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Package 406/462HostnameOS / ArchBUILDCHECKBUILD BIN
seqbias 1.1.0
Daniel Jones
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias
Last Changed Rev: 54802 / Revision: 55359
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 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: seqbias
Version: 1.1.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings seqbias_1.1.0.tar.gz
StartedAt: 2011-05-09 15:33:36 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 15:35:58 -0700 (Mon, 09 May 2011)
EllapsedTime: 142.5 seconds
RetCode: 0
Status:  OK  
CheckDir: seqbias.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/seqbias.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'seqbias/DESCRIPTION' ... OK
* this is package 'seqbias' version '1.1.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'seqbias' 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 ... NOTE
'library' or 'require' call not declared from: 'Rsamtools'
* 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 vignettes ... NOTE
'library' or 'require' calls not declared from:
  'Rsamtools' 'ggplot2'
* 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

seqbias.Rcheck/00install.out:

* installing *source* package 'seqbias' ...

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


** libs
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c sequencing_bias.cpp -o sequencing_bias.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c kmers.cpp -o kmers.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c miscmath.cpp -o miscmath.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c common.cpp -o common.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O3 -Wall  -std=gnu99 -c table.c -o table.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O3 -Wall  -std=gnu99 -c logger.c -o logger.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c seqbias.cpp -o seqbias.o
In file included from E:/biocbld/BBS-2˜1.9-B/R/include/R.h:44:0,
                 from seqbias.cpp:10:
E:/biocbld/BBS-2˜1.9-B/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:\rtools213\mingw\bin\../lib/gcc/mingw32/4.5.0/../../../../include/wingdi.h:313:0: note: this is the location of the previous definition
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/aliascontent.cpp -o yaml-cpp/aliascontent.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/map.cpp -o yaml-cpp/map.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/node.cpp -o yaml-cpp/node.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/null.cpp -o yaml-cpp/null.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/parserstate.cpp -o yaml-cpp/parserstate.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/scalar.cpp -o yaml-cpp/scalar.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/sequence.cpp -o yaml-cpp/sequence.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O2 -Wall  -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O3 -Wall  -std=gnu99 -c gnulib/asprintf.c -o gnulib/asprintf.o
gnulib/asprintf.c: In function 'asprintf':
gnulib/asprintf.c:37:3: warning: implicit declaration of function 'vasprintf'
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O3 -Wall  -std=gnu99 -c gnulib/printf-args.c -o gnulib/printf-args.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O3 -Wall  -std=gnu99 -c gnulib/printf-parse.c -o gnulib/printf-parse.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O3 -Wall  -std=gnu99 -c gnulib/vasnprintf.c -o gnulib/vasnprintf.o
gcc  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DNEED_ASPRINTF   -I"E:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/include"   -Wall   -O3 -Wall  -std=gnu99 -c gnulib/vasprintf.c -o gnulib/vasprintf.o
g++ -shared -s -static-libgcc -o seqbias.dll tmp.def sequencing_bias.o kmers.o miscmath.o common.o table.o logger.o seqbias.o yaml-cpp/aliascontent.o yaml-cpp/conversion.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/map.o yaml-cpp/node.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/parserstate.o yaml-cpp/regex.o yaml-cpp/scalar.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/sequence.o yaml-cpp/simplekey.o yaml-cpp/stream.o yaml-cpp/tag.o gnulib/asprintf.o gnulib/printf-args.o gnulib/printf-parse.o gnulib/vasnprintf.o gnulib/vasprintf.o -LE:/biocbld/bbs-2.9-bioc/R/library/Rsamtools/usrlib/i386 -lbam -lbcf -lRzlib -lws2_32 -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/seqbias.Rcheck/seqbias/libs/i386
** R
** inst
** preparing package for lazy loading
Loading required package: IRanges

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 ...
   'overview.Rnw' 
** testing if installed package can be loaded

* DONE (seqbias)

seqbias.Rcheck/seqbias-Ex.timings:

nameusersystemelapsed
count_reads0.060.000.07
kmer_freq0.560.030.63
random_intervals0.050.060.10
seqbias_fit3.230.003.25
seqbias_load4.911.276.25
seqbias_predict3.680.013.75
seqbias_save4.821.356.24