Rsamtools 2.3.7
Bioconductor Package Maintainer
| Snapshot Date: 2020-04-14 17:00:05 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/Rsamtools |
| Branch: master |
| Last Commit: 54e3b25 |
| Last Changed Date: 2020-03-18 14:13:03 -0400 (Wed, 18 Mar 2020) |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc-testing/src/contrib/Rsamtools_2.3.7.tar.gz && rm -rf Rsamtools.buildbin-libdir && mkdir Rsamtools.buildbin-libdir && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsamtools.buildbin-libdir Rsamtools_2.3.7.tar.gz && C:\Users\bioctesting\bbs-3.11-bioc-testing\R\bin\R.exe CMD INSTALL Rsamtools_2.3.7.zip && rm Rsamtools_2.3.7.tar.gz Rsamtools_2.3.7.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 2659k 100 2659k 0 0 27.4M 0 --:--:-- --:--:-- --:--:-- 29.5M
install for i386
* installing *source* package 'Rsamtools' ...
** using staged installation
** libs
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
/mingw32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PileupBuffer.cpp -o PileupBuffer.o
/mingw32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PosCacheColl.cpp -o PosCacheColl.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_Rsamtools.c -o R_init_Rsamtools.o
/mingw32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ResultManager.cpp -o ResultManager.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c as_bam.c -o as_bam.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam.c -o bam.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_data.c -o bam_data.o
/mingw32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/sam.h:29,
from Template.h:9,
from BamIterator.h:10,
from BamRangeIterator.h:7,
from bam_mate_iter.cpp:2:
BamRangeIterator.h: In member function 'virtual void BamRangeIterator::finalize_inprogress(bamFile)':
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)', declared with attribute warn_unused_result [-Wunused-result]
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
~~~~~~~~~^~~~~~~~~~~~~~
BamRangeIterator.h:138:9: note: in expansion of macro 'bam_seek'
bam_seek(bfile, pos, SEEK_SET);
^~~~~~~~
BamIterator.h: In constructor 'BamIterator::BamIterator(bamFile, const bam_index_t*)':
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)', declared with attribute warn_unused_result [-Wunused-result]
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
~~~~~~~~~^~~~~~~~~~~~~~
BamIterator.h:87:9: note: in expansion of macro 'bam_seek'
bam_seek(bfile, 0, 0);
^~~~~~~~
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_plbuf.c -o bam_plbuf.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_sort.c -o bam_sort.o
In file included from bam_sort.c:1:
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c: In function 'complain_about_memory_setting':
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2256:26: warning: unknown conversion type character 'z' in format [-Wformat=]
"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
^
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2256:29: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
~^
%d
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2263:13:
max_mem, suffix, SORT_MIN_MEGS_PER_THREAD);
~~~~~~~
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2256:74: warning: unknown conversion type character 'z' in format [-Wformat=]
"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
^
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2256:1: warning: too many arguments for format [-Wformat-extra-args]
"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2256:26: warning: unknown conversion type character 'z' in format [-Wformat=]
"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
^
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2256:29: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
~^
%d
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2263:13:
max_mem, suffix, SORT_MIN_MEGS_PER_THREAD);
~~~~~~~
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2256:74: warning: unknown conversion type character 'z' in format [-Wformat=]
"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
^
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2256:1: warning: too many arguments for format [-Wformat-extra-args]
"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c: In function 'bam_sort_core_ext':
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2065:9: warning: 'strncpy' specified bound 2 equals destination size [-Wstringop-truncation]
strncpy(g_sort_tag, sort_by_tag, 2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bambuffer.c -o bambuffer.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bamfile.c -o bamfile.o
bamfile.c: In function 'bamfile_isincomplete':
bamfile.c:168:13: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bamfile.c: In function 'bamfile_open':
bamfile.c:29:17: warning: 'cfile' may be used uninitialized in this function [-Wmaybe-uninitialized]
index = hts_idx_load2(file, indexname);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bamfile.c:73:17: note: 'cfile' was declared here
