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BioC 2.13: CHECK report for Rsamtools on moscato1

This page was generated on 2014-04-05 09:50:03 -0700 (Sat, 05 Apr 2014).

Package 625/750HostnameOS / ArchBUILDCHECKBUILD BIN
Rsamtools 1.14.3
Bioconductor Package Maintainer
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/Rsamtools
Last Changed Rev: 86232 / Revision: 88450
Last Changed Date: 2014-02-08 04:54:55 -0800 (Sat, 08 Feb 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: Rsamtools
Version: 1.14.3
Command: rm -rf Rsamtools.buildbin-libdir && mkdir Rsamtools.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rsamtools.buildbin-libdir Rsamtools_1.14.3.tar.gz >Rsamtools-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=Rsamtools.buildbin-libdir --install="check:Rsamtools-install.out" --force-multiarch --no-vignettes --timings Rsamtools_1.14.3.tar.gz && mv Rsamtools.buildbin-libdir/* Rsamtools.Rcheck/ && rmdir Rsamtools.buildbin-libdir
StartedAt: 2014-04-05 06:31:55 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 06:39:59 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 484.0 seconds
RetCode: 0
Status:  OK  
CheckDir: Rsamtools.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-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 '1.14.3'
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   2.5Mb
* 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
Missing object imported by a ':::' call: 'IRanges:::.makeLow2highFromHigh2low'
Unexported object imported by a ':::' call: 'Biostrings:::.normarg_padding.letter'
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for 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 'D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/i386/Rsamtools.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/x64/Rsamtools.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.  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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'Rsamtools-Overview.Rnw', 'Rsamtools-UsingCLibraries.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [48s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
sequenceLayer          17.37   0.62   19.30
readGAlignmentsFromBam  7.95   0.17    8.75
** running examples for arch 'x64' ... [43s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
sequenceLayer          18.89   0.45   19.36
readGAlignmentsFromBam  6.61   0.16    6.77
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'Rsamtools_unit_tests.R' [48s]
 [49s] OK
** running tests for arch 'x64'
  Running 'Rsamtools_unit_tests.R' [59s]
 [59s] 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

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.Rcheck/00check.log'
for details.

Rsamtools.Rcheck/00install.out:


