Package: Rhtslib

Version: 1.12.1

Command: rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rhtslib.buildbin-libdir Rhtslib_1.12.1.tar.gz

StartedAt: 2018-10-17 06:53:55 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 06:56:14 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 138.3 seconds

RetCode: 0

Status:  OK

PackageFile: Rhtslib_1.12.1.zip

PackageFileSize: 3.07 MiB

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###
### Running command:
###
###   rm -rf Rhtslib.buildbin-libdir && mkdir Rhtslib.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rhtslib.buildbin-libdir Rhtslib_1.12.1.tar.gz
###
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install for i386

* installing *source* package 'Rhtslib' ...
** libs
cd "htslib-1.7" && /cygdrive/c/Rtools/bin/make -f "C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/etc/i386/Makeconf" -f "Makefile.Rhtslib.win"
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqUTyMD/R.INSTALLfe869882c39/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib.win:128: warning: overriding commands for target `.c.o'
C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/etc/i386/Makeconf:208: warning: ignoring old commands for target `.c.o'
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o kfunc.o kfunc.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -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.  -c -o kstring.o kstring.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -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.  -c -o errmod.o errmod.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -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.  -c -o hfile.o hfile.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -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.  -c -o hts.o hts.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o hts_os.o hts_os.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o md5.o md5.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -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.  -c -o probaln.o probaln.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o realn.o realn.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o regidx.o regidx.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -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.  -c -o synced_bcf_reader.o synced_bcf_reader.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o vcf_sweep.o vcf_sweep.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o tbx.o tbx.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o textutils.o textutils.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o thread_pool.o thread_pool.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o vcf.o vcf.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o vcfutils.o vcfutils.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o cram/cram_decode.o cram/cram_decode.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o cram/cram_encode.o cram/cram_encode.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o cram/cram_external.o cram/cram_external.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o cram/cram_index.o cram/cram_index.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o cram/cram_io.o cram/cram_io.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o cram/cram_stats.o cram/cram_stats.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o cram/files.o cram/files.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o cram/mFILE.o cram/mFILE.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o cram/rANS_static.o cram/rANS_static.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o cram/sam_header.o cram/sam_header.c
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -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
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o bgzip.o bgzip.c
C:/Rtools/mingw_32/bin/gcc   -o bgzip bgzip.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o htsfile.o htsfile.c
C:/Rtools/mingw_32/bin/gcc   -o htsfile htsfile.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o tabix.o tabix.c
C:/Rtools/mingw_32/bin/gcc   -o tabix tabix.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o test/hts_endian.o test/hts_endian.c
C:/Rtools/mingw_32/bin/gcc   -o test/hts_endian test/hts_endian.o -lz -lm -lws2_32
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o test/fieldarith.o test/fieldarith.c
C:/Rtools/mingw_32/bin/gcc   -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o test/hfile.o test/hfile.c
C:/Rtools/mingw_32/bin/gcc   -o test/hfile test/hfile.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o test/sam.o test/sam.c
