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Package 390/462HostnameOS / ArchBUILDCHECKBUILD BIN
Rsamtools 1.5.12
Biocore Team c/o BioC user list
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsamtools
Last Changed Rev: 55340 / Revision: 55359
Last Changed Date: 2011-05-08 19:44:09 -0700 (Sun, 08 May 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: Rsamtools
Version: 1.5.12
Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings Rsamtools_1.5.12.tar.gz
StartedAt: 2011-05-09 19:44:31 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 19:47:52 -0700 (Mon, 09 May 2011)
EllapsedTime: 201.0 seconds
RetCode: 0
Status:  OK  
CheckDir: Rsamtools.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/Rsamtools.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: x86_64-pc-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 '1.5.12'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  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

Rsamtools.Rcheck/00install.out:

* installing *source* package 'Rsamtools' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c Biostrings_stubs.c -o Biostrings_stubs.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c IRanges_stubs.c -o IRanges_stubs.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c as_bam.c -o as_bam.o
In file included from D:/biocbld/BBS-2˜1.9-B/R/include/Rdefines.h:26:0,
                 from bamfile.h:4,
                 from as_bam.c:2:
D:/biocbld/BBS-2˜1.9-B/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:/rtools213/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/wingdi.h:63:0: note: this is the location of the previous definition
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c bamfile.c -o bamfile.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c bcffile.c -o bcffile.o
In file included from D:/biocbld/BBS-2˜1.9-B/R/include/Rdefines.h:26:0,
                 from bcffile.h:4,
                 from bcffile.c:5:
D:/biocbld/BBS-2˜1.9-B/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:/rtools213/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/wingdi.h:63:0: note: this is the location of the previous definition
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c encode.c -o encode.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c fafile.c -o fafile.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c io_sam.c -o io_sam.o
In file included from D:/biocbld/BBS-2˜1.9-B/R/include/Rdefines.h:26:0,
                 from bamfile.h:4,
                 from io_sam.c:3:
D:/biocbld/BBS-2˜1.9-B/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:/rtools213/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/wingdi.h:63:0: note: this is the location of the previous definition
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c pileupbam.c -o pileupbam.o
In file included from D:/biocbld/BBS-2˜1.9-B/R/include/Rdefines.h:26:0,
                 from pileupbam.h:4,
                 from pileupbam.c:3:
D:/biocbld/BBS-2˜1.9-B/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:/rtools213/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/wingdi.h:63:0: note: this is the location of the previous definition
pileupbam.c: In function '_pileup_bam1.clone.4':
pileupbam.c:302:10: warning: 's0' may be used uninitialized in this function
pileupbam.c:302:15: warning: 'q0' may be used uninitialized in this function
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools_patch.c -o samtools_patch.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c tabixfile.c -o tabixfile.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c utilities.c -o utilities.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bgzf.c -o samtools/bgzf.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/kstring.c -o samtools/kstring.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bam_aux.c -o samtools/bam_aux.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bam.c -o samtools/bam.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -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'
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/sam.c -o samtools/sam.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bam_index.c -o samtools/bam_index.o
samtools/bam_index.c: In function 'ks_shuffle_off':
samtools/bam_index.c:52:1: warning: implicit declaration of function 'drand48'
samtools/bam_index.c: In function 'bam_idxstats':
samtools/bam_index.c:531:4: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:531:4: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:531:4: warning: too many arguments for format
samtools/bam_index.c:535:2: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:535:2: warning: too many arguments for format
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bam_pileup.c -o samtools/bam_pileup.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
samtools/bam_lpileup.c: In function 'ks_shuffle_node':
samtools/bam_lpileup.c:15:1: warning: implicit declaration of function 'drand48'
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bam_md.c -o samtools/bam_md.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/glf.c -o samtools/glf.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/razf.c -o samtools/razf.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/faidx.c -o samtools/faidx.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -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
samtools/knetfile.c:413:5: warning: too many arguments for format
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bam_sort.c -o samtools/bam_sort.o
samtools/bam_sort.c: In function 'ks_shuffle_heap':
samtools/bam_sort.c:53:1: warning: implicit declaration of function 'drand48'
samtools/bam_sort.c: At top level:
samtools/bam_sort.c:297:1: warning: 'bam1_lt' is static but used in inline function '__ks_insertsort_sort' which is not static
samtools/bam_sort.c:53:1: warning: 'heap_lt' is static but used in inline function '__ks_insertsort_heap' which is not static
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/sam_header.c -o samtools/sam_header.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bam_reheader.c -o samtools/bam_reheader.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/kprobaln.c -o samtools/kprobaln.o
x86_64-w64-mingw32-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/glf.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
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
samtools/bcftools/bcfutils.c: In function 'bcf_shuffle':
samtools/bcftools/bcfutils.c:248:3: warning: implicit declaration of function 'drand48'
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bcftools/ld.c -o samtools/bcftools/ld.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bcftools/index.c -o samtools/bcftools/index.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
x86_64-w64-mingw32-ar crs libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/ld.o samtools/bcftools/kfunc.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c tabix/index.c -o tabix/index.o
tabix/index.c: In function 'ks_shuffle_offt':
tabix/index.c:22:1: warning: implicit declaration of function 'drand48'
x86_64-w64-mingw32-gcc  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include"    -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 -c tabix/bedidx.c -o tabix/bedidx.o
x86_64-w64-mingw32-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-2.9-bioc/meat/Rsamtools.Rcheck/Rsamtools/usretc/x64
cp Rsamtools.mk D:/biocbld/bbs-2.9-bioc/meat/Rsamtools.Rcheck/Rsamtools/usretc/x64
mkdir -p D:/biocbld/bbs-2.9-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/samtools/bcftools
mkdir -p D:/biocbld/bbs-2.9-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/tabix
cp samtools/*.h D:/biocbld/bbs-2.9-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/samtools/
cp samtools/bcftools/*h D:/biocbld/bbs-2.9-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/samtools/bcftools/
cp tabix/*h D:/biocbld/bbs-2.9-bioc/meat/Rsamtools.Rcheck/Rsamtools/include/tabix/
mkdir -p D:/biocbld/bbs-2.9-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib/x64
cp libbam.a libbcf.a libtabix.a D:/biocbld/bbs-2.9-bioc/meat/Rsamtools.Rcheck/Rsamtools/usrlib/x64
C:\Rtools213\MinGW64\bin\x86_64-w64-mingw32-nm.exe: 'libs': No such file
x86_64-w64-mingw32-gcc -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 -L. -lbam -lbcf -ltabix -lRzlib -lws2_32 -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/Rsamtools.Rcheck/Rsamtools/libs/x64
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'Rsamtools-Overview.Rnw' 
   'Rsamtools-UsingCLibraries.Rnw' 
** testing if installed package can be loaded

* DONE (Rsamtools)

Rsamtools.Rcheck/Rsamtools-Ex.timings:

nameusersystemelapsed
BamFile-class0.350.000.34
BamViews-class2.370.002.39
BcfFile-class1.500.031.55
FaFile-class0.140.030.17
PileupFiles-class0.400.010.42
PileupParam-class0.380.040.41
Rsamtools-package0.010.000.01
ScanBamParam-class0.130.000.13
ScanBcfParam-class0.010.000.01
TabixFile-class0.220.000.22
applyPileups0.110.020.12
headerTabix0.020.000.02
indexTabix0.050.000.04
readBamGappedAlignments0.230.000.24
readPileup0.090.000.09
scanBam0.320.040.36
scanBcf0.590.020.61
scanFa0.110.020.13
scanTabix0.090.000.09
seqnamesTabix0.000.010.01
yieldTabix0.280.000.29