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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/Rhtslib_1.26.0.tar.gz && rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rhtslib.buildbin-libdir Rhtslib_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL Rhtslib_1.26.0.zip && rm Rhtslib_1.26.0.tar.gz Rhtslib_1.26.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 1268k 0 1137 0 0 13873 0 0:01:33 --:--:-- 0:01:33 13865
100 1268k 100 1268k 0 0 1261k 0 0:00:01 0:00:01 --:--:-- 1262k
install for i386
* installing *source* package 'Rhtslib' ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && /usr/bin/make -f "C:/Users/BIOCBU~1/BBS-3~1.14-/R/etc/i386/Makeconf" -f "Makefile.Rhtslib.win"
make[1]: Entering directory '/c/Users/biocbuild/bbs-3.14-bioc/tmpdir/Rtmp2Fhw4a/R.INSTALL10e44c593a95/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib.win:131: warning: overriding recipe for target '.c.o'
C:/Users/BIOCBU~1/BBS-3~1.14-/R/etc/i386/Makeconf:238: warning: ignoring old recipe for target '.c.o'
echo '/* Default config.h generated by Makefile */' > config.h
echo '#define HAVE_FSEEKO 1' >> config.h
echo '#define HAVE_LIBCURL 1' >> config.h
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o kfunc.o kfunc.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o knetfile.o knetfile.c
knetfile.c: In function 'khttp_connect_file':
knetfile.c:416:61: 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:416:45: warning: too many arguments for format [-Wformat-extra-args]
if (fp->offset != 0) l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
^~~~~~~~~~~~~~~~~~~~~~~~
knetfile.c:416:61: 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:416:45: warning: too many arguments for format [-Wformat-extra-args]
if (fp->offset != 0) l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
^~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o kstring.o kstring.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o bcf_sr_sort.o bcf_sr_sort.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o bgzf.o bgzf.c
In file included from htslib/hts.h:35,
from bgzf.c:38:
bgzf.c: In function 'bgzf_read':
bgzf.c:888:31: 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);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
#define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
^~~~~~~~~~~
bgzf.c:888:31: 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);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
#define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
^~~~~~~~~~~
bgzf.c:888:31: warning: too many arguments for format [-Wformat-extra-args]
hts_log_error("Read block operation failed with error %d after %zd of %zu bytes", ret, bytes_read, length);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
#define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o errmod.o errmod.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o faidx.o faidx.c
In file included from htslib/hts.h:35,
from hts_internal.h:29,
from faidx.c:43:
faidx.c: In function 'fai_read':
faidx.c:222:27: warning: unknown conversion type character 'z' in format [-Wformat=]
hts_log_error("Could not understand FAI %s line %zd", fname, lnum);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
#define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
^~~~~~~~~~~
faidx.c:222:27: warning: too many arguments for format [-Wformat-extra-args]
hts_log_error("Could not understand FAI %s line %zd", fname, lnum);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
#define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o hfile.o hfile.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o hts.o hts.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o hts_os.o hts_os.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o md5.o md5.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o multipart.o multipart.c
In file included from htslib/hts.h:35,
from hts_internal.h:29,
from multipart.c:33:
multipart.c: In function 'multipart_read':
multipart.c:81:27: warning: unknown conversion type character 'z' in format [-Wformat=]
hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:84:61: note: in definition of macro 'hts_log_debug'
#define hts_log_debug(...) hts_log(HTS_LOG_DEBUG, __func__, __VA_ARGS__)
^~~~~~~~~~~
multipart.c:81:27: warning: unknown conversion type character 'z' in format [-Wformat=]
hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:84:61: note: in definition of macro 'hts_log_debug'
#define hts_log_debug(...) hts_log(HTS_LOG_DEBUG, __func__, __VA_ARGS__)
^~~~~~~~~~~
multipart.c:81:27: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fp->current+1, fp->nparts, p->url,
~~~~~~~~~~~~~
htslib/hts_log.h:84:61: note: in definition of macro 'hts_log_debug'
#define hts_log_debug(...) hts_log(HTS_LOG_DEBUG, __func__, __VA_ARGS__)
^~~~~~~~~~~
multipart.c:81:27: warning: format '%s' expects argument of type 'char *', but argument 5 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fp->current+1, fp->nparts, p->url,
~~~~~~~~~~
htslib/hts_log.h:84:61: note: in definition of macro 'hts_log_debug'
#define hts_log_debug(...) hts_log(HTS_LOG_DEBUG, __func__, __VA_ARGS__)
^~~~~~~~~~~
multipart.c:81:27: warning: too many arguments for format [-Wformat-extra-args]
hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:84:61: note: in definition of macro 'hts_log_debug'
#define hts_log_debug(...) hts_log(HTS_LOG_DEBUG, __func__, __VA_ARGS__)
^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o probaln.o probaln.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o realn.o realn.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o regidx.o regidx.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o sam.o sam.c
