BitSeq 1.17.0
Antti Honkela , Panagiotis Papastamoulis
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BitSeq | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
###
### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings BitSeq_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/BitSeq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-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 ‘1.17.0’
* 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 13.7Mb
sub-directories of 1Mb or more:
extdata 4.5Mb
libs 8.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
Artistic-2.0 + file LICENSE
Versioned 'LinkingTo' value for ‘Rsamtools’ is only usable in R >= 3.0.2
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘Rsamtools’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getExpression: no visible global function definition for ‘read.table’
loadSamples: no visible global function definition for ‘read.table’
tri.load: no visible global function definition for ‘read.table’
tri.save: no visible global function definition for ‘is’
tri.save: no visible global function definition for ‘write.table’
tri.setGeneNames: no visible global function definition for ‘is’
writeSamples: no visible global function definition for ‘is’
writeSamples: no visible global function definition for ‘write.table’
Undefined global functions or variables:
is read.table write.table
Consider adding
importFrom("methods", "is")
importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘BitSeq/libs/BitSeq.so’:
Found ‘rand’, possibly from ‘rand’ (C)
Object: ‘PosteriorSamples.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/BitSeq.Rcheck/00check.log’
for details.
* installing *source* package ‘BitSeq’ ...
configure: Version def: -DBS_VERSION=\"1.17.0\"
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for g++ option to support OpenMP... -fopenmp
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/Makevars.win
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c ArgumentParser.cpp -o ArgumentParser.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c FileHeader.cpp -o FileHeader.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c GibbsParameters.cpp -o GibbsParameters.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c GibbsSampler.cpp -o GibbsSampler.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c MyTimer.cpp -o MyTimer.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp: In member function ‘bool ReadDistribution::observed(ns_rD::fragmentP)’:
ReadDistribution.cpp:265:30: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘˜’ [-Wparentheses]
(! frag->second->core.flag & BAM_FREVERSE))){
^
ReadDistribution.cpp: In member function ‘bool ReadDistribution::getP(ns_rD::fragmentP, double&, double&)’:
ReadDistribution.cpp:687:35: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘˜’ [-Wparentheses]
(! frag->second->core.flag & BAM_FREVERSE))){
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c Sampler.cpp -o Sampler.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c SimpleSparse.cpp -o SimpleSparse.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c TagAlignments.cpp -o TagAlignments.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c TranscriptExpression.cpp -o TranscriptExpression.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c TranscriptInfo.cpp -o TranscriptInfo.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c TranscriptSequence.cpp -o TranscriptSequence.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c VariationalBayes.cpp -o VariationalBayes.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c common.cpp -o common.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c estimateDE.cpp -o estimateDE.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c estimateExpression.cpp -o estimateExpression.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c estimateHyperPar.cpp -o estimateHyperPar.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c estimateVBExpression.cpp -o estimateVBExpression.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c getGeneExpression.cpp -o getGeneExpression.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c getVariance.cpp -o getVariance.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c lowess.cpp -o lowess.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c misc.cpp -o misc.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c parseAlignment.cpp -o parseAlignment.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.17.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -Wall -c transposeFiles.cpp -o transposeFiles.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o BitSeq.so ArgumentParser.o CollapsedSampler.o FileHeader.o GibbsParameters.o GibbsSampler.o MyTimer.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Sampler.o SimpleSparse.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o VariationalBayes.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o estimateVBExpression.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o misc.o parseAlignment.o transposeFiles.o /home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -fopenmp -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/BitSeq.Rcheck/BitSeq/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BitSeq)