BioC 3.4: CHECK report for Rsamtools on moscato1

Package: Rsamtools

Version: 1.25.2

Command: rm -rf Rsamtools.buildbin-libdir Rsamtools.Rcheck && mkdir Rsamtools.buildbin-libdir Rsamtools.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rsamtools.buildbin-libdir Rsamtools_1.25.2.tar.gz >Rsamtools.Rcheck\00install.out 2>&1 && cp Rsamtools.Rcheck\00install.out Rsamtools-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Rsamtools.buildbin-libdir --install="check:Rsamtools-install.out" --force-multiarch --no-vignettes --timings Rsamtools_1.25.2.tar.gz

StartedAt: 2016-09-20 15:53:24 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 16:01:35 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 491.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Rsamtools.Rcheck

Warnings: 1

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### Running command:
###
###   rm -rf Rsamtools.buildbin-libdir Rsamtools.Rcheck && mkdir Rsamtools.buildbin-libdir Rsamtools.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rsamtools.buildbin-libdir Rsamtools_1.25.2.tar.gz >Rsamtools.Rcheck\00install.out 2>&1 && cp Rsamtools.Rcheck\00install.out Rsamtools-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=Rsamtools.buildbin-libdir --install="check:Rsamtools-install.out" --force-multiarch --no-vignettes --timings Rsamtools_1.25.2.tar.gz
###
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* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rsamtools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rsamtools' version '1.25.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Rsamtools' can be installed ... WARNING
Found the following significant warnings:
  samtools/faidx.c:191:3: warning: too many arguments for format [-Wformat-extra-args]
See 'D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'S4Vectors:::explodeIntBits' 'S4Vectors:::implodeIntBits'
  'S4Vectors:::makePowersOfTwo' 'S4Vectors:::quick_unlist'
  'S4Vectors:::selectSome'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... 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 ... 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-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/i386/Rsamtools.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
pileup 41.09   0.08   42.65
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
pileup 36.66   0.06    36.8
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'Rsamtools_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'Rsamtools_unit_tests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'Rsamtools' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c PileupBuffer.cpp -o PileupBuffer.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c PosCacheColl.cpp -o PosCacheColl.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c ResultManager.cpp -o ResultManager.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c as_bam.c -o as_bam.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c bam_data.c -o bam_data.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from BamRangeIterator.h:7:0,
                 from bam_mate_iter.cpp:2:
BamIterator.h: In constructor 'BamIterator::BamIterator(bamFile, const bam_index_t*)':
BamIterator.h:80:10: warning: 'BamIterator::iter_done' will be initialized after [-Wreorder]
     bool iter_done;
          ^
BamIterator.h:29:13: warning:   'bam1_t* BamIterator::bam' [-Wreorder]
     bam1_t *bam;
             ^
BamIterator.h:83:5: warning:   when initialized here [-Wreorder]
     BamIterator(bamFile bfile, const bam_index_t *bindex) :
     ^
BamIterator.h:29:13: warning: 'BamIterator::bam' will be initialized after [-Wreorder]
     bam1_t *bam;
             ^
BamIterator.h:15:14: warning:   '_BAM_DATA* BamIterator::bam_data' [-Wreorder]
     BAM_DATA bam_data;
              ^
BamIterator.h:83:5: warning:   when initialized here [-Wreorder]
     BamIterator(bamFile bfile, const bam_index_t *bindex) :
     ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c bambuffer.c -o bambuffer.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c bamfile.c -o bamfile.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c bcffile.c -o bcffile.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c encode.c -o encode.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c fafile.c -o fafile.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c idxstats.c -o idxstats.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c io_sam.c -o io_sam.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
C:/Rtools/mingw_32/bin/g++  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c pileup.cpp -o pileup.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c pileupbam.c -o pileupbam.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools_patch.c -o samtools_patch.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c scan_bam_data.c -o scan_bam_data.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c tabixfile.c -o tabixfile.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c tagfilter.c -o tagfilter.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c zip_compression.c -o zip_compression.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=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]
  int i, tmp, stop = 0;
         ^
samtools/bgzf.c: In function 'bgzf_close':
samtools/bgzf.c:592:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int ret, count, block_length;
           ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/kstring.c -o samtools/kstring.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_aux.c -o samtools/bam_aux.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam.c -o samtools/bam.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=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]
  abort();
  ^
samtools/bam_import.c: In function 'append_text':
samtools/bam_import.c:181:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat=]
             fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
             ^
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t' [-Wformat=]
         fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,(long)header->n_text,x,y);
         ^
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=]
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat=]
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/sam.c -o samtools/sam.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_index.c -o samtools/bam_index.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_pileup.c -o samtools/bam_pileup.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_md.c -o samtools/bam_md.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=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]
                 abort();
                 ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=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=]
   sscanf(p, "%d%lld%d%d", &len, &offset, &line_blen, &line_len);
   ^
samtools/faidx.c:191:3: warning: format '%d' expects argument of type 'int *', but argument 4 has type 'long long int *' [-Wformat=]
samtools/faidx.c:191:3: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/knetfile.c -o samtools/knetfile.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_sort.c -o samtools/bam_sort.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/sam_header.c -o samtools/sam_header.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=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]
  bam_header_t *old;
                ^
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=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]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
C:/Rtools/mingw_32/bin/ar crs libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/index.c -o samtools/bcftools/index.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
C:/Rtools/mingw_32/bin/ar crs libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c tabix/index.c -o tabix/index.o