test/sam.c: In function 'aux_fields1':
test/sam.c:185:22: warning: unknown conversion type character 'z' in format [-Wformat=]
                      bam_auxB_len(p), nvals);
                      ^
test/sam.c:185:22: warning: too many arguments for format [-Wformat-extra-args]
test/sam.c:191:26: warning: unknown conversion type character 'z' in format [-Wformat=]
                          i, bam_auxB2f(p, i), bfvals[i]);
                          ^
test/sam.c:191:26: warning: format '%f' expects argument of type 'double', but argument 2 has type 'size_t' [-Wformat=]
test/sam.c:191:26: warning: too many arguments for format [-Wformat-extra-args]
test/sam.c: In function 'samrecord_layout':
test/sam.c:309:9: warning: unknown conversion type character 'z' in format [-Wformat=]
         fail("sizeof bam1_core_t is %zu, expected 36", sizeof (bam1_core_t));
         ^
test/sam.c:309:9: warning: too many arguments for format [-Wformat-extra-args]
test/sam.c:313:14: warning: unknown conversion type character 'z' in format [-Wformat=]
              sizeof(bam1_t), bam1_t_size, bam1_t_size2);
              ^
test/sam.c:313:14: warning: unknown conversion type character 'z' in format [-Wformat=]
test/sam.c:313:14: warning: unknown conversion type character 'z' in format [-Wformat=]
test/sam.c:313:14: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc   -o test/sam test/sam.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o test/test_bgzf.o test/test_bgzf.c
test/test_bgzf.c: In function 'try_bgzf_getc':
test/test_bgzf.c:262:17: warning: unknown conversion type character 'z' in format [-Wformat=]
                 func, c, name, pos, expected);
                 ^
test/test_bgzf.c:262:17: warning: too many arguments for format [-Wformat-extra-args]
test/test_bgzf.c: In function 'test_write_read':
test/test_bgzf.c:430:21: warning: unknown conversion type character 'z' in format [-Wformat=]
                     __func__, f->tmp_bgzf, pos);
                     ^
test/test_bgzf.c:430:21: warning: too many arguments for format [-Wformat-extra-args]
test/test_bgzf.c:438:17: warning: unknown conversion type character 'z' in format [-Wformat=]
                 __func__, pos, bg_put);
                 ^
test/test_bgzf.c:438:17: warning: unknown conversion type character 'z' in format [-Wformat=]
test/test_bgzf.c:438:17: warning: too many arguments for format [-Wformat-extra-args]
test/test_bgzf.c: In function 'test_embed_eof':
test/test_bgzf.c:503:21: warning: unknown conversion type character 'z' in format [-Wformat=]
                     __func__, f->tmp_bgzf, pos);
                     ^
test/test_bgzf.c:503:21: warning: too many arguments for format [-Wformat-extra-args]
test/test_bgzf.c:511:17: warning: unknown conversion type character 'z' in format [-Wformat=]
                 __func__, pos, f->ltext);
                 ^
test/test_bgzf.c:511:17: warning: unknown conversion type character 'z' in format [-Wformat=]
test/test_bgzf.c:511:17: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc   -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o test/test-regidx.o test/test-regidx.c
C:/Rtools/mingw_32/bin/gcc   -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o test/test_view.o test/test_view.c
C:/Rtools/mingw_32/bin/gcc   -o test/test_view test/test_view.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o test/test-vcf-api.o test/test-vcf-api.c
C:/Rtools/mingw_32/bin/gcc   -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
C:/Rtools/mingw_32/bin/gcc   -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o test/test-bcf-sr.o test/test-bcf-sr.c
C:/Rtools/mingw_32/bin/gcc   -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_32/bin/gcc  -g -Wall -O2 -I.  -c -o test/test-bcf-translate.o test/test-bcf-translate.c
C:/Rtools/mingw_32/bin/gcc   -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lm -lws2_32 -lpthread
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpqUTyMD/R.INSTALLfe869882c39/Rhtslib/src/htslib-1.7'
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/i386"
cd "htslib-1.7" && cp libhts.a "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/i386"
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include"
cd "htslib-1.7/htslib" && cp * "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include"
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-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
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o Rhtslib.dll tmp.def R_init_Rhtslib.o C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-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
In R CMD INSTALL

