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Package 355/419HostnameOS / ArchBUILDCHECKBUILD BIN
Rsamtools 1.2.3
Biocore Team c/o BioC user list
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/Rsamtools
Last Changed Rev: 51873 / Revision: 54281
Last Changed Date: 2011-01-11 16:14:33 -0800 (Tue, 11 Jan 2011)
lamb2 Linux (openSUSE 11.2) / 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: 1.2.3
Command: D:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings Rsamtools_1.2.3.tar.gz
StartedAt: 2011-03-31 10:28:48 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 10:31:30 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 161.1 seconds
RetCode: 0
Status:  OK  
CheckDir: Rsamtools.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/Rsamtools.Rcheck'
* using R version 2.12.2 (2011-02-25)
* 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 '1.2.3'
* 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 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 package vignettes in 'inst/doc' ... 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˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c io_sam.c -o io_sam.o
In file included from D:/biocbld/BBS-2˜1.7-B/R/include/Rdefines.h:26:0,
                 from D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include/IRanges_defines.h:18,
                 from D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include/IRanges_interface.h:12,
                 from io_sam.c:5:
D:/biocbld/BBS-2˜1.7-B/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:/rtools212/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˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c utilities.c -o utilities.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c encode.c -o encode.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c Biostrings_stubs.c -o Biostrings_stubs.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c IRanges_stubs.c -o IRanges_stubs.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c R_init_Rsamtools.c -o R_init_Rsamtools.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c samtools/bam.c -o samtools/bam.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -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:166:2: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:166:2: warning: format '%s' expects type 'char *', but argument 3 has type 'int64_t'
samtools/bam_import.c:166:2: warning: too many arguments for format
samtools/bam_import.c: In function 'append_text':
samtools/bam_import.c:179:13: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
samtools/bam_import.c:186:9: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t'
samtools/bam_import.c:186:9: warning: format '%ld' expects type 'long int', but argument 4 has type 'size_t'
samtools/bam_import.c:186:9: warning: format '%ld' expects type 'long int', but argument 5 has type 'size_t'
samtools/bam_import.c:186:9: warning: format '%ld' expects type 'long int', but argument 6 has type 'size_t'
samtools/bam_import.c: In function 'sam_read1':
samtools/bam_import.c:318:5: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:318:5: warning: too many arguments for format
samtools/bam_import.c:387:10: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:387:10: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:387:10: warning: too many arguments for format
samtools/bam_import.c:401:10: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:401:10: warning: unknown conversion type character 'l' in format
samtools/bam_import.c:401:10: warning: too many arguments for format
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c samtools/bam_sort.c -o samtools/bam_sort.o
samtools/bam_sort.c:273:1: 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˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c samtools/bam_index.c -o samtools/bam_index.o
samtools/bam_index.c: In function 'bam_index_core':
samtools/bam_index.c:205:6: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:205:6: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:205:6: warning: too many arguments for format
samtools/bam_index.c: In function 'bam_idxstats':
samtools/bam_index.c:524:4: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:524:4: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:524:4: warning: too many arguments for format
samtools/bam_index.c:528:2: warning: unknown conversion type character 'l' in format
samtools/bam_index.c:528:2: warning: too many arguments for format
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c samtools/kstring.c -o samtools/kstring.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c samtools/bam_aux.c -o samtools/bam_aux.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c samtools/sam_header.c -o samtools/sam_header.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c samtools/bgzf.c -o samtools/bgzf.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c samtools/razf.c -o samtools/razf.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c samtools/knetfile.c -o samtools/knetfile.o
samtools/knetfile.c: In function 'khttp_connect_file':
samtools/knetfile.c:414:5: warning: unknown conversion type character 'l' in format
samtools/knetfile.c:414:5: warning: too many arguments for format
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c samtools/sam.c -o samtools/sam.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c samtools/bam_pileup.c -o samtools/bam_pileup.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/BBS-2˜1.7-B/R/include"   -I"D:/biocbld/BBS-2˜1.7-B/R/library/Biostrings/include" -I"D:/biocbld/BBS-2˜1.7-B/R/library/IRanges/include"   -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64   -O2 -Wall  -std=gnu99 -c samtools/faidx.c -o samtools/faidx.o
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o Rsamtools.dll tmp.def io_sam.o utilities.o encode.o Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o samtools/bam.o samtools/bam_import.o samtools/bam_sort.o samtools/bam_index.o samtools/kstring.o samtools/bam_aux.o samtools/sam_header.o samtools/bgzf.o samtools/razf.o samtools/knetfile.o samtools/sam.o samtools/bam_pileup.o samtools/faidx.o -lRzlib -lws2_32 -LD:/biocbld/BBS-2˜1.7-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.7-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, mapply, order, paste, pmax, pmax.int, pmin,
    pmin.int, rbind, rep.int, table

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (Rsamtools)

Rsamtools.Rcheck/Rsamtools-Ex.timings:

nameusersystemelapsed
BamViews-class1.590.031.64
Rsamtools-package0.030.000.03
ScanBamParam-class0.280.000.29
readBamGappedAlignments0.030.020.04
readPileup0.110.000.11
scanBam0.200.050.25