In file included from htslib/hts.h:35,
from htslib/sam.h:31,
from sam.c:35:
sam.c: In function 'sam_read1':
sam.c:1439:29: warning: unknown conversion type character 'l' in format [-Wformat=]
hts_log_warning("Parse error at line %lld", (long long)fp->lineno);
^~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:78:65: note: in definition of macro 'hts_log_warning'
#define hts_log_warning(...) hts_log(HTS_LOG_WARNING, __func__, __VA_ARGS__)
^~~~~~~~~~~
sam.c:1439:29: warning: too many arguments for format [-Wformat-extra-args]
hts_log_warning("Parse error at line %lld", (long long)fp->lineno);
^~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:78:65: note: in definition of macro 'hts_log_warning'
#define hts_log_warning(...) hts_log(HTS_LOG_WARNING, __func__, __VA_ARGS__)
^~~~~~~~~~~
sam.c: In function 'bam_hdr_write':
sam.c:233:5: warning: 'strncpy' output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
strncpy(buf, "BAM\1", 4);
^~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o synced_bcf_reader.o synced_bcf_reader.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o vcf_sweep.o vcf_sweep.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o tbx.o tbx.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o textutils.o textutils.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o thread_pool.o thread_pool.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o vcf.o vcf.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o vcfutils.o vcfutils.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/cram_codecs.o cram/cram_codecs.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/cram_decode.o cram/cram_decode.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/cram_encode.o cram/cram_encode.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/cram_external.o cram/cram_external.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/cram_index.o cram/cram_index.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/cram_io.o cram/cram_io.c
cram/cram_io.c: In function 'cram_populate_ref':
cram/cram_io.c:2178:27: warning: '.tmp_' directive writing 5 bytes into a region of size between 1 and 260 [-Wformat-overflow=]
sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
^~~~~
cram/cram_io.c:2178:24: note: using the range [0, 4294967295] for directive argument
sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
^~~~~~~~~~~~~~~~~
cram/cram_io.c:2178:24: note: using the range [0, 4294967295] for directive argument
cram/cram_io.c:2178:6: note: 'sprintf' output between 11 and 298 bytes into a destination of size 260
sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cram/cram_io.c:2071:2: warning: 'strncpy' specified bound 260 equals destination size [-Wstringop-truncation]
strncpy(path, path2, PATH_MAX);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'full_path',
inlined from 'cram_write_SAM_hdr' at cram/cram_io.c:3752:3:
cram/cram_io.c:3677:6: warning: 'strncpy' specified bound 260 equals destination size [-Wstringop-truncation]
strncpy(out, in, PATH_MAX);
^~~~~~~~~~~~~~~~~~~~~~~~~~
cram/cram_io.c:3669:2: warning: 'strncpy' specified bound 260 equals destination size [-Wstringop-truncation]
strncpy(out, in, PATH_MAX);
^~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/cram_samtools.o cram/cram_samtools.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/cram_stats.o cram/cram_stats.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/files.o cram/files.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/mFILE.o cram/mFILE.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/open_trace_file.o cram/open_trace_file.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/pooled_alloc.o cram/pooled_alloc.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/rANS_static.o cram/rANS_static.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/sam_header.o cram/sam_header.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/string_alloc.o cram/string_alloc.c
"C:/rtools40/mingw32/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o hfile_libcurl.o hfile_libcurl.c
"C:/rtools40/mingw32/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 hfile_libcurl.o
"C:/rtools40/mingw32/bin/"ranlib libhts.a
"C:/rtools40/mingw32/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 hfile_libcurl.o -Wl,--no-whole-archive -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -lpthread
make[1]: Leaving directory '/c/Users/biocbuild/bbs-3.14-bioc/tmpdir/Rtmp2Fhw4a/R.INSTALL10e44c593a95/Rhtslib/src/htslib-1.7'
mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/i386"
cd "htslib-1.7" && cp libhts.a "C:/Users/biocbuild/bbs-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/i386"
mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib"
cd "htslib-1.7/htslib" && cp * "C:/Users/biocbuild/bbs-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "C:/Users/biocbuild/bbs-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include"
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include" -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_Rhtslib.c -o R_init_Rhtslib.o
mkdir -p "C:/Users/biocbuild/bbs-3.14-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-3.14-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-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata/tabix" 2>/dev/null || true)
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o Rhtslib.dll tmp.def R_init_Rhtslib.o C:/Users/biocbuild/bbs-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-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" && /usr/bin/make -f "C:/Users/BIOCBU~1/BBS-3~1.14-/R/etc/x64/Makeconf" -f "Makefile.Rhtslib.win"