C:/Rtools/mingw_32/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O3 -Wall  -std=gnu99 -mtune=core2 -c tabix/bedidx.c -o tabix/bedidx.o
C:/Rtools/mingw_32/bin/ar crs libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386"
cp ../Rsamtools.mk.win "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386/Rsamtools.mk"
mkdir -p "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386"
cp libbam.a libbcf.a libtabix.a "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386"
C:\Rtools\mingw_32\bin\nm.exe: 'libs': No such file
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Rsamtools.dll tmp.def Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -pthread -fopenmp D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libbam.a D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libbcf.a D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -LD:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Lc:/local323/lib/i386 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.4-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
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c PileupBuffer.cpp -o PileupBuffer.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c PosCacheColl.cpp -o PosCacheColl.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c ResultManager.cpp -o ResultManager.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c as_bam.c -o as_bam.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c bam_data.c -o bam_data.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from BamRangeIterator.h:7:0,
                 from bam_mate_iter.cpp:2:
BamIterator.h: In constructor 'BamIterator::BamIterator(bamFile, const bam_index_t*)':
BamIterator.h:80:10: warning: 'BamIterator::iter_done' will be initialized after [-Wreorder]
     bool iter_done;
          ^
BamIterator.h:29:13: warning:   'bam1_t* BamIterator::bam' [-Wreorder]
     bam1_t *bam;
             ^
BamIterator.h:83:5: warning:   when initialized here [-Wreorder]
     BamIterator(bamFile bfile, const bam_index_t *bindex) :
     ^
BamIterator.h:29:13: warning: 'BamIterator::bam' will be initialized after [-Wreorder]
     bam1_t *bam;
             ^
BamIterator.h:15:14: warning:   '_BAM_DATA* BamIterator::bam_data' [-Wreorder]
     BAM_DATA bam_data;
              ^
BamIterator.h:83:5: warning:   when initialized here [-Wreorder]
     BamIterator(bamFile bfile, const bam_index_t *bindex) :
     ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c bambuffer.c -o bambuffer.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c bamfile.c -o bamfile.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c bcffile.c -o bcffile.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c encode.c -o encode.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c fafile.c -o fafile.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c idxstats.c -o idxstats.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c io_sam.c -o io_sam.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
C:/Rtools/mingw_64/bin/g++  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O2 -Wall  -mtune=core2 -c pileup.cpp -o pileup.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c pileupbam.c -o pileupbam.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools_patch.c -o samtools_patch.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c scan_bam_data.c -o scan_bam_data.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c tabixfile.c -o tabixfile.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c tagfilter.c -o tagfilter.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c zip_compression.c -o zip_compression.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=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]
  int i, tmp, stop = 0;
         ^
samtools/bgzf.c: In function 'bgzf_close':
samtools/bgzf.c:592:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
  int ret, count, block_length;
           ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/kstring.c -o samtools/kstring.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_aux.c -o samtools/bam_aux.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam.c -o samtools/bam.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=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]
  abort();
  ^
samtools/bam_import.c: In function 'append_text':
samtools/bam_import.c:181:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat=]
             fprintf(stderr,"realloc failed to alloc %ld bytes\n", y);
             ^
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat=]
         fprintf(stderr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n",  header->l_text+str->l+1,(long)header->n_text,x,y);
         ^
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=]
samtools/bam_import.c:188:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat=]
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/sam.c -o samtools/sam.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_index.c -o samtools/bam_index.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_pileup.c -o samtools/bam_pileup.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_md.c -o samtools/bam_md.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=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]
                 abort();
                 ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=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=]
   sscanf(p, "%d%lld%d%d", &len, &offset, &line_blen, &line_len);
   ^
samtools/faidx.c:191:3: warning: format '%d' expects argument of type 'int *', but argument 4 has type 'long long int *' [-Wformat=]
samtools/faidx.c:191:3: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/knetfile.c -o samtools/knetfile.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bam_sort.c -o samtools/bam_sort.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/sam_header.c -o samtools/sam_header.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=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]
  bam_header_t *old;
                ^
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=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]
  int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
                     ^
C:/Rtools/mingw_64/bin/ar crs libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/index.c -o samtools/bcftools/index.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
C:/Rtools/mingw_64/bin/ar crs libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c tabix/index.c -o tabix/index.o
C:/Rtools/mingw_64/bin/gcc  -I"D:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.4-B/R/include" -DNDEBUG    -I"D:/biocbld/bbs-3.4-bioc/R/library/S4Vectors/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/XVector/include" -I"D:/biocbld/bbs-3.4-bioc/R/library/Biostrings/include" -I"c:/local323/include"  -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE   -O2 -Wall  -std=gnu99 -mtune=core2 -c tabix/bedidx.c -o tabix/bedidx.o
C:/Rtools/mingw_64/bin/ar crs libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x64"
cp ../Rsamtools.mk.win "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x64/Rsamtools.mk"
mkdir -p "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64"
cp libbam.a libbcf.a libtabix.a "D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64"
C:\Rtools\mingw_64\bin\nm.exe: 'libs': No such file
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Rsamtools.dll tmp.def Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -pthread -fopenmp D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libbcf.a D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -LD:/biocbld/bbs-3.4-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Lc:/local323/lib/x64 -Lc:/local323/lib -LD:/biocbld/BBS-3˜1.4-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.4-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsamtools' as Rsamtools_1.25.2.zip
* DONE (Rsamtools)

