Rsamtools 2.2.3
Bioconductor Package Maintainer
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/Rsamtools |
| Branch: RELEASE_3_10 |
| Last Commit: 073d892 |
| Last Changed Date: 2020-02-22 20:14:42 -0400 (Sat, 22 Feb 2020) |
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf Rsamtools.buildbin-libdir && mkdir Rsamtools.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsamtools.buildbin-libdir Rsamtools_2.2.3.tar.gz
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install for i386
* installing *source* package 'Rsamtools' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c PileupBuffer.cpp -o PileupBuffer.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c PosCacheColl.cpp -o PosCacheColl.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c ResultManager.cpp -o ResultManager.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c as_bam.c -o as_bam.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bam.c -o bam.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bam_data.c -o bam_data.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from bam_mate_iter.cpp:2:0:
BamRangeIterator.h: In member function 'virtual void BamRangeIterator::finalize_inprogress(bamFile)':
BamRangeIterator.h:138:39: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)', declared with attribute warn_unused_result [-Wunused-result]
bam_seek(bfile, pos, SEEK_SET);
^
In file included from BamRangeIterator.h:7:0,
from bam_mate_iter.cpp:2:
BamIterator.h: In constructor 'BamIterator::BamIterator(bamFile, const bam_index_t*)':
BamIterator.h:87:30: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)', declared with attribute warn_unused_result [-Wunused-result]
bam_seek(bfile, 0, 0);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bam_sort.c -o bam_sort.o
In file included from bam_sort.c:1:0:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c: In function 'complain_about_memory_setting':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: unknown conversion type character 'z' in format [-Wformat=]
max_mem, suffix, SORT_MIN_MEGS_PER_THREAD);
^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'size_t' [-Wformat=]
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: unknown conversion type character 'z' in format [-Wformat=]
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bambuffer.c -o bambuffer.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -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:29:15: 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;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c bcffile.c -o bcffile.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c encode.c -o encode.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c fafile.c -o fafile.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c idxstats.c -o idxstats.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/sam.h:29:0,
from bamfile.h:5,
from idxstats.c:1:
idxstats.c: In function 'idxstats_bamfile':
C:/Users/biocbuild/bbs-3.10-bioc/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);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c io_sam.c -o io_sam.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/sam.h:29:0,
from io_sam.c:2:
io_sam.c: In function '_scan_bam_all':
C:/Users/biocbuild/bbs-3.10-bioc/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);
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c pileup.cpp -o pileup.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c pileupbam.c -o pileupbam.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sam.c -o sam.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sam_opts.c -o sam_opts.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sam_utils.c -o sam_utils.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c samtools_patch.c -o samtools_patch.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c scan_bam_data.c -o scan_bam_data.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c tabixfile.c -o tabixfile.o
tabixfile.c: In function 'index_tabix':
tabixfile.c:190:5: warning: 'bgzf_is_bgzf' is deprecated (declared at C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/bgzf.h:243): Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
if (bgzf_is_bgzf(fn) != 1)
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c tagfilter.c -o tagfilter.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c zip_compression.c -o zip_compression.o
C:/Rtools/mingw_32/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/biocbuild/bbs-3.10-bioc/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/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/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/biocbuild/bbs-3.10-bioc/tmpdir/RtmpiQo7OW/R.INSTALL31d43595cd1/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/biocbuild/bbs-3.10-bioc/tmpdir/RtmpiQo7OW/R.INSTALL31d43595cd1/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/biocbuild/bbs-3.10-bioc/tmpdir/RtmpiQo7OW/R.INSTALL31d43595cd1/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/biocbuild/bbs-3.10-bioc/tmpdir/RtmpiQo7OW/R.INSTALL31d43595cd1/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/biocbuild/bbs-3.10-bioc/tmpdir/RtmpiQo7OW/R.INSTALL31d43595cd1/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/biocbuild/bbs-3.10-bioc/tmpdir/RtmpiQo7OW/R.INSTALL31d43595cd1/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/biocbuild/bbs-3.10-bioc/tmpdir/RtmpiQo7OW/R.INSTALL31d43595cd1/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/biocbuild/bbs-3.10-bioc/tmpdir/RtmpiQo7OW/R.INSTALL31d43595cd1/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/biocbuild/bbs-3.10-bioc/tmpdir/RtmpiQo7OW/R.INSTALL31d43595cd1/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
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c PileupBuffer.cpp -o PileupBuffer.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c PosCacheColl.cpp -o PosCacheColl.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c ResultManager.cpp -o ResultManager.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c as_bam.c -o as_bam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bam.c -o bam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bam_data.c -o bam_data.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from bam_mate_iter.cpp:2:0:
BamRangeIterator.h: In member function 'virtual void BamRangeIterator::finalize_inprogress(bamFile)':
BamRangeIterator.h:138:39: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)', declared with attribute warn_unused_result [-Wunused-result]
bam_seek(bfile, pos, SEEK_SET);
^
In file included from BamRangeIterator.h:7:0,
from bam_mate_iter.cpp:2:
BamIterator.h: In constructor 'BamIterator::BamIterator(bamFile, const bam_index_t*)':
BamIterator.h:87:30: warning: ignoring return value of 'int64_t bgzf_seek(BGZF*, int64_t, int)', declared with attribute warn_unused_result [-Wunused-result]
bam_seek(bfile, 0, 0);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bam_sort.c -o bam_sort.o
In file included from bam_sort.c:1:0:
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c: In function 'complain_about_memory_setting':
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: unknown conversion type character 'z' in format [-Wformat=]
max_mem, suffix, SORT_MIN_MEGS_PER_THREAD);
^
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'size_t' [-Wformat=]
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: unknown conversion type character 'z' in format [-Wformat=]
C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/bam_sort.c:2263:13: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bambuffer.c -o bambuffer.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -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:29:15: 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;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c bcffile.c -o bcffile.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c encode.c -o encode.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c fafile.c -o fafile.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c idxstats.c -o idxstats.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/sam.h:29:0,
from bamfile.h:5,
from idxstats.c:1:
idxstats.c: In function 'idxstats_bamfile':
C:/Users/biocbuild/bbs-3.10-bioc/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);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c io_sam.c -o io_sam.o
In file included from C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/sam.h:29:0,
from io_sam.c:2:
io_sam.c: In function '_scan_bam_all':
C:/Users/biocbuild/bbs-3.10-bioc/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);
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c pileup.cpp -o pileup.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c pileupbam.c -o pileupbam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sam.c -o sam.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sam_opts.c -o sam_opts.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sam_utils.c -o sam_utils.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c samtools_patch.c -o samtools_patch.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c scan_bam_data.c -o scan_bam_data.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c tabixfile.c -o tabixfile.o
tabixfile.c: In function 'index_tabix':
tabixfile.c:190:5: warning: 'bgzf_is_bgzf' is deprecated (declared at C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include/htslib/bgzf.h:243): Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
if (bgzf_is_bgzf(fn) != 1)
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c tagfilter.c -o tagfilter.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Biostrings/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c zip_compression.c -o zip_compression.o
C:/Rtools/mingw_64/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/biocbuild/bbs-3.10-bioc/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/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsamtools' as Rsamtools_2.2.3.zip
* DONE (Rsamtools)