BioC 3.5: CHECK report for chromstaR on veracruz2

Package: chromstaR

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromstaR_1.2.0.tar.gz

StartedAt: 2017-08-16 00:59:45 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:06:26 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 401.2 seconds

RetCode: 0

Status:  OK

CheckDir: chromstaR.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 chromstaR_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/chromstaR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chromstaR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromstaR’ version ‘1.2.0’
* 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 ‘chromstaR’ 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 ... NOTE
Chromstar: multiple local function definitions for ‘parallel.helper’
  with different formal arguments
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
enrichment_analysis   12.766  0.370  16.883
readCustomBedFile     11.097  0.125  11.517
combineMultivariates   9.764  0.474  10.479
Chromstar              7.847  0.252  42.549
callPeaksMultivariate  6.209  0.215   6.619
transitionFrequencies  5.850  0.286  48.883
readBedFileAsGRanges   4.800  0.150   5.075
plotExpression         2.155  0.051   5.374
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/chromstaR.Rcheck/00check.log’
for details.

* installing *source* package ‘chromstaR’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c R_interface.cpp -o R_interface.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c densities.cpp -o densities.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c scalehmm.cpp -o scalehmm.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2  -c utility.cpp -o utility.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 chromstaR.so R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/chromstaR.Rcheck/chromstaR/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 (chromstaR)

name	user	system	elapsed
Chromstar	7.847	0.252	42.549
binReads	0.420	0.016	0.490
callPeaksMultivariate	6.209	0.215	6.619
callPeaksReplicates	3.548	0.193	3.851
callPeaksUnivariate	1.609	0.065	1.802
changeFDR	2.997	0.111	3.202
changePostCutoff	2.487	0.113	2.685
collapseBins	0.502	0.021	0.533
combinatorialStates	2.991	0.114	3.204
combineMultivariates	9.764	0.474	10.479
combined_model	0.181	0.014	0.203
conversion	0.001	0.000	0.002
enrichment_analysis	12.766	0.370	16.883
experiment.table	0.006	0.001	0.007
exportFiles	0.593	0.016	0.616
exportGRangesAsBedFile	0.651	0.036	0.707
fixedWidthBins	0.062	0.001	0.064
genes_rn4	0.120	0.005	0.131
genomicFrequencies	0.136	0.014	0.152
getCombinations	0.155	0.007	0.166
getDistinctColors	0.029	0.003	0.033
getStateColors	0.020	0.001	0.022
heatmapCombinations	0.489	0.010	0.520
heatmapCountCorrelation	0.307	0.010	0.326
heatmapTransitionProbs	0.297	0.007	0.323
loadHmmsFromFiles	0.816	0.039	0.875
multiHMM	0.117	0.009	0.126
multivariate_model	0.537	0.010	0.560
plotExpression	2.155	0.051	5.374
plotHistogram	1.511	0.071	1.637
readBamFileAsGRanges	0.884	0.078	1.008
readBedFileAsGRanges	4.800	0.150	5.075
readCustomBedFile	11.097	0.125	11.517
removeCondition	1.084	0.082	1.196
state.brewer	0.013	0.000	0.013
stateBrewer	0.034	0.002	0.035
transitionFrequencies	5.850	0.286	48.883
unis2pseudomulti	2.378	0.131	2.578
variableWidthBins	2.701	0.316	3.110