Package: Rhtslib

Version: 1.15.5

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rhtslib.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Rhtslib_1.15.5.tar.gz

StartedAt: 2019-04-09 05:23:28 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:24:00 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 31.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Rhtslib.Rcheck

Warnings: 2

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rhtslib.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Rhtslib_1.15.5.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rhtslib/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rhtslib' version '1.15.5'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  src/htslib-1.7/.appveyor.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'Rhtslib' can be installed ... WARNING
Found the following significant warnings:
  knetfile.c:416:2: warning: too many arguments for format [-Wformat-extra-args]
  bgzf.c:888:17: warning: too many arguments for format [-Wformat-extra-args]
  faidx.c:222:13: warning: too many arguments for format [-Wformat-extra-args]
  multipart.c:81:13: warning: too many arguments for format [-Wformat-extra-args]
  sam.c:1439:13: warning: too many arguments for format [-Wformat-extra-args]
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs       1.1Mb
    testdata   4.1Mb
    usrlib     6.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
  src/htslib-1.7/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section 'Writing portable
packages' in the 'Writing R Extensions' manual.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/libs/i386/Rhtslib.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/libs/x64/Rhtslib.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rhtslib.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/Rhtslib_1.15.5.tar.gz && 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_1.15.5.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL Rhtslib_1.15.5.zip && rm Rhtslib_1.15.5.tar.gz Rhtslib_1.15.5.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1265k  100 1265k    0     0  7051k      0 --:--:-- --:--:-- --:--:-- 7313k

install for i386

* installing *source* package 'Rhtslib' ...
** libs
cd "htslib-1.7" && /cygdrive/c/Rtools/bin/make -f "C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/etc/i386/Makeconf" -f "Makefile.Rhtslib.win"
make[1]: Entering directory `/cygdrive/c/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUhnokX/R.INSTALLde47c80288c/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'
echo '/* Default config.h generated by Makefile */' > config.h
echo '#define HAVE_FSEEKO 1' >> config.h
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
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUhnokX/R.INSTALLde47c80288c/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 -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' ...
** 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/RtmpuOhc0w/R.INSTALL191069c416ce/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'
echo '/* Default config.h generated by Makefile */' > config.h
echo '#define HAVE_FSEEKO 1' >> config.h
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
make[1]: Leaving directory `/cygdrive/c/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpuOhc0w/R.INSTALL191069c416ce/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 -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_1.15.5.zip
* DONE (Rhtslib)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'Rhtslib' successfully unpacked and MD5 sums checked