BioC 3.6: CHECK report for chromstaR on veracruz1

Package: chromstaR

Version: 1.3.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromstaR_1.3.1.tar.gz

StartedAt: 2017-08-16 01:10:41 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:18:28 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 466.8 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_1.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.3.1’
* 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
combineMultivariates  19.520  1.306  21.478
enrichment_analysis   13.541  0.599  17.925
callPeaksMultivariate 10.022  0.533  10.860
readCustomBedFile      9.383  0.126   9.755
Chromstar              8.693  0.291  50.575
callPeaksReplicates    7.367  0.536   8.115
transitionFrequencies  6.543  0.389  68.450
unis2pseudomulti       5.573  0.387   6.085
combinatorialStates    4.734  0.364   5.240
plotExpression         2.191  0.087   5.613
* 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-3.6-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-3.6-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	8.693	0.291	50.575
binReads	0.614	0.028	0.700
callPeaksMultivariate	10.022	0.533	10.860
callPeaksReplicates	7.367	0.536	8.115
callPeaksUnivariate	2.357	0.152	2.581
changeFDR	3.505	0.197	3.814
changePostCutoff	3.411	0.226	3.737
collapseBins	0.784	0.034	0.842
combinatorialStates	4.734	0.364	5.240
combineMultivariates	19.520	1.306	21.478
combined_model	0.104	0.017	0.121
conversion	0.001	0.000	0.001
enrichment_analysis	13.541	0.599	17.925
experiment.table	0.003	0.001	0.004
exportFiles	0.790	0.025	0.826
exportGRangesAsBedFile	0.848	0.044	0.915
fixedWidthBins	0.066	0.002	0.073
genes_rn4	0.129	0.005	0.135
genomicFrequencies	0.146	0.017	0.170
getCombinations	0.164	0.009	0.173
getDistinctColors	0.029	0.003	0.037
getStateColors	0.019	0.000	0.018
heatmapCombinations	0.465	0.011	0.494
heatmapCountCorrelation	0.308	0.012	0.330
heatmapTransitionProbs	0.303	0.010	0.326
loadHmmsFromFiles	1.816	0.121	2.007
multiHMM	0.126	0.012	0.145
multivariate_model	0.125	0.009	0.138
plotExpression	2.191	0.087	5.613
plotHistogram	2.355	0.165	2.600
readBamFileAsGRanges	0.788	0.086	0.894
readBedFileAsGRanges	4.388	0.142	4.628
readCustomBedFile	9.383	0.126	9.755
removeCondition	0.736	0.092	0.853
state.brewer	0.013	0.001	0.014
stateBrewer	0.042	0.001	0.045
transitionFrequencies	6.543	0.389	68.450
unis2pseudomulti	5.573	0.387	6.085
variableWidthBins	2.986	0.341	3.434