make[1]: Entering directory '/c/Users/biocbuild/bbs-3.14-bioc/tmpdir/Rtmpi0LbkO/R.INSTALL108c12003c9a/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib.win:131: warning: overriding recipe for target '.c.o'
C:/Users/BIOCBU~1/BBS-3~1.14-/R/etc/x64/Makeconf:238: warning: ignoring old recipe for target '.c.o'
echo '/* Default config.h generated by Makefile */' > config.h
echo '#define HAVE_FSEEKO 1' >> config.h
echo '#define HAVE_LIBCURL 1' >> config.h
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o kfunc.o kfunc.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o knetfile.o knetfile.c
knetfile.c: In function 'khttp_connect_file':
knetfile.c:416:61: 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:416:45: warning: too many arguments for format [-Wformat-extra-args]
if (fp->offset != 0) l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
^~~~~~~~~~~~~~~~~~~~~~~~
knetfile.c:416:61: 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:416:45: warning: too many arguments for format [-Wformat-extra-args]
if (fp->offset != 0) l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
^~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o kstring.o kstring.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o bcf_sr_sort.o bcf_sr_sort.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o bgzf.o bgzf.c
In file included from htslib/hts.h:35,
from bgzf.c:38:
bgzf.c: In function 'bgzf_read':
bgzf.c:888:31: 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);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
#define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
^~~~~~~~~~~
bgzf.c:888:31: 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);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
#define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
^~~~~~~~~~~
bgzf.c:888:31: warning: too many arguments for format [-Wformat-extra-args]
hts_log_error("Read block operation failed with error %d after %zd of %zu bytes", ret, bytes_read, length);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
#define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o errmod.o errmod.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o faidx.o faidx.c
In file included from htslib/hts.h:35,
from hts_internal.h:29,
from faidx.c:43:
faidx.c: In function 'fai_read':
faidx.c:222:27: warning: unknown conversion type character 'z' in format [-Wformat=]
hts_log_error("Could not understand FAI %s line %zd", fname, lnum);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
#define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
^~~~~~~~~~~
faidx.c:222:27: warning: too many arguments for format [-Wformat-extra-args]
hts_log_error("Could not understand FAI %s line %zd", fname, lnum);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:75:61: note: in definition of macro 'hts_log_error'
#define hts_log_error(...) hts_log(HTS_LOG_ERROR, __func__, __VA_ARGS__)
^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o hfile.o hfile.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o hts.o hts.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o hts_os.o hts_os.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o md5.o md5.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o multipart.o multipart.c
In file included from htslib/hts.h:35,
from hts_internal.h:29,
from multipart.c:33:
multipart.c: In function 'multipart_read':
multipart.c:81:27: warning: unknown conversion type character 'z' in format [-Wformat=]
hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:84:61: note: in definition of macro 'hts_log_debug'
#define hts_log_debug(...) hts_log(HTS_LOG_DEBUG, __func__, __VA_ARGS__)
^~~~~~~~~~~
multipart.c:81:27: warning: unknown conversion type character 'z' in format [-Wformat=]
hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:84:61: note: in definition of macro 'hts_log_debug'
#define hts_log_debug(...) hts_log(HTS_LOG_DEBUG, __func__, __VA_ARGS__)
^~~~~~~~~~~
multipart.c:81:27: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fp->current+1, fp->nparts, p->url,
~~~~~~~~~~~~~
htslib/hts_log.h:84:61: note: in definition of macro 'hts_log_debug'
#define hts_log_debug(...) hts_log(HTS_LOG_DEBUG, __func__, __VA_ARGS__)
^~~~~~~~~~~
multipart.c:81:27: warning: format '%s' expects argument of type 'char *', but argument 5 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
fp->current+1, fp->nparts, p->url,
~~~~~~~~~~
htslib/hts_log.h:84:61: note: in definition of macro 'hts_log_debug'
#define hts_log_debug(...) hts_log(HTS_LOG_DEBUG, __func__, __VA_ARGS__)
^~~~~~~~~~~
multipart.c:81:27: warning: too many arguments for format [-Wformat-extra-args]
hts_log_debug("Opening part #%zu of %zu: \"%.120s%s\"",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:84:61: note: in definition of macro 'hts_log_debug'
#define hts_log_debug(...) hts_log(HTS_LOG_DEBUG, __func__, __VA_ARGS__)
^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o probaln.o probaln.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o realn.o realn.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o regidx.o regidx.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o sam.o sam.c
In file included from htslib/hts.h:35,
from htslib/sam.h:31,
from sam.c:35:
sam.c: In function 'sam_read1':
sam.c:1439:29: warning: unknown conversion type character 'l' in format [-Wformat=]
hts_log_warning("Parse error at line %lld", (long long)fp->lineno);
^~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:78:65: note: in definition of macro 'hts_log_warning'
#define hts_log_warning(...) hts_log(HTS_LOG_WARNING, __func__, __VA_ARGS__)
