Package: Rsamtools

Version: 1.32.3

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rsamtools.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Rsamtools_1.32.3.tar.gz

StartedAt: 2018-10-17 04:34:06 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 04:39:11 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 305.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Rsamtools.Rcheck

Warnings: 2

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Rsamtools.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Rsamtools_1.32.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rsamtools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rsamtools' version '1.32.3'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Rsamtools' can be installed ... WARNING
Found the following significant warnings:
  BamIterator.h:80:10: warning: 'BamIterator::iter_done' will be initialized after [-Wreorder]
  BamIterator.h:29:13: warning:   'bam1_t* BamIterator::bam' [-Wreorder]
  BamIterator.h:83:5: warning:   when initialized here [-Wreorder]
  BamIterator.h:29:13: warning: 'BamIterator::bam' will be initialized after [-Wreorder]
  BamIterator.h:15:14: warning:   '_BAM_DATA* BamIterator::bam_data' [-Wreorder]
  samtools/faidx.c:191:3: warning: too many arguments for format [-Wformat-extra-args]
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/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-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/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-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/Rsamtools/man/BamFile-class.Rd:354: file link 'summarizeOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/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-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/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-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/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-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/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-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/Rsamtools/man/ScanBcfParam-class.Rd:139: file link 'ScanVcfParam' in package 'VariantAnnotation' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/Rsamtools/man/readPileup.Rd:34: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'S4Vectors:::explodeIntBits' 'S4Vectors:::implodeIntBits'
  'S4Vectors:::makePowersOfTwo' 'S4Vectors:::quick_unlist'
  'S4Vectors:::selectSome'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'PileupFiles' but not in code:
  open.PileupFiles close.PileupFiles

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/libs/i386/Rsamtools.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
pileup 47.25   0.53   47.95
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
pileup 39.97   0.77   40.74
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'Rsamtools_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'Rsamtools_unit_tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Rsamtools_1.32.3.tar.gz && rm -rf Rsamtools.buildbin-libdir && mkdir Rsamtools.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Rsamtools.buildbin-libdir Rsamtools_1.32.3.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Rsamtools_1.32.3.zip && rm Rsamtools_1.32.3.tar.gz Rsamtools_1.32.3.zip
###
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100 2695k  100 2695k    0     0  25.6M      0 --:--:-- --:--:-- --:--:-- 27.4M

