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: 2017-10-18 01:43:41 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:50:33 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 412.3 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 3.4.2 (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 ‘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   13.246  0.393  17.708
readCustomBedFile     10.863  0.172  11.302
combineMultivariates  10.242  0.535  11.078
Chromstar              8.231  0.288  44.534
callPeaksMultivariate  6.477  0.266   7.005
transitionFrequencies  5.676  0.311  49.462
plotExpression         2.491  0.060   5.761
* 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	8.231	0.288	44.534
binReads	0.953	0.031	1.081
callPeaksMultivariate	6.477	0.266	7.005
callPeaksReplicates	3.279	0.183	3.607
callPeaksUnivariate	1.543	0.074	1.670
changeFDR	2.760	0.116	3.005
changePostCutoff	2.223	0.117	2.431
collapseBins	0.947	0.024	1.002
combinatorialStates	2.969	0.126	3.184
combineMultivariates	10.242	0.535	11.078
combined_model	0.186	0.015	0.204
conversion	0.001	0.000	0.001
enrichment_analysis	13.246	0.393	17.708
experiment.table	0.004	0.001	0.007
exportFiles	0.594	0.016	0.637
exportGRangesAsBedFile	0.718	0.036	0.768
fixedWidthBins	0.081	0.005	0.087
genes_rn4	0.118	0.007	0.132
genomicFrequencies	0.116	0.010	0.130
getCombinations	0.172	0.011	0.187
getDistinctColors	0.030	0.004	0.034
getStateColors	0.02	0.00	0.02
heatmapCombinations	0.502	0.015	0.533
heatmapCountCorrelation	0.325	0.010	0.340
heatmapTransitionProbs	0.346	0.009	0.396
loadHmmsFromFiles	0.822	0.037	0.890
multiHMM	0.117	0.012	0.132
multivariate_model	0.112	0.012	0.126
plotExpression	2.491	0.060	5.761
plotHistogram	1.453	0.079	1.570
readBamFileAsGRanges	0.854	0.062	0.944
readBedFileAsGRanges	4.707	0.125	4.951
readCustomBedFile	10.863	0.172	11.302
removeCondition	1.094	0.073	1.195
state.brewer	0.015	0.000	0.016
stateBrewer	0.040	0.002	0.044
transitionFrequencies	5.676	0.311	49.462
unis2pseudomulti	2.822	0.153	3.054
variableWidthBins	2.397	0.348	2.820