2_32 -LD:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/rtools44/x86_64-w64-mingw32.static.posix/lib -liconv -lcharset -lz -lbrotlidec -LD:/rtools44/x86_64-w64-mingw32.static.posix/lib -lbrotlicommon -lzstd -lssl -LD:/rtools44/x86_64-w64-mingw32.static.posix -lz -lws2_32 -lgdi32 -lcrypt32 -lcrypto -lz -lgdi32 -lcrypt32 -lunistring -liconv -lcharset -lssh2 -lgcrypt -lgpg-error -lws2_32 -LD:/rtools44/x86_64-w64-mingw32.static.posix/lib -lgcrypt -lgpg-error -lws2_32 -LD:/rtools44/x86_64-w64-mingw32.static.posix/lib -lgcrypt -LD:/rtools44/x86_64-w64-mingw32.static.posix/lib -lgpg-error -LD:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/rtools44/x86_64-w64-mingw32.static.posix/lib -lz -lpsl -lunistring -lws2_32 -lidn2 -lunistring -liconv -lcharset -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools44/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.4.2/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2024_12_08_01_50_01_8405/RtmpMjuKrR/R.INSTALL2cb343dbf8a9/vcfppR/src'
make[1]: Entering directory '/d/temp/2024_12_08_01_50_01_8405/RtmpMjuKrR/R.INSTALL2cb343dbf8a9/vcfppR/src'
make[1]: Leaving directory '/d/temp/2024_12_08_01_50_01_8405/RtmpMjuKrR/R.INSTALL2cb343dbf8a9/vcfppR/src'
installing to d:/Rcompile/CRANpkg/lib/4.4/00LOCK-vcfppR/00new/vcfppR/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'vcfppR' as vcfppR_0.6.0.zip
* DONE (vcfppR)