BioC 3.5: CHECK report for RJMCMCNucleosomes on veracruz2

Package: RJMCMCNucleosomes

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RJMCMCNucleosomes_1.0.0.tar.gz

StartedAt: 2017-10-18 08:22:43 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 08:27:58 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 315.4 seconds

RetCode: 0

Status:  OK

CheckDir: RJMCMCNucleosomes.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RJMCMCNucleosomes_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RJMCMCNucleosomes.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RJMCMCNucleosomes/DESCRIPTION’ ... OK
* this is package ‘RJMCMCNucleosomes’ version ‘1.0.0’
* 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   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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 -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	1.274	0.028	1.337
mergeAllRDSFiles	0.410	0.002	0.419
mergeAllRDSFilesFromDirectory	0.076	0.002	0.078
mergeRDSFiles	0.057	0.001	0.059
plotNucleosomes	0.383	0.005	0.399
postMerge	0.728	0.007	0.750
postTreatment	0.393	0.004	0.406
print.rjmcmcNucleosomes	0.005	0.001	0.006
print.rjmcmcNucleosomesBeforeAndAfterPostTreatment	0.269	0.006	0.285
print.rjmcmcNucleosomesMerge	0.054	0.001	0.059
reads_demo_01	0.034	0.001	0.038
reads_demo_02	0.048	0.002	0.050
rjmcmc	0.103	0.002	0.109
rjmcmcCHR	0.376	0.005	0.404
rjmcmcNucleo	0.084	0.002	0.089
runCHR	0.464	0.009	0.487
segmentation	0.109	0.009	0.123
validateDirectoryParameters	0.002	0.000	0.002
validatePlotNucleosomesParameters	0.045	0.003	0.049
validatePrepMergeParameters	0.004	0.002	0.005
validateRDSFilesParameters	0.008	0.000	0.009
validateRJMCMCParameters	0.010	0.001	0.010
validateSegmentationParameters	0.018	0.002	0.019