seqbias 1.0.0
Daniel Jones
| Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/seqbias | | Last Changed Rev: 54800 / Revision: 59457 | | Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/seqbias.Rcheck’
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqbias/DESCRIPTION’ ... OK
* this is package ‘seqbias’ version ‘1.0.0’
* checking package namespace 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 ... NOTE
installed size is 11.6Mb
sub-directories of 1Mb or more:
libs 10.7Mb
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 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 ... 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
* installing *source* package ‘seqbias’ ...
** libs
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c sequencing_bias.cpp -o sequencing_bias.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c kmers.cpp -o kmers.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c miscmath.cpp -o miscmath.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c common.cpp -o common.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c table.c -o table.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c logger.c -o logger.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c seqbias.cpp -o seqbias.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/aliascontent.cpp -o yaml-cpp/aliascontent.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/map.cpp -o yaml-cpp/map.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/node.cpp -o yaml-cpp/node.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/null.cpp -o yaml-cpp/null.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/parserstate.cpp -o yaml-cpp/parserstate.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/scalar.cpp -o yaml-cpp/scalar.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/sequence.cpp -o yaml-cpp/sequence.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/include" -Wall -D_GNU_SOURCE -fpic -g -O2 -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
g++ -shared -L/usr/local/lib64 -o seqbias.so 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 -L/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rsamtools/usrlib/ -lbam -lbcf -lz -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/seqbias.Rcheck/seqbias/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (seqbias)