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###
### Running command:
###
###   set _R_INSTALL_TIME_PATCHES_=no&& F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL Rhtslib
###
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* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'Rhtslib' ...
** using non-staged installation via StagedInstall field
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
cd "htslib-1.18" && /usr/bin/make -f "Makefile.Rhtslib.win"
make[1]: Entering directory '/f/biocbuild/bbs-3.19-bioc/meat/Rhtslib/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 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o kfunc.o kfunc.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o kstring.o kstring.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o bgzf.o bgzf.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o errmod.o errmod.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o faidx.o faidx.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o header.o header.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -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' \
'-O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden' \
'-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 -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts.o hts.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts_expr.o hts_expr.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o hts_os.o hts_os.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o md5.o md5.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o multipart.o multipart.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o probaln.o probaln.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o realn.o realn.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o regidx.o regidx.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o region.o region.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o sam.o sam.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o sam_mods.o sam_mods.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcf_sweep.o vcf_sweep.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o tbx.o tbx.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o textutils.o textutils.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o thread_pool.o thread_pool.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcf.o vcf.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o vcfutils.o vcfutils.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_decode.o cram/cram_decode.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_encode.o cram/cram_encode.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_external.o cram/cram_external.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_index.o cram/cram_index.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_io.o cram/cram_io.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/cram_stats.o cram/cram_stats.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/mFILE.o cram/mFILE.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o cram/string_alloc.o cram/string_alloc.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -I. -D_FILE_OFFSET_BITS=64 -DCURL_STATICLIB -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
gcc -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fpic -fvisibility=hidden  -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
sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp
sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk
sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc
make[1]: Leaving directory '/f/biocbuild/bbs-3.19-bioc/meat/Rhtslib/src/htslib-1.18'
mkdir -p "F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/usrlib/x64"
cd "htslib-1.18" && cp libhts.a "F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/usrlib/x64"
mkdir -p "F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include/htslib"
cd "htslib-1.18/htslib" && cp * "F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include/htslib"
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/include" -I'F:/biocbuild/bbs-3.19-bioc/R/library/zlibbioc/include'   -I"c:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_Rhtslib.c -o R_init_Rhtslib.o
mkdir -p "F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/testdata/tabix"
cd "htslib-1.18/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/testdata/tabix" 2>/dev/null || true)
gcc -shared -s -static-libgcc -o Rhtslib.dll tmp.def R_init_Rhtslib.o F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -Lc:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/Rhtslib/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rhtslib)