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CHECK report for BitSeq on malbec2

This page was generated on 2018-10-17 08:24:16 -0400 (Wed, 17 Oct 2018).

Package 157/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BitSeq 1.24.0
Antti Honkela , Panagiotis Papastamoulis
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/BitSeq
Branch: RELEASE_3_7
Last Commit: 6cfb2ae
Last Changed Date: 2018-04-30 10:35:24 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BitSeq
Version: 1.24.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:BitSeq.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BitSeq_1.24.0.tar.gz
StartedAt: 2018-10-15 22:51:21 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 22:52:23 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 61.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BitSeq.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:BitSeq.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings BitSeq_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/BitSeq.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.24.0’
* 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 13.4Mb
  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 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 shell scripts ... 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
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.7-bioc/R/library/BitSeq/libs/BitSeq.so’:
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.7-bioc/R/library/BitSeq/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.7-bioc/R/library/BitSeq/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.7-bioc/R/library/BitSeq/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.7-bioc/R/library/BitSeq/extdata’, resetting
* 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: 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/BitSeq.Rcheck/00check.log’
for details.

Installation output

BitSeq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL BitSeq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘BitSeq’ ...
configure: Version def: -DBS_VERSION=\"1.24.0\"
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-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c ArgumentParser.cpp -o ArgumentParser.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c CollapsedSampler.cpp -o CollapsedSampler.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c FileHeader.cpp -o FileHeader.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c GibbsParameters.cpp -o GibbsParameters.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c GibbsSampler.cpp -o GibbsSampler.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c MyTimer.cpp -o MyTimer.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c PosteriorSamples.cpp -o PosteriorSamples.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/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-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c Sampler.cpp -o Sampler.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c SimpleSparse.cpp -o SimpleSparse.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c TagAlignments.cpp -o TagAlignments.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c TranscriptExpression.cpp -o TranscriptExpression.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c TranscriptInfo.cpp -o TranscriptInfo.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c TranscriptSequence.cpp -o TranscriptSequence.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c VariationalBayes.cpp -o VariationalBayes.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c common.cpp -o common.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c estimateDE.cpp -o estimateDE.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c estimateExpression.cpp -o estimateExpression.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c estimateHyperPar.cpp -o estimateHyperPar.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c estimateVBExpression.cpp -o estimateVBExpression.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c getGeneExpression.cpp -o getGeneExpression.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c getVariance.cpp -o getVariance.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c lowess.cpp -o lowess.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c misc.cpp -o misc.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c parseAlignment.cpp -o parseAlignment.o
g++  -I"/home/biocbuild/bbs-3.7-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=\"1.24.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I/usr/local/include  -I. -fopenmp -fpic  -g -O2  -Wall -c transposeFiles.cpp -o transposeFiles.o
g++ -shared -L/home/biocbuild/bbs-3.7-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-3.7-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -fopenmp -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/BitSeq/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BitSeq)

Tests output

Example timings

BitSeq.Rcheck/BitSeq-Ex.timings

nameusersystemelapsed
BitSeq-package0.0040.0000.001
estimateDE000
estimateExpression0.0000.0000.001
estimateHyperPar0.0000.0040.001
estimateVBExpression0.0000.0000.001
getDE000
getExpression0.0000.0040.001
loadSamples0.0000.0000.001
parseAlignment0.0000.0000.001