install for i386

* installing *source* package 'Rsamtools' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c PileupBuffer.cpp -o PileupBuffer.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c PosCacheColl.cpp -o PosCacheColl.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_Rsamtools.c -o R_init_Rsamtools.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ResultManager.cpp -o ResultManager.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c as_bam.c -o as_bam.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c bam_data.c -o bam_data.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bam_mate_iter.cpp -o bam_mate_iter.o
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:80:10: warning: 'BamIterator::iter_done' will be initialized after [-Wreorder]
     bool iter_done;
          ^
BamIterator.h:29:13: warning:   'bam1_t* BamIterator::bam' [-Wreorder]
     bam1_t *bam;
             ^
BamIterator.h:83:5: warning:   when initialized here [-Wreorder]
     BamIterator(bamFile bfile, const bam_index_t *bindex) :
     ^
BamIterator.h:29:13: warning: 'BamIterator::bam' will be initialized after [-Wreorder]
     bam1_t *bam;
             ^
BamIterator.h:15:14: warning:   '_BAM_DATA* BamIterator::bam_data' [-Wreorder]
     BAM_DATA bam_data;
              ^
BamIterator.h:83:5: warning:   when initialized here [-Wreorder]
     BamIterator(bamFile bfile, const bam_index_t *bindex) :
     ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c bambuffer.c -o bambuffer.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c bamfile.c -o bamfile.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c bcffile.c -o bcffile.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c encode.c -o encode.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c fafile.c -o fafile.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c idxstats.c -o idxstats.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c io_sam.c -o io_sam.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pileup.cpp -o pileup.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c pileupbam.c -o pileupbam.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools_patch.c -o samtools_patch.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c scan_bam_data.c -o scan_bam_data.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c tabixfile.c -o tabixfile.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c tagfilter.c -o tagfilter.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c utilities.c -o utilities.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c zip_compression.c -o zip_compression.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bgzf.c -o samtools/bgzf.o
samtools/bgzf.c: In function 'worker_aux':
samtools/bgzf.c:412:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
  int i, tmp, stop = 0;
         ^
samtools/bgzf.c: In function 'bgzf_close':
samtools/bgzf.c:592:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int ret, count, block_length;
           ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/kstring.c -o samtools/kstring.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_aux.c -o samtools/bam_aux.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam.c -o samtools/bam.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_import.c -o samtools/bam_import.o
samtools/bam_import.c: In function 'parse_error':
samtools/bam_import.c:169:2: warning: implicit declaration of function '_samtools_abort' [-Wimplicit-function-declaration]
  abort();
  ^
samtools/bam_import.c: In function 'append_text':
samtools/bam_import.c:181:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat=]
             fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
             ^
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t' [-Wformat=]
         fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,(long)header->n_text,x,y);
         ^
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=]
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat=]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/sam.c -o samtools/sam.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_index.c -o samtools/bam_index.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_pileup.c -o samtools/bam_pileup.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_md.c -o samtools/bam_md.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/razf.c -o samtools/razf.o
samtools/razf.c: In function 'razf_seek':
samtools/razf.c:761:17: warning: implicit declaration of function '_samtools_abort' [-Wimplicit-function-declaration]
                 abort();
                 ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/faidx.c -o samtools/faidx.o
samtools/faidx.c: In function 'fai_read':
samtools/faidx.c:191:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   sscanf(p, "%d%lld%d%d", &len, &offset, &line_blen, &line_len);
   ^
samtools/faidx.c:191:3: warning: format '%d' expects argument of type 'int *', but argument 4 has type 'long long int *' [-Wformat=]
samtools/faidx.c:191:3: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/knetfile.c -o samtools/knetfile.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_sort.c -o samtools/bam_sort.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/sam_header.c -o samtools/sam_header.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_reheader.c -o samtools/bam_reheader.o
samtools/bam_reheader.c: In function 'bam_reheader':
samtools/bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
  bam_header_t *old;
                ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/kprobaln.c -o samtools/kprobaln.o
samtools/kprobaln.c: In function 'kpa_glocal':
samtools/kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
C:/Rtools/mingw_32/bin/ar crs libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/index.c -o samtools/bcftools/index.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
C:/Rtools/mingw_32/bin/ar crs libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c tabix/index.c -o tabix/index.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=generic -c tabix/bedidx.c -o tabix/bedidx.o
C:/Rtools/mingw_32/bin/ar crs libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386"
cp ../Rsamtools.mk.win "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386/Rsamtools.mk"
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386"
cp libbam.a libbcf.a libtabix.a "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386"
C:\Rtools\mingw_32\bin\nm.exe: 'libs': No such file
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Rsamtools.dll tmp.def Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -pthread -fopenmp C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libbcf.a C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/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-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/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-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/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-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/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-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/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-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/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-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/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-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/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-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/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-3.7-bioc/tmpdir/RtmpYhD6Ep/R.INSTALLa08bab2e33/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
In R CMD INSTALL

