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BioC 3.0: CHECK report for Rsamtools on moscato1

This page was generated on 2015-04-10 09:46:18 -0700 (Fri, 10 Apr 2015).

Package 777/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsamtools 1.18.3
Bioconductor Package Maintainer
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/Rsamtools
Last Changed Rev: 100077 / Revision: 102249
Last Changed Date: 2015-03-02 13:57:17 -0800 (Mon, 02 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: Rsamtools
Version: 1.18.3
Command: rm -rf Rsamtools.buildbin-libdir Rsamtools.Rcheck && mkdir Rsamtools.buildbin-libdir Rsamtools.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rsamtools.buildbin-libdir Rsamtools_1.18.3.tar.gz >Rsamtools.Rcheck\00install.out 2>&1 && cp Rsamtools.Rcheck\00install.out Rsamtools-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=Rsamtools.buildbin-libdir --install="check:Rsamtools-install.out" --force-multiarch --no-vignettes --timings Rsamtools_1.18.3.tar.gz
StartedAt: 2015-04-10 05:15:54 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 05:25:41 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 587.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: Rsamtools.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Rsamtools.buildbin-libdir Rsamtools.Rcheck && mkdir Rsamtools.buildbin-libdir Rsamtools.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rsamtools.buildbin-libdir Rsamtools_1.18.3.tar.gz >Rsamtools.Rcheck\00install.out 2>&1 && cp Rsamtools.Rcheck\00install.out Rsamtools-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=Rsamtools.buildbin-libdir --install="check:Rsamtools-install.out" --force-multiarch --no-vignettes --timings Rsamtools_1.18.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.Rcheck'
* using R version 3.1.3 (2015-03-09)
* 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 '1.18.3'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'S4Vectors' 'IRanges' 'GenomeInfoDb' 'GenomicRanges' 'XVector'
  'Biostrings'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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:
  samtools/faidx.c:191:3: warning: too many arguments for format [-Wformat-extra-args]
  samtools/knetfile.c:416:5: warning: too many arguments for format [-Wformat-extra-args]
See 'D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   2.5Mb
    libs      1.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'ShortRead' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  'BiocGenerics:::selectSome' 'S4Vectors:::explodeIntBits'
  'S4Vectors:::implodeIntBits' 'S4Vectors:::makePowersOfTwo'
  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 ... NOTE
scanFa,FaFile-missing: no visible global function definition for
  'readRNAStringSet'
scanFa,FaFile-missing: no visible global function definition for
  'readAAStringSet'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  src/Makevars
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section 'Writing portable packages' in
the 'Writing R Extensions' manual.
* 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-3.0-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)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'D:/biocbld/bbs-3.0-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)
  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 the system RNG.
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [65s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
pileup 49.02   0.68   49.85
** running examples for arch 'x64' ... [69s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
pileup 53.76   0.68   54.54
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'Rsamtools_unit_tests.R' [55s]
 [55s] OK
** running tests for arch 'x64' ...
  Running 'Rsamtools_unit_tests.R' [65s]
 [65s] 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

WARNING: There were 2 warnings.
NOTE: There were 5 notes.
See
  'D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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
g++ -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c PileupBuffer.cpp -o PileupBuffer.o
g++ -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c PosCacheColl.cpp -o PosCacheColl.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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
g++ -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c ResultManager.cpp -o ResultManager.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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 S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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
bamfile.c: In function '_bamfile_close':
bamfile.c:44:9: warning: implicit declaration of function 'pileup_pbuffer_destroy' [-Wimplicit-function-declaration]
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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
g++ -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pileup.cpp -o pileup.o
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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
samtools/faidx.c: In function 'fai_read':
samtools/faidx.c:191:3: warning: unknown conversion type character 'l' in format [-Wformat]
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]
gcc -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386"
cp ../Rsamtools.mk.win "D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386/Rsamtools.mk"
mkdir -p "D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386"
cp libbam.a libbcf.a libtabix.a "D:/biocbld/bbs-3.0-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 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 io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o utilities.o zip_compression.o -pthread -fopenmp D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libbam.a D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libbcf.a D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -LD:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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
g++ -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c PileupBuffer.cpp -o PileupBuffer.o
g++ -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c PosCacheColl.cpp -o PosCacheColl.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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
g++ -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c ResultManager.cpp -o ResultManager.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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 S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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
bamfile.c: In function '_bamfile_close':
bamfile.c:44:9: warning: implicit declaration of function 'pileup_pbuffer_destroy' [-Wimplicit-function-declaration]
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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
g++ -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c pileup.cpp -o pileup.o
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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
samtools/faidx.c: In function 'fai_read':
samtools/faidx.c:191:3: warning: unknown conversion type character 'l' in format [-Wformat]
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]
gcc -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.0-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.0-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.0-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-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x64"
cp ../Rsamtools.mk.win "D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x64/Rsamtools.mk"
mkdir -p "D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64"
cp libbam.a libbcf.a libtabix.a "D:/biocbld/bbs-3.0-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 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 io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o utilities.o zip_compression.o -pthread -fopenmp D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libbcf.a D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -LD:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsamtools' as Rsamtools_1.18.3.zip
* DONE (Rsamtools)

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

nameusersystemelapsed
ApplyPileupsParam-class0.440.020.45
BamFile-class0.810.032.15
BamSampler-class2.030.092.12
BamViews-class0.060.000.07
BcfFile-class0.640.000.63
FaFile-class0.050.000.05
PileupFiles-class0.170.000.17
Rsamtools-package0.010.000.02
ScanBamParam-class0.470.020.48
ScanBcfParam-class000
TabixFile-class0.050.000.05
applyPileups0.090.000.09
headerTabix000
indexTabix0.040.000.05
pileup49.02 0.6849.85
quickBamFlagSummary0.030.000.03
readPileup0.090.000.10
scanBam0.440.020.45
scanBcf0.230.010.25
scanFa0.070.000.06
scanTabix0.040.020.49
seqnamesTabix0.020.000.01
zip0.010.010.03

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

nameusersystemelapsed
ApplyPileupsParam-class0.560.000.56
BamFile-class0.720.000.72
BamSampler-class1.950.112.05
BamViews-class0.080.000.08
BcfFile-class1.110.021.13
FaFile-class0.060.000.06
PileupFiles-class0.120.010.64
Rsamtools-package0.020.000.02
ScanBamParam-class0.670.020.69
ScanBcfParam-class000
TabixFile-class0.030.000.03
applyPileups0.110.010.13
headerTabix000
indexTabix0.020.040.04
pileup53.76 0.6854.54
quickBamFlagSummary0.030.000.03
readPileup0.110.000.11
scanBam0.520.050.56
scanBcf0.310.000.70
scanFa0.070.000.06
scanTabix0.080.000.08
seqnamesTabix000
zip0.010.010.03