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###
### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL Rhtslib
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
cd "htslib-1.18" && make -f "Makefile.Rhtslib"
make[1]: Entering directory '/home/biocbuild/bbs-3.20-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 -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o header.o header.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -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' \
'-I/usr/local/include -D_FILE_OFFSET_BITS=64' \
'-g -O2 -Wall -fpic -fvisibility=hidden' \
'-L/usr/local/lib -fvisibility=hidden' \
'-lz -lm -lbz2 -llzma -lcurl' > config_vars.h
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_expr.o hts_expr.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o region.o region.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam_mods.o sam_mods.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -g -O2 -Wall -fpic -fvisibility=hidden  -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
htscodecs/htscodecs/rANS_static4x16pr.c: In function 'have_neon':
htscodecs/htscodecs/rANS_static4x16pr.c:1022:35: error: 'HWCAP_ASIMD' undeclared (first use in this function)
 1022 |     return (getauxval(AT_HWCAP) & HWCAP_ASIMD) != 0;
      |                                   ^~~~~~~~~~~
htscodecs/htscodecs/rANS_static4x16pr.c:1022:35: note: each undeclared identifier is reported only once for each function it appears in
htscodecs/htscodecs/rANS_static4x16pr.c:1038:1: warning: control reaches end of non-void function [-Wreturn-type]
 1038 | }
      | ^
make[1]: *** [Makefile.Rhtslib:160: htscodecs/htscodecs/rANS_static4x16pr.o] Error 1
make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rhtslib/src/htslib-1.18'
make: *** [Makevars.common:22: htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/home/biocbuild/R/R-4.4.1/site-library/Rhtslib’
* restoring previous ‘/home/biocbuild/R/R-4.4.1/site-library/Rhtslib’