Rsamtools 1.10.2
Bioconductor Package Maintainer
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/Rsamtools | | Last Changed Rev: 71100 / Revision: 74773 | | Last Changed Date: 2012-11-09 14:22:35 -0800 (Fri, 09 Nov 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory 'D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rsamtools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rsamtools' version '1.10.2'
* 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 whether package 'Rsamtools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 for unstated dependencies in R code ... OK
* 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 for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/i386/Rsamtools.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/x64/Rsamtools.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'putchar', possibly from 'putchar' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console. The detected symbols
are linked into the code but might come from libraries and not actually
be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
BamFile-class 20.16 0.31 21.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
BamFile-class 20.89 0.22 21.12
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There was 1 note.
See
'D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'Rsamtools' ...
** libs
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
In file included from D:/biocbld/BBS-2˜1.11-/R/include/Rdefines.h:26:0,
from bamfile.h:4,
from as_bam.c:2:
D:/biocbld/BBS-2˜1.11-/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/wingdi.h:70:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c bamfile.c -o bamfile.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
In file included from D:/biocbld/BBS-2˜1.11-/R/include/Rdefines.h:26:0,
from bcffile.h:4,
from bcffile.c:5:
D:/biocbld/BBS-2˜1.11-/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/wingdi.h:70:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c encode.c -o encode.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c fafile.c -o fafile.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
In file included from D:/biocbld/BBS-2˜1.11-/R/include/Rdefines.h:26:0,
from bamfile.h:4,
from io_sam.c:4:
D:/biocbld/BBS-2˜1.11-/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/wingdi.h:70:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
In file included from D:/biocbld/BBS-2˜1.11-/R/include/Rdefines.h:26:0,
from pileupbam.h:4,
from pileupbam.c:3:
D:/biocbld/BBS-2˜1.11-/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/wingdi.h:70:0: note: this is the location of the previous definition
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools_patch.c -o samtools_patch.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c tabixfile.c -o tabixfile.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c zip_compression.c -o zip_compression.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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:47:0: warning: "ftello" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/stdio.h:431:0: note: this is the location of the previous definition
samtools/bgzf.c:48:0: warning: "fseeko" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/stdio.h:416:0: note: this is the location of the previous definition
samtools/bgzf.c: In function 'bgzf_close':
samtools/bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/kstring.c -o samtools/kstring.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/bam.c -o samtools/bam.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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:167:2: warning: implicit declaration of function '_samtools_abort' [-Wimplicit-function-declaration]
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/sam.c -o samtools/sam.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
samtools/bam_index.c: In function 'bam_idxstats':
samtools/bam_index.c:544:4: warning: unknown conversion type character 'l' in format [-Wformat]
samtools/bam_index.c:544:4: warning: unknown conversion type character 'l' in format [-Wformat]
samtools/bam_index.c:544:4: warning: too many arguments for format [-Wformat-extra-args]
samtools/bam_index.c:548:2: warning: unknown conversion type character 'l' in format [-Wformat]
samtools/bam_index.c:548:2: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
samtools/bam_pileup.c: In function 'resolve_cigar2':
samtools/bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/bam_md.c -o samtools/bam_md.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/razf.c -o samtools/razf.o
samtools/razf.c: In function 'razf_seek':
samtools/razf.c:761:17: warning: implicit declaration of function '_samtools_abort' [-Wimplicit-function-declaration]
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/faidx.c -o samtools/faidx.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/knetfile.c -o samtools/knetfile.o
samtools/knetfile.c: In function 'khttp_connect_file':
samtools/knetfile.c:413:5: warning: unknown conversion type character 'l' in format [-Wformat]
samtools/knetfile.c:413:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/bam_sort.c -o samtools/bam_sort.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/sam_header.c -o samtools/sam_header.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/kprobaln.c -o samtools/kprobaln.o
samtools/kprobaln.c: In function 'kpa_glocal':
samtools/kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
ar crs libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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/kfunc.c -o samtools/bcftools/kfunc.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/bcftools/index.c -o samtools/bcftools/index.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
ar crs libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/kfunc.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c tabix/index.c -o tabix/index.o
gcc -m32 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O3 -Wall -std=gnu99 -mtune=core2 -c tabix/bedidx.c -o tabix/bedidx.o
ar crs libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386"
cp ../Rsamtools.mk.win "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386/Rsamtools.mk"
mkdir -p "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386"
cp libbam.a libbcf.a libtabix.a "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386"
C:\Rtools216\gcc-4.6.3\bin\nm.exe: 'libs': No such file
gcc -m32 -shared -s -static-libgcc -o Rsamtools.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o bcffile.o encode.o fafile.o io_sam.o pileupbam.o samtools_patch.o tabixfile.o utilities.o zip_compression.o -fopenmp D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libbam.a D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libbcf.a D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -LD:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.11-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'Rsamtools-Overview.Rnw'
'Rsamtools-UsingCLibraries.Rnw'
** testing if installed package can be loaded
install for x64
* installing *source* package 'Rsamtools' ...