install for i386

* installing *source* package 'Rsamtools' ...
** libs
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c as_bam.c -o as_bam.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c bam_data.c -o bam_data.o
g++ -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c bam_mate_iter.cpp -o bam_mate_iter.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c bambuffer.c -o bambuffer.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c bamfile.c -o bamfile.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c bcffile.c -o bcffile.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c encode.c -o encode.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c fafile.c -o fafile.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c io_sam.c -o io_sam.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c pileupbam.c -o pileupbam.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools_patch.c -o samtools_patch.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c scan_bam_data.c -o scan_bam_data.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c tabixfile.c -o tabixfile.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c zip_compression.c -o zip_compression.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -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]
samtools/bgzf.c: In function 'bgzf_close':
samtools/bgzf.c:592:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/kstring.c -o samtools/kstring.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam.c -o samtools/bam.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -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]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/sam.c -o samtools/sam.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_index.c -o samtools/bam_index.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_md.c -o samtools/bam_md.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -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]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/faidx.c -o samtools/faidx.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/knetfile.c -o samtools/knetfile.o
samtools/knetfile.c: In function 'khttp_connect_file':
samtools/knetfile.c:416:5: warning: unknown conversion type character 'l' in format [-Wformat]
samtools/knetfile.c:416:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_sort.c -o samtools/bam_sort.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/sam_header.c -o samtools/sam_header.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -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]
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -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]
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
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/index.c -o samtools/bcftools/index.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
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
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c tabix/index.c -o tabix/index.o
gcc -m32 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c tabix/bedidx.c -o tabix/bedidx.o
ar crs libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386"
cp ../Rsamtools.mk.win "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386/Rsamtools.mk"
mkdir -p "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386"
cp libbam.a libbcf.a libtabix.a "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386"
C:\Rtools31\gcc-4.6.3\bin\nm.exe: 'libs': No such file
g++ -m32 -shared -s -static-libgcc -o Rsamtools.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o io_sam.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o utilities.o zip_compression.o -pthread -fopenmp D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libbam.a D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libbcf.a D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -LD:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'Rsamtools' ...
** libs
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c as_bam.c -o as_bam.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c bam_data.c -o bam_data.o
g++ -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c bam_mate_iter.cpp -o bam_mate_iter.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c bambuffer.c -o bambuffer.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c bamfile.c -o bamfile.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c bcffile.c -o bcffile.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c encode.c -o encode.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c fafile.c -o fafile.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c io_sam.c -o io_sam.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c pileupbam.c -o pileupbam.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools_patch.c -o samtools_patch.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c scan_bam_data.c -o scan_bam_data.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c tabixfile.c -o tabixfile.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c zip_compression.c -o zip_compression.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -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]
samtools/bgzf.c: In function 'bgzf_close':
samtools/bgzf.c:592:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/kstring.c -o samtools/kstring.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam.c -o samtools/bam.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -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]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/sam.c -o samtools/sam.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_index.c -o samtools/bam_index.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_md.c -o samtools/bam_md.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -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]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/faidx.c -o samtools/faidx.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/knetfile.c -o samtools/knetfile.o
samtools/knetfile.c: In function 'khttp_connect_file':
samtools/knetfile.c:416:5: warning: unknown conversion type character 'l' in format [-Wformat]
samtools/knetfile.c:416:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_sort.c -o samtools/bam_sort.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/sam_header.c -o samtools/sam_header.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -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]
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -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]
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
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/index.c -o samtools/bcftools/index.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
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
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c tabix/index.c -o tabix/index.o
gcc -m64 -I"D:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c tabix/bedidx.c -o tabix/bedidx.o
ar crs libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x64"
cp ../Rsamtools.mk.win "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x64/Rsamtools.mk"
mkdir -p "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64"
cp libbam.a libbcf.a libtabix.a "D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64"
C:\Rtools31\gcc-4.6.3\bin\nm.exe: 'libs': No such file
g++ -m64 -shared -s -static-libgcc -o Rsamtools.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o io_sam.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o utilities.o zip_compression.o -pthread -fopenmp D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libbcf.a D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -LD:/biocbld/bbs-2.13-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsamtools' as Rsamtools_1.14.3.zip
* DONE (Rsamtools)

Rsamtools.Rcheck/examples_i386/Rsamtools-Ex.timings:

nameusersystemelapsed
BamFile-class0.690.020.70
BamSampler-class0.400.000.41
BamViews-class4.050.034.09
BcfFile-class1.190.001.18
FaFile-class0.240.010.27
PileupFiles-class0.210.000.20
PileupParam-class0.160.000.15
Rsamtools-package0.030.000.03
ScanBamParam-class0.500.000.64
ScanBcfParam-class0.000.020.02
TabixFile-class0.080.000.08
applyPileups0.150.010.17
findMateAlignment0.920.000.92
headerTabix0.020.000.01
indexTabix0.050.000.05
quickCountBam0.030.000.03
readGAlignmentsFromBam7.950.178.75
readPileup0.110.020.12
scanBam0.740.030.77
scanBcf0.520.000.52
scanFa0.250.000.25
scanTabix0.060.030.43
seqnamesTabix0.010.000.02
sequenceLayer17.37 0.6219.30
stackStringsFromBam1.820.031.85
zip0.030.020.05

Rsamtools.Rcheck/examples_x64/Rsamtools-Ex.timings:

nameusersystemelapsed
BamFile-class0.750.010.76
BamSampler-class0.30.00.3
BamViews-class2.810.022.83
BcfFile-class1.520.021.53
FaFile-class0.190.000.19
PileupFiles-class0.420.000.43
PileupParam-class0.250.000.24
Rsamtools-package0.040.000.04
ScanBamParam-class0.580.000.58
ScanBcfParam-class0.000.010.01
TabixFile-class0.060.000.07
applyPileups0.110.000.11
findMateAlignment0.870.020.89
headerTabix0.020.000.01
indexTabix0.030.010.05
quickCountBam0.050.000.04
readGAlignmentsFromBam6.610.166.77
readPileup0.130.010.15
scanBam0.590.040.63
scanBcf0.340.000.35
scanFa0.170.000.18
scanTabix0.080.000.12
seqnamesTabix0.010.000.02
sequenceLayer18.89 0.4519.36
stackStringsFromBam1.910.011.91
zip0.030.000.04