BioC 3.5: CHECK report for RJMCMCNucleosomes on oaxaca

Package: RJMCMCNucleosomes

Version: 0.99.13

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RJMCMCNucleosomes_0.99.13.tar.gz

StartedAt: 2017-03-04 08:17:07 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 08:22:01 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 294.4 seconds

RetCode: 0

Status:  OK

CheckDir: RJMCMCNucleosomes.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RJMCMCNucleosomes_0.99.13.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RJMCMCNucleosomes.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RJMCMCNucleosomes/DESCRIPTION’ ... OK
* this is package ‘RJMCMCNucleosomes’ version ‘0.99.13’
* package encoding: UTF-8
* 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 ‘RJMCMCNucleosomes’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... 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 loading without being on the library search path ... OK
* checking 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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: OK

* installing *source* package ‘RJMCMCNucleosomes’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `gsl-config --cflags` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c NucleoDirichlet.cpp -o NucleoDirichlet.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `gsl-config --cflags` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c NucleoDirichletPA.cpp -o NucleoDirichletPA.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `gsl-config --cflags` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c Nucleosome.cpp -o Nucleosome.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `gsl-config --cflags` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c RJMCMCNucleosomes_init.c -o RJMCMCNucleosomes_init.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `gsl-config --cflags` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `gsl-config --cflags` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c SegmentSeq.cpp -o SegmentSeq.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG `gsl-config --cflags` -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c rjmcmcNucleo.cpp -o rjmcmcNucleo.o
clang++ -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 RJMCMCNucleosomes.so NucleoDirichlet.o NucleoDirichletPA.o Nucleosome.o RJMCMCNucleosomes_init.o RcppExports.o SegmentSeq.o rjmcmcNucleo.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/RJMCMCNucleosomes.Rcheck/RJMCMCNucleosomes/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RJMCMCNucleosomes)

name	user	system	elapsed
RJMCMC_result	1.506	0.036	1.543
mergeAllRDSFiles	0.455	0.001	0.457
mergeAllRDSFilesFromDirectory	0.095	0.000	0.095
mergeRDSFiles	0.080	0.001	0.081
plotNucleosomes	0.460	0.006	0.466
postMerge	0.949	0.008	0.958
postTreatment	0.433	0.004	0.437
print.rjmcmcNucleosomes	0.004	0.001	0.005
print.rjmcmcNucleosomesBeforeAndAfterPostTreatment	0.259	0.004	0.263
print.rjmcmcNucleosomesMerge	0.054	0.001	0.055
reads_demo_01	0.030	0.001	0.032
reads_demo_02	0.041	0.001	0.042
rjmcmc	0.093	0.002	0.095
rjmcmcCHR	0.716	0.003	0.720
rjmcmcNucleo	0.087	0.003	0.090
runCHR	0.119	0.014	0.133
segmentation	0.125	0.011	0.136
validateDirectoryParameters	0.001	0.000	0.001
validatePlotNucleosomesParameters	0.036	0.008	0.044
validatePrepMergeParameters	0.005	0.010	0.015
validateRDSFilesParameters	0.010	0.001	0.011
validateRJMCMCParameters	0.011	0.000	0.011
validateSegmentationParameters	0.018	0.002	0.020