const char *cfile;
^~~~~
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bcffile.c -o bcffile.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c encode.c -o encode.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fafile.c -o fafile.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c idxstats.c -o idxstats.o
In file included from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/sam.h:29,
from bamfile.h:5,
from idxstats.c:1:
idxstats.c: In function 'idxstats_bamfile':
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
^~~~~~~~~~~~~~~~~~~~~~~
idxstats.c:20:5: note: in expansion of macro 'bam_seek'
bam_seek(fp, 0, 0);
^~~~~~~~
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io_sam.c -o io_sam.o
In file included from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/sam.h:29,
from io_sam.c:2:
io_sam.c: In function '_scan_bam_all':
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
^~~~~~~~~~~~~~~~~~~~~~~
io_sam.c:304:5: note: in expansion of macro 'bam_seek'
bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
^~~~~~~~
/mingw32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
/mingw32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pileup.cpp -o pileup.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pileupbam.c -o pileupbam.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam.c -o sam.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam_opts.c -o sam_opts.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam_utils.c -o sam_utils.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c samtools_patch.c -o samtools_patch.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c scan_bam_data.c -o scan_bam_data.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tabixfile.c -o tabixfile.o
tabixfile.c: In function 'index_tabix':
tabixfile.c:190:5: warning: 'bgzf_is_bgzf' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
if (bgzf_is_bgzf(fn) != 1)
^~
In file included from tabixfile.c:3:
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/htslib/bgzf.h:243:9: note: declared here
int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
^~~~~~~~~~~~
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tagfilter.c -o tagfilter.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utilities.c -o utilities.o
/mingw32/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c zip_compression.c -o zip_compression.o
/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Rsamtools.dll tmp.def Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/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/BIOCTE~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/Rsamtools.buildbin-libdir/00LOCK-Rsamtools/00new/Rsamtools/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Rsamtools'
finding HTML links ... done
ApplyPileupsParam-class html
BamFile-class html
finding level-2 HTML links ... done
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpuoMoq1/R.INSTALLc40158a7986/Rsamtools/man/BamFile-class.Rd:350: file link 'readGAlignmentPairs' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpuoMoq1/R.INSTALLc40158a7986/Rsamtools/man/BamFile-class.Rd:351: file link 'readGAlignmentsList' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpuoMoq1/R.INSTALLc40158a7986/Rsamtools/man/BamFile-class.Rd:354: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
BamViews-class html
BcfFile-class html
FaFile-class html
PileupFiles-class html
Rsamtools-package html
RsamtoolsFile-class html
RsamtoolsFileList-class html
ScanBamParam-class html
ScanBcfParam-class html
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpuoMoq1/R.INSTALLc40158a7986/Rsamtools/man/ScanBcfParam-class.Rd:62: file link 'scanVcfHeader' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpuoMoq1/R.INSTALLc40158a7986/Rsamtools/man/ScanBcfParam-class.Rd:65: file link 'scanVcfHeader' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpuoMoq1/R.INSTALLc40158a7986/Rsamtools/man/ScanBcfParam-class.Rd:69: file link 'scanVcfHeader' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpuoMoq1/R.INSTALLc40158a7986/Rsamtools/man/ScanBcfParam-class.Rd:138: file link 'scanVcf' in package 'VariantAnnotation' does not exist and so has been treated as a topic
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpuoMoq1/R.INSTALLc40158a7986/Rsamtools/man/ScanBcfParam-class.Rd:139: file link 'ScanVcfParam' in package 'VariantAnnotation' does not exist and so has been treated as a topic
TabixFile-class html
applyPileups html
defunct html
deprecated html
headerTabix html
indexTabix html
pileup html
quickBamFlagSummary html
readPileup html
Rd warning: C:/Users/bioctesting/bbs-3.11-bioc-testing/tmpdir/RtmpuoMoq1/R.INSTALLc40158a7986/Rsamtools/man/readPileup.Rd:34: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
scanBam html
scanBcf html
scanFa html
scanTabix html
seqnamesTabix html
testPairedEndBam html
zip html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'Rsamtools' ...
