BitSeq 1.2.2
Peter Glaus
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/BitSeq | | Last Changed Rev: 73009 / Revision: 74773 | | Last Changed Date: 2013-01-29 15:22:51 -0800 (Tue, 29 Jan 2013) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/BitSeq.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.2.2’
* 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 whether package ‘BitSeq’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 11.4Mb
sub-directories of 1Mb or more:
extdata 4.5Mb
libs 6.5Mb
* 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 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-2.11-bioc/meat/BitSeq.Rcheck/00check.log’
for details.
* installing *source* package ‘BitSeq’ ...
** libs
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c ArgumentParser.cpp -o ArgumentParser.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c GibbsParameters.cpp -o GibbsParameters.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c GibbsSampler.cpp -o GibbsSampler.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp:562:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
ReadDistribution.cpp:571:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
ReadDistribution.cpp:587:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ReadDistribution.cpp:618:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
ReadDistribution.cpp:621:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c Sampler.cpp -o Sampler.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c TagAlignments.cpp -o TagAlignments.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c TranscriptExpression.cpp -o TranscriptExpression.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c TranscriptInfo.cpp -o TranscriptInfo.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c TranscriptSequence.cpp -o TranscriptSequence.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c common.cpp -o common.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c estimateDE.cpp -o estimateDE.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:171:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
estimateExpression.cpp:195:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c estimateHyperPar.cpp -o estimateHyperPar.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c getGeneExpression.cpp -o getGeneExpression.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c getVariance.cpp -o getVariance.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c lowess.cpp -o lowess.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c parseAlignment.cpp -o parseAlignment.o
g++ -I/home/biocbuild/bbs-2.11-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-2.11-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.11-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -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-2.11-bioc/R/library/Rsamtools/usrlib//libbam.a /loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/usrlib//libbcf.a /loc/home/biocbuild/bbs-2.11-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -L/home/biocbuild/bbs-2.11-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.11-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)