BitSeq 1.3.1
Peter Glaus
| Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BitSeq | | Last Changed Rev: 71014 / Revision: 72575 | | Last Changed Date: 2012-11-06 16:03:09 -0800 (Tue, 06 Nov 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/BitSeq.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BitSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BitSeq’ version ‘1.3.1’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BitSeq’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 15.4Mb
sub-directories of 1Mb or more:
extdata 4.5Mb
libs 10.5Mb
* checking package directory ... 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
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... 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
‘/loc/home/biocbuild/bbs-2.12-bioc/meat/BitSeq.Rcheck/00check.log’
for details.
* installing *source* package ‘BitSeq’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c ArgumentParser.cpp -o ArgumentParser.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c GibbsParameters.cpp -o GibbsParameters.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c GibbsSampler.cpp -o GibbsSampler.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c ReadDistribution.cpp -o ReadDistribution.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c Sampler.cpp -o Sampler.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c TagAlignments.cpp -o TagAlignments.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c TranscriptExpression.cpp -o TranscriptExpression.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c TranscriptInfo.cpp -o TranscriptInfo.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c TranscriptSequence.cpp -o TranscriptSequence.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c common.cpp -o common.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c estimateDE.cpp -o estimateDE.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c estimateExpression.cpp -o estimateExpression.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c estimateHyperPar.cpp -o estimateHyperPar.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c getGeneExpression.cpp -o getGeneExpression.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c getVariance.cpp -o getVariance.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c lowess.cpp -o lowess.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c parseAlignment.cpp -o parseAlignment.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBIOC_BUILD -I. -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/zlibbioc/include" -fpic -g -O2 -c transposeFiles.cpp -o transposeFiles.o
g++ -shared -L/usr/local/lib64 -o BitSeq.so ArgumentParser.o CollapsedSampler.o GibbsParameters.o GibbsSampler.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Sampler.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o parseAlignment.o transposeFiles.o /loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libbam.a /loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libbcf.a /loc/home/biocbuild/bbs-2.12-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.12-bioc/meat/BitSeq.Rcheck/BitSeq/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘BitSeq.Rnw’
** testing if installed package can be loaded
* DONE (BitSeq)