BitSeq 1.0.1
Peter Glaus
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/BitSeq | | Last Changed Rev: 65606 / Revision: 69725 | | Last Changed Date: 2012-04-30 11:27:00 -0700 (Mon, 30 Apr 2012) |
| 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-2.10-bioc/meat/BitSeq.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘1.0.1’
* 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 whether package ‘BitSeq’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 14.8Mb
sub-directories of 1Mb or more:
extdata 4.5Mb
libs 9.9Mb
* 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 ... NOTE
writeSamples: warning in write.table(as.data.frame(data), fileName,
append = TRUE, row.name = FALSE, col.names = FALSE): partial argument
match of 'row.name' to 'row.names'
* 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 ... NOTE
File ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/BitSeq.Rcheck/BitSeq/libs/BitSeq.so’:
Found ‘stdout’, possibly from ‘stdout’ (C)
Objects: ‘estimateHyperPar.o’, ‘transposeFiles.o’
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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 were 3 notes.
See
‘/loc/home/biocbuild/bbs-2.10-bioc/meat/BitSeq.Rcheck/00check.log’
for details.
* installing *source* package ‘BitSeq’ ...
** libs
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c argumentParser.cpp -o argumentParser.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c collapsedSampler.cpp -o collapsedSampler.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c common.cpp -o common.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c estimateDE.cpp -o estimateDE.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:182:0: warning: ignoring #pragma omp parallel
estimateExpression.cpp:206:0: warning: ignoring #pragma omp parallel
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c estimateHyperPar.cpp -o estimateHyperPar.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c getGeneExpression.cpp -o getGeneExpression.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c getVariance.cpp -o getVariance.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c gibbsParameters.cpp -o gibbsParameters.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c gibbsSampler.cpp -o gibbsSampler.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c lowess.cpp -o lowess.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c parseAlignment.cpp -o parseAlignment.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c posteriorSamples.cpp -o posteriorSamples.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c readDistribution.cpp -o readDistribution.o
readDistribution.cpp:482:0: warning: ignoring #pragma omp critical
readDistribution.cpp:491:0: warning: ignoring #pragma omp critical
readDistribution.cpp:507:0: warning: ignoring #pragma omp parallel
readDistribution.cpp:538:0: warning: ignoring #pragma omp parallel
readDistribution.cpp:541:0: warning: ignoring #pragma omp critical
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c sampler.cpp -o sampler.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c transcriptExpression.cpp -o transcriptExpression.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c transcriptInfo.cpp -o transcriptInfo.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c transcriptSequence.cpp -o transcriptSequence.o
g++ -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/library/Rsamtools/include" -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/zlibbioc/include" -fpic -g -O2 -Wall -c transposeFiles.cpp -o transposeFiles.o
g++ -shared -L/usr/local/lib64 -o BitSeq.so R_init_BitSeq.o argumentParser.o collapsedSampler.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o getGeneExpression.o getVariance.o getWithinGeneExpression.o gibbsParameters.o gibbsSampler.o lowess.o parseAlignment.o posteriorSamples.o readDistribution.o sampler.o transcriptExpression.o transcriptInfo.o transcriptSequence.o transposeFiles.o /loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/usrlib//libbam.a /loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/usrlib//libbcf.a /loc/home/biocbuild/bbs-2.10-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-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)