name	user	system	elapsed
ApplyPileupsParam-class	0.19	0.00	0.19
BamFile-class	0.42	0.05	2.95
BamViews-class	0.03	0.00	0.03
BcfFile-class	0.39	0.01	0.40
FaFile-class	0.03	0.00	0.03
PileupFiles-class	0.11	0.00	0.11
Rsamtools-package	0.02	0.00	0.02
ScanBamParam-class	0.56	0.03	0.59
ScanBcfParam-class	0	0	0
TabixFile-class	0.03	0.00	0.03
applyPileups	0.09	0.00	0.10
headerTabix	0	0	0
indexTabix	0.04	0.00	0.03
pileup	41.09	0.08	42.65
quickBamFlagSummary	0.03	0.00	0.03
readPileup	0.06	0.00	0.06
scanBam	0.48	0.05	0.53
scanBcf	0.25	0.01	0.27
scanFa	0.03	0.00	0.03
scanTabix	0.05	0.00	0.05
seqnamesTabix	0	0	0
testPairedEndBam	0.03	0.00	0.03
zip	0.03	0.00	0.03

name	user	system	elapsed
ApplyPileupsParam-class	0.2	0.0	0.2
BamFile-class	0.53	0.02	0.55
BamViews-class	0.03	0.00	0.03
BcfFile-class	0.70	0.01	0.72
FaFile-class	0.03	0.00	0.03
PileupFiles-class	0.13	0.00	0.13
Rsamtools-package	0.01	0.00	0.01
ScanBamParam-class	0.83	0.02	0.85
ScanBcfParam-class	0	0	0
TabixFile-class	0.03	0.00	0.03
applyPileups	0.09	0.00	0.09
headerTabix	0.02	0.00	0.02
indexTabix	0.03	0.00	0.03
pileup	36.66	0.06	36.80
quickBamFlagSummary	0.03	0.00	0.04
readPileup	0.06	0.00	0.06
scanBam	0.50	0.03	0.53
scanBcf	0.22	0.05	0.26
scanFa	0.03	0.00	0.03
scanTabix	0.05	0.00	0.05
seqnamesTabix	0.01	0.00	0.02
testPairedEndBam	0.02	0.00	0.01
zip	0.03	0.00	0.03