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CHECK report for BitSeq on celaya2

This page was generated on 2020-01-16 13:34:47 -0500 (Thu, 16 Jan 2020).

Package 186/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BitSeq 1.31.0
Antti Honkela , Panagiotis Papastamoulis
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/BitSeq
Branch: master
Last Commit: b3ffcee
Last Changed Date: 2019-10-29 13:36:08 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  ERROR  ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BitSeq
Version: 1.31.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BitSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BitSeq_1.31.0.tar.gz
StartedAt: 2020-01-16 02:17:22 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 02:19:59 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 157.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BitSeq.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BitSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BitSeq_1.31.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/BitSeq.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.31.0’
* 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  5.7Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.0Mb
* 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 ‘Rhtslib’ 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BitSeq/libs/BitSeq.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_srand48’, possibly from ‘srand48’ (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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BitSeq/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BitSeq/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BitSeq/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/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, 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/BitSeq.Rcheck/00check.log’
for details.

Installation output

BitSeq.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BitSeq
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘BitSeq’ ...
** using staged installation
configure: Version def: -DBS_VERSION=\"1.31.0\"
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 clang++ -std=gnu++11 accepts -g... yes
checking for clang++ -std=gnu++11 option to support OpenMP... -fopenmp
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/Makevars.win
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c ArgumentParser.cpp -o ArgumentParser.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c CollapsedSampler.cpp -o CollapsedSampler.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c FileHeader.cpp -o FileHeader.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c GibbsParameters.cpp -o GibbsParameters.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c GibbsSampler.cpp -o GibbsSampler.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c MyTimer.cpp -o MyTimer.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c PosteriorSamples.cpp -o PosteriorSamples.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c R_init_BitSeq.cpp -o R_init_BitSeq.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp:265:9: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
       (! frag->second->core.flag & BAM_FREVERSE))){
        ^                         ~
ReadDistribution.cpp:265:9: note: add parentheses after the '!' to evaluate the bitwise operator first
       (! frag->second->core.flag & BAM_FREVERSE))){
        ^
          (                                     )
ReadDistribution.cpp:265:9: note: add parentheses around left hand side expression to silence this warning
       (! frag->second->core.flag & BAM_FREVERSE))){
        ^
        (                        )
ReadDistribution.cpp:687:14: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses]
            (! frag->second->core.flag & BAM_FREVERSE))){
             ^                         ~
ReadDistribution.cpp:687:14: note: add parentheses after the '!' to evaluate the bitwise operator first
            (! frag->second->core.flag & BAM_FREVERSE))){
             ^
               (                                     )
ReadDistribution.cpp:687:14: note: add parentheses around left hand side expression to silence this warning
            (! frag->second->core.flag & BAM_FREVERSE))){
             ^
             (                        )
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c Sampler.cpp -o Sampler.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c SimpleSparse.cpp -o SimpleSparse.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c TagAlignments.cpp -o TagAlignments.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c TranscriptExpression.cpp -o TranscriptExpression.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c TranscriptInfo.cpp -o TranscriptInfo.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c TranscriptSequence.cpp -o TranscriptSequence.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c VariationalBayes.cpp -o VariationalBayes.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam_plbuf.c -o bam_plbuf.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c common.cpp -o common.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c estimateDE.cpp -o estimateDE.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c estimateExpression.cpp -o estimateExpression.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c estimateHyperPar.cpp -o estimateHyperPar.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c estimateVBExpression.cpp -o estimateVBExpression.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c getGeneExpression.cpp -o getGeneExpression.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c getVariance.cpp -o getVariance.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c lowess.cpp -o lowess.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c misc.cpp -o misc.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c parseAlignment.cpp -o parseAlignment.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c sam.c -o sam.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.31.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c transposeFiles.cpp -o transposeFiles.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 bam_plbuf.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o estimateVBExpression.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o misc.o parseAlignment.o sam.o transposeFiles.o /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-BitSeq/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BitSeq)

Tests output

Example timings

BitSeq.Rcheck/BitSeq-Ex.timings

nameusersystemelapsed
BitSeq-package0.0010.0010.001
estimateDE0.0000.0010.001
estimateExpression0.0000.0000.001
estimateHyperPar0.0000.0000.001
estimateVBExpression0.0010.0010.001
getDE0.0000.0000.001
getExpression0.0010.0000.001
loadSamples000
parseAlignment000