^~~~~~~~~~~
sam.c:1439:29: warning: too many arguments for format [-Wformat-extra-args]
hts_log_warning("Parse error at line %lld", (long long)fp->lineno);
^~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/hts_log.h:78:65: note: in definition of macro 'hts_log_warning'
#define hts_log_warning(...) hts_log(HTS_LOG_WARNING, __func__, __VA_ARGS__)
^~~~~~~~~~~
sam.c: In function 'bam_hdr_write':
sam.c:233:5: warning: 'strncpy' output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
strncpy(buf, "BAM\1", 4);
^~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o synced_bcf_reader.o synced_bcf_reader.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o vcf_sweep.o vcf_sweep.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o tbx.o tbx.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o textutils.o textutils.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o thread_pool.o thread_pool.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o vcf.o vcf.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o vcfutils.o vcfutils.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/cram_codecs.o cram/cram_codecs.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/cram_decode.o cram/cram_decode.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/cram_encode.o cram/cram_encode.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/cram_external.o cram/cram_external.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/cram_index.o cram/cram_index.c
In file included from ./textutils_internal.h:32,
from ./hts_internal.h:31,
from cram/cram_index.c:65:
In function 'kputsn',
inlined from 'kputs' at ./htslib/kstring.h:156:9,
inlined from 'cram_index_build' at cram/cram_index.c:571:9:
./htslib/kstring.h:148:2: warning: 'memcpy' pointer overflow between offset 0 and size [-2, 9223372036854775807] [-Warray-bounds]
memcpy(s->s + s->l, p, l);
^~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/cram_io.o cram/cram_io.c
cram/cram_io.c: In function 'cram_populate_ref':
cram/cram_io.c:2178:27: warning: '.tmp_' directive writing 5 bytes into a region of size between 1 and 260 [-Wformat-overflow=]
sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
^~~~~
cram/cram_io.c:2178:24: note: using the range [0, 4294967295] for directive argument
sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
^~~~~~~~~~~~~~~~~
cram/cram_io.c:2178:24: note: using the range [0, 4294967295] for directive argument
cram/cram_io.c:2178:6: note: 'sprintf' output between 11 and 298 bytes into a destination of size 260
sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cram/cram_io.c:2071:2: warning: 'strncpy' specified bound 260 equals destination size [-Wstringop-truncation]
strncpy(path, path2, PATH_MAX);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'full_path',
inlined from 'cram_write_SAM_hdr' at cram/cram_io.c:3752:3:
cram/cram_io.c:3677:6: warning: 'strncpy' specified bound 260 equals destination size [-Wstringop-truncation]
strncpy(out, in, PATH_MAX);
^~~~~~~~~~~~~~~~~~~~~~~~~~
cram/cram_io.c:3669:2: warning: 'strncpy' specified bound 260 equals destination size [-Wstringop-truncation]
strncpy(out, in, PATH_MAX);
^~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/cram_samtools.o cram/cram_samtools.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/cram_stats.o cram/cram_stats.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/files.o cram/files.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/mFILE.o cram/mFILE.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/open_trace_file.o cram/open_trace_file.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/pooled_alloc.o cram/pooled_alloc.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/rANS_static.o cram/rANS_static.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/sam_header.o cram/sam_header.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o cram/string_alloc.o cram/string_alloc.c
"C:/rtools40/mingw64/bin/"gcc -g -Wall -O2 -I. -D_FILE_OFFSET_BITS=64 -IC:/extsoft/include -DCURL_STATICLIB -c -o hfile_libcurl.o hfile_libcurl.c
"C:/rtools40/mingw64/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 hfile_libcurl.o
"C:/rtools40/mingw64/bin/"ranlib libhts.a
"C:/rtools40/mingw64/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 hfile_libcurl.o -Wl,--no-whole-archive -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lpthread
make[1]: Leaving directory '/c/Users/biocbuild/bbs-3.14-bioc/tmpdir/Rtmpi0LbkO/R.INSTALL108c12003c9a/Rhtslib/src/htslib-1.7'
mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/x64"
cd "htslib-1.7" && cp libhts.a "C:/Users/biocbuild/bbs-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/x64"
mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib"
cd "htslib-1.7/htslib" && cp * "C:/Users/biocbuild/bbs-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "C:/Users/biocbuild/bbs-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include"
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include" -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_Rhtslib.c -o R_init_Rhtslib.o
mkdir -p "C:/Users/biocbuild/bbs-3.14-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-3.14-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-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/testdata/tabix" 2>/dev/null || true)
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o Rhtslib.dll tmp.def R_init_Rhtslib.o C:/Users/biocbuild/bbs-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rhtslib' as Rhtslib_1.26.0.zip
* DONE (Rhtslib)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'Rhtslib' successfully unpacked and MD5 sums checked
