Rsamtools 1.28.0
Bioconductor Package Maintainer
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/Rsamtools | | Branch: RELEASE_3_5 | | Last Commit: dfa5b6a | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf Rsamtools.buildbin-libdir Rsamtools.Rcheck && mkdir Rsamtools.buildbin-libdir Rsamtools.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rsamtools.buildbin-libdir Rsamtools_1.28.0.tar.gz >Rsamtools.Rcheck\00install.out 2>&1 && cp Rsamtools.Rcheck\00install.out Rsamtools-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=Rsamtools.buildbin-libdir --install="check:Rsamtools-install.out" --force-multiarch --no-vignettes --timings Rsamtools_1.28.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.28.0'
* 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 'C:/Users/biocbuild/bbs-3.5-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 'C:/Users/biocbuild/bbs-3.5-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 43.85 0.14 44.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
pileup 23.14 0.04 23.19
* 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
'C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'Rsamtools' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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 "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386"
cp ../Rsamtools.mk.win "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386/Rsamtools.mk"
mkdir -p "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386"
cp libbam.a libbcf.a libtabix.a "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386"
C:\Rtools\mingw_32\bin\nm.exe: 'libs': No such file
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o Rsamtools.dll tmp.def Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -pthread -fopenmp C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libbcf.a C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-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 "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x64"
cp ../Rsamtools.mk.win "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x64/Rsamtools.mk"
mkdir -p "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64"
cp libbam.a libbcf.a libtabix.a "C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64"
C:\Rtools\mingw_64\bin\nm.exe: 'libs': No such file
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o Rsamtools.dll tmp.def Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -pthread -fopenmp C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsamtools' as Rsamtools_1.28.0.zip
* DONE (Rsamtools)