BioC 3.5: CHECK report for RJMCMCNucleosomes on toluca2

Package: RJMCMCNucleosomes

Version: 0.99.15

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RJMCMCNucleosomes_0.99.15.tar.gz

StartedAt: 2017-04-23 09:08:39 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 09:13:59 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 319.9 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_0.99.15.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RJMCMCNucleosomes.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘0.99.15’
* 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 -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	1.493	0.034	1.531
mergeAllRDSFiles	0.507	0.001	0.510
mergeAllRDSFilesFromDirectory	0.091	0.000	0.092
mergeRDSFiles	0.073	0.001	0.074
plotNucleosomes	0.408	0.004	0.413
postMerge	0.890	0.006	0.915
postTreatment	0.490	0.004	0.496
print.rjmcmcNucleosomes	0.005	0.001	0.006
print.rjmcmcNucleosomesBeforeAndAfterPostTreatment	0.311	0.004	0.316
print.rjmcmcNucleosomesMerge	0.076	0.001	0.078
reads_demo_01	0.041	0.003	0.044
reads_demo_02	0.051	0.002	0.053
rjmcmc	0.105	0.002	0.108
rjmcmcCHR	0.855	0.004	0.861
rjmcmcNucleo	0.090	0.003	0.093
runCHR	0.102	0.012	0.116
segmentation	0.140	0.011	0.152
validateDirectoryParameters	0.002	0.000	0.001
validatePlotNucleosomesParameters	0.059	0.009	0.068
validatePrepMergeParameters	0.004	0.008	0.013
validateRDSFilesParameters	0.012	0.000	0.012
validateRJMCMCParameters	0.01	0.00	0.01
validateSegmentationParameters	0.018	0.002	0.019