** libs
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
In file included from D:/biocbld/BBS-2˜1.11-/R/include/Rdefines.h:26:0,
from bamfile.h:4,
from as_bam.c:2:
D:/biocbld/BBS-2˜1.11-/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/wingdi.h:70:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c bamfile.c -o bamfile.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
In file included from D:/biocbld/BBS-2˜1.11-/R/include/Rdefines.h:26:0,
from bcffile.h:4,
from bcffile.c:5:
D:/biocbld/BBS-2˜1.11-/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/wingdi.h:70:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c encode.c -o encode.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c fafile.c -o fafile.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
In file included from D:/biocbld/BBS-2˜1.11-/R/include/Rdefines.h:26:0,
from bamfile.h:4,
from io_sam.c:4:
D:/biocbld/BBS-2˜1.11-/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/wingdi.h:70:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
In file included from D:/biocbld/BBS-2˜1.11-/R/include/Rdefines.h:26:0,
from pileupbam.h:4,
from pileupbam.c:3:
D:/biocbld/BBS-2˜1.11-/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/wingdi.h:70:0: note: this is the location of the previous definition
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools_patch.c -o samtools_patch.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c tabixfile.c -o tabixfile.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c zip_compression.c -o zip_compression.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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:47:0: warning: "ftello" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/stdio.h:431:0: note: this is the location of the previous definition
samtools/bgzf.c:48:0: warning: "fseeko" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/stdio.h:416:0: note: this is the location of the previous definition
samtools/bgzf.c: In function 'bgzf_close':
samtools/bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/kstring.c -o samtools/kstring.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/bam.c -o samtools/bam.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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:167:2: warning: implicit declaration of function '_samtools_abort' [-Wimplicit-function-declaration]
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/sam.c -o samtools/sam.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
samtools/bam_index.c: In function 'bam_idxstats':
samtools/bam_index.c:544:4: warning: unknown conversion type character 'l' in format [-Wformat]
samtools/bam_index.c:544:4: warning: unknown conversion type character 'l' in format [-Wformat]
samtools/bam_index.c:544:4: warning: too many arguments for format [-Wformat-extra-args]
samtools/bam_index.c:548:2: warning: unknown conversion type character 'l' in format [-Wformat]
samtools/bam_index.c:548:2: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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
samtools/bam_pileup.c: In function 'resolve_cigar2':
samtools/bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/bam_md.c -o samtools/bam_md.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/razf.c -o samtools/razf.o
samtools/razf.c: In function 'razf_seek':
samtools/razf.c:761:17: warning: implicit declaration of function '_samtools_abort' [-Wimplicit-function-declaration]
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/faidx.c -o samtools/faidx.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/knetfile.c -o samtools/knetfile.o
samtools/knetfile.c: In function 'khttp_connect_file':
samtools/knetfile.c:413:5: warning: unknown conversion type character 'l' in format [-Wformat]
samtools/knetfile.c:413:5: warning: too many arguments for format [-Wformat-extra-args]
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/bam_sort.c -o samtools/bam_sort.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/sam_header.c -o samtools/sam_header.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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:11:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/kprobaln.c -o samtools/kprobaln.o
samtools/kprobaln.c: In function 'kpa_glocal':
samtools/kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
ar crs libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -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/kfunc.c -o samtools/bcftools/kfunc.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/bcftools/index.c -o samtools/bcftools/index.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
ar crs libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/kfunc.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c tabix/index.c -o tabix/index.o
gcc -m64 -I"D:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -I"D:/biocbld/bbs-2.11-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.11-bioc/R/library/IRanges/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -D_LARGEFILE64_SOURCE -O2 -Wall -std=gnu99 -mtune=core2 -c tabix/bedidx.c -o tabix/bedidx.o
ar crs libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x64"
cp ../Rsamtools.mk.win "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x64/Rsamtools.mk"
mkdir -p "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64"
cp libbam.a libbcf.a libtabix.a "D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64"
C:\Rtools216\gcc-4.6.3\bin\nm.exe: 'libs': No such file
gcc -m64 -shared -s -static-libgcc -o Rsamtools.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o bcffile.o encode.o fafile.o io_sam.o pileupbam.o samtools_patch.o tabixfile.o utilities.o zip_compression.o -fopenmp D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libbcf.a D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -LD:/biocbld/bbs-2.11-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.11-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.11-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rsamtools' as Rsamtools_1.10.2.zip
* DONE (Rsamtools)