** libs
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Biostrings_stubs.c -o Biostrings_stubs.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c IRanges_stubs.c -o IRanges_stubs.o
/mingw64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PileupBuffer.cpp -o PileupBuffer.o
/mingw64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PosCacheColl.cpp -o PosCacheColl.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_Rsamtools.c -o R_init_Rsamtools.o
/mingw64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ResultManager.cpp -o ResultManager.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c XVector_stubs.c -o XVector_stubs.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c as_bam.c -o as_bam.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam.c -o bam.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_data.c -o bam_data.o
/mingw64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/sam.h:29,
from Template.h:9,
from BamIterator.h:10,
from BamRangeIterator.h:7,
from bam_mate_iter.cpp:2:
BamRangeIterator.h: In member function 'virtual void BamRangeIterator::finalize_inprogress(bamFile)':
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)', declared with attribute warn_unused_result [-Wunused-result]
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
~~~~~~~~~^~~~~~~~~~~~~~
BamRangeIterator.h:138:9: note: in expansion of macro 'bam_seek'
bam_seek(bfile, pos, SEEK_SET);
^~~~~~~~
BamIterator.h: In constructor 'BamIterator::BamIterator(bamFile, const bam_index_t*)':
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)', declared with attribute warn_unused_result [-Wunused-result]
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
~~~~~~~~~^~~~~~~~~~~~~~
BamIterator.h:87:9: note: in expansion of macro 'bam_seek'
bam_seek(bfile, 0, 0);
^~~~~~~~
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_plbuf.c -o bam_plbuf.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_sort.c -o bam_sort.o
In file included from bam_sort.c:1:
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c: In function 'complain_about_memory_setting':
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2256:26: warning: unknown conversion type character 'z' in format [-Wformat=]
"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
^
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2256:29: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
~^
%I64d
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2263:13:
max_mem, suffix, SORT_MIN_MEGS_PER_THREAD);
~~~~~~~
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2256:74: warning: unknown conversion type character 'z' in format [-Wformat=]
"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
^
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2256:1: warning: too many arguments for format [-Wformat-extra-args]
"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2256:26: warning: unknown conversion type character 'z' in format [-Wformat=]
"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
^
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2256:29: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'size_t' {aka 'long long unsigned int'} [-Wformat=]
"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
~^
%I64d
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2263:13:
max_mem, suffix, SORT_MIN_MEGS_PER_THREAD);
~~~~~~~
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2256:74: warning: unknown conversion type character 'z' in format [-Wformat=]
"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
^
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2256:1: warning: too many arguments for format [-Wformat-extra-args]
"[bam_sort] -m setting (%zu%s bytes) is less than the minimum required (%zuM).\n\n"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c: In function 'bam_sort_core_ext':
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam_sort.c:2065:9: warning: 'strncpy' specified bound 2 equals destination size [-Wstringop-truncation]
strncpy(g_sort_tag, sort_by_tag, 2);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bambuffer.c -o bambuffer.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bamfile.c -o bamfile.o
bamfile.c: In function 'bamfile_isincomplete':
bamfile.c:168:13: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bamfile.c: In function 'bamfile_open':
bamfile.c:29:17: warning: 'cfile' may be used uninitialized in this function [-Wmaybe-uninitialized]
index = hts_idx_load2(file, indexname);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bamfile.c:73:17: note: 'cfile' was declared here
const char *cfile;
^~~~~
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bcffile.c -o bcffile.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c encode.c -o encode.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fafile.c -o fafile.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c idxstats.c -o idxstats.o
In file included from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/sam.h:29,
from bamfile.h:5,
from idxstats.c:1:
idxstats.c: In function 'idxstats_bamfile':
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
^~~~~~~~~~~~~~~~~~~~~~~
idxstats.c:20:5: note: in expansion of macro 'bam_seek'
bam_seek(fp, 0, 0);
^~~~~~~~
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c io_sam.c -o io_sam.o
In file included from C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/sam.h:29,
from io_sam.c:2:
io_sam.c: In function '_scan_bam_all':
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
#define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
^~~~~~~~~~~~~~~~~~~~~~~
io_sam.c:304:5: note: in expansion of macro 'bam_seek'
bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
^~~~~~~~
/mingw64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
/mingw64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pileup.cpp -o pileup.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pileupbam.c -o pileupbam.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam.c -o sam.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam_opts.c -o sam_opts.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam_utils.c -o sam_utils.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c samtools_patch.c -o samtools_patch.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c scan_bam_data.c -o scan_bam_data.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tabixfile.c -o tabixfile.o
tabixfile.c: In function 'index_tabix':
tabixfile.c:190:5: warning: 'bgzf_is_bgzf' is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
if (bgzf_is_bgzf(fn) != 1)
^~
In file included from tabixfile.c:3:
C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include/htslib/bgzf.h:243:9: note: declared here
int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
^~~~~~~~~~~~
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c tagfilter.c -o tagfilter.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c utilities.c -o utilities.o
/mingw64/bin/gcc -I"C:/Users/BIOCTE~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Rhtslib/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/S4Vectors/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/IRanges/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/XVector/include' -I'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/Biostrings/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c zip_compression.c -o zip_compression.o
/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o Rsamtools.dll tmp.def Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library/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/BIOCTE~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/bioctesting/bbs-3.11-bioc-testing/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsamtools' as Rsamtools_2.3.7.zip
* DONE (Rsamtools)
* installing to library 'C:/Users/bioctesting/bbs-3.11-bioc-testing/R/library'
package 'Rsamtools' successfully unpacked and MD5 sums checked