install for x64

* installing *source* package 'Rhtslib' ...
** libs
cd "htslib-1.7" && /cygdrive/c/Rtools/bin/make -f "C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/etc/x64/Makeconf" -f "Makefile.Rhtslib.win"
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYx8piu/R.INSTALL253c337040f0/Rhtslib/src/htslib-1.7'
Makefile.Rhtslib.win:128: warning: overriding commands for target `.c.o'
C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/etc/x64/Makeconf:208: warning: ignoring old commands for target `.c.o'
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o kfunc.o kfunc.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -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.  -c -o kstring.o kstring.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -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.  -c -o errmod.o errmod.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -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.  -c -o hfile.o hfile.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -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.  -c -o hts.o hts.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o hts_os.o hts_os.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o md5.o md5.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -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.  -c -o probaln.o probaln.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o realn.o realn.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o regidx.o regidx.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -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.  -c -o synced_bcf_reader.o synced_bcf_reader.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o vcf_sweep.o vcf_sweep.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o tbx.o tbx.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o textutils.o textutils.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o thread_pool.o thread_pool.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o vcf.o vcf.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o vcfutils.o vcfutils.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o cram/cram_decode.o cram/cram_decode.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o cram/cram_encode.o cram/cram_encode.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o cram/cram_external.o cram/cram_external.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o cram/cram_index.o cram/cram_index.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o cram/cram_io.o cram/cram_io.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o cram/cram_stats.o cram/cram_stats.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o cram/files.o cram/files.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o cram/mFILE.o cram/mFILE.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o cram/rANS_static.o cram/rANS_static.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o cram/sam_header.o cram/sam_header.c
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -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
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o bgzip.o bgzip.c
C:/Rtools/mingw_64/bin/gcc   -o bgzip bgzip.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o htsfile.o htsfile.c
C:/Rtools/mingw_64/bin/gcc   -o htsfile htsfile.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o tabix.o tabix.c
C:/Rtools/mingw_64/bin/gcc   -o tabix tabix.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o test/hts_endian.o test/hts_endian.c
C:/Rtools/mingw_64/bin/gcc   -o test/hts_endian test/hts_endian.o -lz -lm -lws2_32
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o test/fieldarith.o test/fieldarith.c
C:/Rtools/mingw_64/bin/gcc   -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o test/hfile.o test/hfile.c
C:/Rtools/mingw_64/bin/gcc   -o test/hfile test/hfile.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o test/sam.o test/sam.c
test/sam.c: In function 'aux_fields1':
test/sam.c:185:22: warning: unknown conversion type character 'z' in format [-Wformat=]
                      bam_auxB_len(p), nvals);
                      ^
test/sam.c:185:22: warning: too many arguments for format [-Wformat-extra-args]
test/sam.c:191:26: warning: unknown conversion type character 'z' in format [-Wformat=]
                          i, bam_auxB2f(p, i), bfvals[i]);
                          ^
test/sam.c:191:26: warning: format '%f' expects argument of type 'double', but argument 2 has type 'size_t' [-Wformat=]
test/sam.c:191:26: warning: too many arguments for format [-Wformat-extra-args]
test/sam.c: In function 'samrecord_layout':
test/sam.c:309:9: warning: unknown conversion type character 'z' in format [-Wformat=]
         fail("sizeof bam1_core_t is %zu, expected 36", sizeof (bam1_core_t));
         ^
test/sam.c:309:9: warning: too many arguments for format [-Wformat-extra-args]
test/sam.c:313:14: warning: unknown conversion type character 'z' in format [-Wformat=]
              sizeof(bam1_t), bam1_t_size, bam1_t_size2);
              ^
test/sam.c:313:14: warning: unknown conversion type character 'z' in format [-Wformat=]
test/sam.c:313:14: warning: unknown conversion type character 'z' in format [-Wformat=]
test/sam.c:313:14: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc   -o test/sam test/sam.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o test/test_bgzf.o test/test_bgzf.c
test/test_bgzf.c: In function 'try_bgzf_getc':
test/test_bgzf.c:262:17: warning: unknown conversion type character 'z' in format [-Wformat=]
                 func, c, name, pos, expected);
                 ^
test/test_bgzf.c:262:17: warning: format '%d' expects argument of type 'int', but argument 6 has type 'size_t' [-Wformat=]
test/test_bgzf.c:262:17: warning: too many arguments for format [-Wformat-extra-args]
test/test_bgzf.c: In function 'test_write_read':
test/test_bgzf.c:430:21: warning: unknown conversion type character 'z' in format [-Wformat=]
                     __func__, f->tmp_bgzf, pos);
                     ^
test/test_bgzf.c:430:21: warning: too many arguments for format [-Wformat-extra-args]
test/test_bgzf.c:438:17: warning: unknown conversion type character 'z' in format [-Wformat=]
                 __func__, pos, bg_put);
                 ^
test/test_bgzf.c:438:17: warning: unknown conversion type character 'z' in format [-Wformat=]
test/test_bgzf.c:438:17: warning: too many arguments for format [-Wformat-extra-args]
test/test_bgzf.c: In function 'test_embed_eof':
test/test_bgzf.c:503:21: warning: unknown conversion type character 'z' in format [-Wformat=]
                     __func__, f->tmp_bgzf, pos);
                     ^
test/test_bgzf.c:503:21: warning: too many arguments for format [-Wformat-extra-args]
test/test_bgzf.c:511:17: warning: unknown conversion type character 'z' in format [-Wformat=]
                 __func__, pos, f->ltext);
                 ^
test/test_bgzf.c:511:17: warning: unknown conversion type character 'z' in format [-Wformat=]
test/test_bgzf.c:511:17: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc   -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o test/test-regidx.o test/test-regidx.c
C:/Rtools/mingw_64/bin/gcc   -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o test/test_view.o test/test_view.c
C:/Rtools/mingw_64/bin/gcc   -o test/test_view test/test_view.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o test/test-vcf-api.o test/test-vcf-api.c
C:/Rtools/mingw_64/bin/gcc   -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
C:/Rtools/mingw_64/bin/gcc   -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o test/test-bcf-sr.o test/test-bcf-sr.c
C:/Rtools/mingw_64/bin/gcc   -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lws2_32 -lpthread
C:/Rtools/mingw_64/bin/gcc  -g -Wall -O2 -I.  -c -o test/test-bcf-translate.o test/test-bcf-translate.c
C:/Rtools/mingw_64/bin/gcc   -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lm -lws2_32 -lpthread
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYx8piu/R.INSTALL253c337040f0/Rhtslib/src/htslib-1.7'
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/x64"
cd "htslib-1.7" && cp libhts.a "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/usrlib/x64"
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include"
cd "htslib-1.7/htslib" && cp * "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include"
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.7-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
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Rhtslib.dll tmp.def R_init_Rhtslib.o C:/Users/biocbuild/bbs-3.7-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˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Rhtslib.buildbin-libdir/Rhtslib/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rhtslib' as Rhtslib_1.12.1.zip
* DONE (Rhtslib)
In R CMD INSTALL
In R CMD INSTALL