Package: Rhtslib

Version: 1.16.3

Command: rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rhtslib.buildbin-libdir Rhtslib_1.16.3.tar.gz

StartedAt: 2019-10-16 10:04:30 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 10:06:25 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 114.8 seconds

RetCode: 0

Status:  OK

PackageFile: Rhtslib_1.16.3.zip

PackageFileSize: 3.789 MiB

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###
### Running command:
###
###   rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rhtslib.buildbin-libdir Rhtslib_1.16.3.tar.gz
###
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install for i386

* installing *source* package 'Rhtslib' ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && /cygdrive/c/Rtools/bin/make -f "C:/Users/BIOCBU~1/BBS-3~1.9-B/R/etc/i386/Makeconf" -f "Makefile.Rhtslib.win"
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpADEnKh/R.INSTALL129016326f17/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib.win:128: warning: overriding commands for target `.c.o'
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/etc/i386/Makeconf:208: warning: ignoring old commands for target `.c.o'
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c
knetfile.c: In function 'khttp_connect_file':
knetfile.c:416:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  if (fp->offset != 0) l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
  ^
knetfile.c:416:2: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
bgzf.c: In function 'bgzf_read':
bgzf.c:888:17: warning: unknown conversion type character 'z' in format [-Wformat=]
                 hts_log_error("Read block operation failed with error %d after %zd of %zu bytes", ret, bytes_read, length);
                 ^
bgzf.c:888:17: warning: unknown conversion type character 'z' in format [-Wformat=]
bgzf.c:888:17: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
faidx.c: In function 'fai_read':
faidx.c:222:13: warning: unknown conversion type character 'z' in format [-Wformat=]
             hts_log_error("Could not understand FAI %s line %zd", fname, lnum);
             ^
faidx.c:222:13: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
multipart.c: In function 'multipart_read':
multipart.c:81:13: warning: unknown conversion type character 'z' in format [-Wformat=]
             hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
             ^
multipart.c:81:13: warning: unknown conversion type character 'z' in format [-Wformat=]
multipart.c:81:13: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'size_t' [-Wformat=]
multipart.c:81:13: warning: format '%s' expects argument of type 'char *', but argument 5 has type 'size_t' [-Wformat=]
multipart.c:81:13: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
sam.c: In function 'sam_read1':
sam.c:1439:13: warning: unknown conversion type character 'l' in format [-Wformat=]
             hts_log_warning("Parse error at line %lld", (long long)fp->lineno);
             ^
sam.c:1439:13: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.o cram/cram_samtools.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/files.o cram/files.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.o cram/rANS_static.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.o cram/sam_header.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c
C:/Rtools/mingw_32/bin/ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.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_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
C:/Rtools/mingw_32/bin/ranlib libhts.a
C:/Rtools/mingw_32/bin/gcc  -shared -Wl,--out-implib=libhts.dll.a -Wl,--export-all-symbols -Wl,--enable-auto-import  -o cyghts-2.dll -Wl,--whole-archive kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.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_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o -Wl,--no-whole-archive -lz -lm -lws2_32 -lpthread
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpADEnKh/R.INSTALL129016326f17/Rhtslib/src/htslib-1.7'
mkdir -p "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/i386"
cd "htslib-1.7" && cp libhts.a "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/i386"
mkdir -p "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib"
cd "htslib-1.7/htslib" && cp * "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include"
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_Rhtslib.c -o R_init_Rhtslib.o
mkdir -p "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata/tabix"
cd "htslib-1.7/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata/tabix" 2>/dev/null || true)
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o Rhtslib.dll tmp.def R_init_Rhtslib.o C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/i386/libhts.a -lz -lm -lws2_32 -lpthread -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Rhtslib'
    finding HTML links ... done
    Rhtslib-package                         html  
    pkgconfig                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Rhtslib' ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && /cygdrive/c/Rtools/bin/make -f "C:/Users/BIOCBU~1/BBS-3~1.9-B/R/etc/x64/Makeconf" -f "Makefile.Rhtslib.win"
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEFUvVN/R.INSTALL2b401aff6aff/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib.win:128: warning: overriding commands for target `.c.o'
C:/Users/BIOCBU~1/BBS-3~1.9-B/R/etc/x64/Makeconf:208: warning: ignoring old commands for target `.c.o'
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c
knetfile.c: In function 'khttp_connect_file':
knetfile.c:416:2: warning: unknown conversion type character 'l' in format [-Wformat=]
  if (fp->offset != 0) l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
  ^
knetfile.c:416:2: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
bgzf.c: In function 'bgzf_read':
bgzf.c:888:17: warning: unknown conversion type character 'z' in format [-Wformat=]
                 hts_log_error("Read block operation failed with error %d after %zd of %zu bytes", ret, bytes_read, length);
                 ^
bgzf.c:888:17: warning: unknown conversion type character 'z' in format [-Wformat=]
bgzf.c:888:17: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
faidx.c: In function 'fai_read':
faidx.c:222:13: warning: unknown conversion type character 'z' in format [-Wformat=]
             hts_log_error("Could not understand FAI %s line %zd", fname, lnum);
             ^
faidx.c:222:13: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
multipart.c: In function 'multipart_read':
multipart.c:81:13: warning: unknown conversion type character 'z' in format [-Wformat=]
             hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
             ^
multipart.c:81:13: warning: unknown conversion type character 'z' in format [-Wformat=]
multipart.c:81:13: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'size_t' [-Wformat=]
multipart.c:81:13: warning: format '%s' expects argument of type 'char *', but argument 5 has type 'size_t' [-Wformat=]
multipart.c:81:13: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
sam.c: In function 'sam_read1':
sam.c:1439:13: warning: unknown conversion type character 'l' in format [-Wformat=]
             hts_log_warning("Parse error at line %lld", (long long)fp->lineno);
             ^
sam.c:1439:13: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.o cram/cram_samtools.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/files.o cram/files.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.o cram/rANS_static.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.o cram/sam_header.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c
C:/Rtools/mingw_64/bin/ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.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_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
C:/Rtools/mingw_64/bin/ranlib libhts.a
C:/Rtools/mingw_64/bin/gcc  -shared -Wl,--out-implib=libhts.dll.a -Wl,--export-all-symbols -Wl,--enable-auto-import  -o cyghts-2.dll -Wl,--whole-archive kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.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_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o -Wl,--no-whole-archive -lz -lm -lws2_32 -lpthread
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpEFUvVN/R.INSTALL2b401aff6aff/Rhtslib/src/htslib-1.7'
mkdir -p "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/x64"
cd "htslib-1.7" && cp libhts.a "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/x64"
mkdir -p "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib"
cd "htslib-1.7/htslib" && cp * "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include"
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_Rhtslib.c -o R_init_Rhtslib.o
mkdir -p "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata/tabix"
cd "htslib-1.7/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata/tabix" 2>/dev/null || true)
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Rhtslib.dll tmp.def R_init_Rhtslib.o C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/x64/libhts.a -lz -lm -lws2_32 -lpthread -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rhtslib' as Rhtslib_1.16.3.zip
* DONE (Rhtslib)