install for x64

* installing *source* package 'Rsamtools' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c PileupBuffer.cpp -o PileupBuffer.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c PosCacheColl.cpp -o PosCacheColl.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_Rsamtools.c -o R_init_Rsamtools.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c ResultManager.cpp -o ResultManager.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c as_bam.c -o as_bam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c bam_data.c -o bam_data.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bam_mate_iter.cpp -o bam_mate_iter.o
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:80:10: warning: 'BamIterator::iter_done' will be initialized after [-Wreorder]
     bool iter_done;
          ^
BamIterator.h:29:13: warning:   'bam1_t* BamIterator::bam' [-Wreorder]
     bam1_t *bam;
             ^
BamIterator.h:83:5: warning:   when initialized here [-Wreorder]
     BamIterator(bamFile bfile, const bam_index_t *bindex) :
     ^
BamIterator.h:29:13: warning: 'BamIterator::bam' will be initialized after [-Wreorder]
     bam1_t *bam;
             ^
BamIterator.h:15:14: warning:   '_BAM_DATA* BamIterator::bam_data' [-Wreorder]
     BAM_DATA bam_data;
              ^
BamIterator.h:83:5: warning:   when initialized here [-Wreorder]
     BamIterator(bamFile bfile, const bam_index_t *bindex) :
     ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c bambuffer.c -o bambuffer.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c bamfile.c -o bamfile.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c bcffile.c -o bcffile.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c encode.c -o encode.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c fafile.c -o fafile.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c idxstats.c -o idxstats.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c io_sam.c -o io_sam.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pileup.cpp -o pileup.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c pileupbam.c -o pileupbam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools_patch.c -o samtools_patch.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c scan_bam_data.c -o scan_bam_data.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c tabixfile.c -o tabixfile.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c tagfilter.c -o tagfilter.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c utilities.c -o utilities.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c zip_compression.c -o zip_compression.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bgzf.c -o samtools/bgzf.o
samtools/bgzf.c: In function 'worker_aux':
samtools/bgzf.c:412:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
  int i, tmp, stop = 0;
         ^
samtools/bgzf.c: In function 'bgzf_close':
samtools/bgzf.c:592:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int ret, count, block_length;
           ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/kstring.c -o samtools/kstring.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_aux.c -o samtools/bam_aux.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam.c -o samtools/bam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_import.c -o samtools/bam_import.o
samtools/bam_import.c: In function 'parse_error':
samtools/bam_import.c:169:2: warning: implicit declaration of function '_samtools_abort' [-Wimplicit-function-declaration]
  abort();
  ^
samtools/bam_import.c: In function 'append_text':
samtools/bam_import.c:181:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat=]
             fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
             ^
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat=]
         fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,(long)header->n_text,x,y);
         ^
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=]
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat=]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/sam.c -o samtools/sam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_index.c -o samtools/bam_index.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_pileup.c -o samtools/bam_pileup.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_md.c -o samtools/bam_md.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/razf.c -o samtools/razf.o
samtools/razf.c: In function 'razf_seek':
samtools/razf.c:761:17: warning: implicit declaration of function '_samtools_abort' [-Wimplicit-function-declaration]
                 abort();
                 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/faidx.c -o samtools/faidx.o
samtools/faidx.c: In function 'fai_read':
samtools/faidx.c:191:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   sscanf(p, "%d%lld%d%d", &len, &offset, &line_blen, &line_len);
   ^
samtools/faidx.c:191:3: warning: format '%d' expects argument of type 'int *', but argument 4 has type 'long long int *' [-Wformat=]
samtools/faidx.c:191:3: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/knetfile.c -o samtools/knetfile.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_sort.c -o samtools/bam_sort.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/sam_header.c -o samtools/sam_header.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bam_reheader.c -o samtools/bam_reheader.o
samtools/bam_reheader.c: In function 'bam_reheader':
samtools/bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
  bam_header_t *old;
                ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/kprobaln.c -o samtools/kprobaln.o
samtools/kprobaln.c: In function 'kpa_glocal':
samtools/kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
C:/Rtools/mingw_64/bin/ar crs libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/index.c -o samtools/bcftools/index.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
C:/Rtools/mingw_64/bin/ar crs libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c tabix/index.c -o tabix/index.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Biostrings/include"   -I"C:/extsoft/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=generic -c tabix/bedidx.c -o tabix/bedidx.o
C:/Rtools/mingw_64/bin/ar crs libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x64"
cp ../Rsamtools.mk.win "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x64/Rsamtools.mk"
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64"
cp libbam.a libbcf.a libtabix.a "C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64"
C:\Rtools\mingw_64\bin\nm.exe: 'libs': No such file
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Rsamtools.dll tmp.def Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -pthread -fopenmp C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsamtools' as Rsamtools_1.32.3.zip
* DONE (Rsamtools)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'Rsamtools' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage('Rsamtools')

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Timing stopped at: 0 0 0
Error in DEACTIVATED("remote scanBcFHeader not supported on Windows") : 
  remote scanBcFHeader not supported on Windows
Timing stopped at: 0 0 0
Error in DEACTIVATED("remote tabix not supported on Windows") : 
  remote tabix not supported on Windows


RUNIT TEST PROTOCOL -- Wed Oct 17 04:38:29 2018 
*********************************************** 
Number of test functions: 183 
Number of deactivated test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Rsamtools RUnit Tests - 183 test functions, 0 errors, 0 failures
Number of test functions: 183 
Number of deactivated test functions: 2 
Number of errors: 0 
Number of failures: 0 
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[khttp_connect_file] fail to open file (HTTP code: 504).
Warning messages:
1: In read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
2: In read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
3: In read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
4: In read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
> 
> proc.time()
   user  system elapsed 
  13.01    0.71   34.03 

R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage('Rsamtools')

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Timing stopped at: 0 0 0
Error in DEACTIVATED("remote scanBcFHeader not supported on Windows") : 
  remote scanBcFHeader not supported on Windows
Timing stopped at: 0 0 0
Error in DEACTIVATED("remote tabix not supported on Windows") : 
  remote tabix not supported on Windows


RUNIT TEST PROTOCOL -- Wed Oct 17 04:39:04 2018 
*********************************************** 
Number of test functions: 183 
Number of deactivated test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Rsamtools RUnit Tests - 183 test functions, 0 errors, 0 failures
Number of test functions: 183 
Number of deactivated test functions: 2 
Number of errors: 0 
Number of failures: 0 
[samopen] SAM header is present: 2 sequences.
[samopen] SAM header is present: 2 sequences.
[khttp_connect_file] fail to open file (HTTP code: 504).
Warning messages:
1: In read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
2: In read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
3: In read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
4: In read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
> 
> proc.time()
   user  system elapsed 
  13.81    0.51   34.23