BioC 3.5: CHECK report for chromstaR on malbec2

Package: chromstaR

Version: 1.2.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings chromstaR_1.2.0.tar.gz

StartedAt: 2017-08-15 21:56:38 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:02:30 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 351.3 seconds

RetCode: 0

Status:  OK

CheckDir: chromstaR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings chromstaR_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/chromstaR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 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  11.200  0.036  11.316
enrichment_analysis    9.924  0.012  14.500
readCustomBedFile      9.544  0.012   9.563
Chromstar              7.068  0.376  35.233
transitionFrequencies  6.212  0.244  44.740
callPeaksMultivariate  6.300  0.032   6.406
plotExpression         2.236  0.012   5.787
* 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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/chromstaR.Rcheck/00check.log’
for details.

* installing *source* package ‘chromstaR’ ...
** libs
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c R_interface.cpp -o R_interface.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c densities.cpp -o densities.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c scalehmm.cpp -o scalehmm.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG   -I/usr/local/include  -fopenmp -fpic  -g -O2  -Wall -c utility.cpp -o utility.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o chromstaR.so R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/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	7.068	0.376	35.233
binReads	0.372	0.000	0.428
callPeaksMultivariate	6.300	0.032	6.406
callPeaksReplicates	4.268	0.012	4.330
callPeaksUnivariate	1.616	0.004	1.620
changeFDR	2.920	0.012	2.937
changePostCutoff	2.368	0.004	2.375
collapseBins	0.416	0.004	0.421
combinatorialStates	3.264	0.008	3.273
combineMultivariates	11.200	0.036	11.316
combined_model	0.184	0.012	0.193
conversion	0.000	0.000	0.001
enrichment_analysis	9.924	0.012	14.500
experiment.table	0.000	0.004	0.004
exportFiles	0.504	0.012	0.515
exportGRangesAsBedFile	0.572	0.000	0.572
fixedWidthBins	0.056	0.000	0.053
genes_rn4	0.104	0.012	0.117
genomicFrequencies	0.136	0.012	0.147
getCombinations	0.164	0.008	0.175
getDistinctColors	0.016	0.004	0.019
getStateColors	0.016	0.000	0.014
heatmapCombinations	0.392	0.012	0.403
heatmapCountCorrelation	0.276	0.016	0.292
heatmapTransitionProbs	0.324	0.000	0.325
loadHmmsFromFiles	1.344	0.000	1.346
multiHMM	0.108	0.008	0.114
multivariate_model	0.100	0.012	0.112
plotExpression	2.236	0.012	5.787
plotHistogram	1.332	0.000	1.332
readBamFileAsGRanges	1.276	0.004	1.280
readBedFileAsGRanges	4.420	0.028	4.468
readCustomBedFile	9.544	0.012	9.563
removeCondition	0.532	0.000	0.533
state.brewer	0.008	0.000	0.010
stateBrewer	0.032	0.000	0.029
transitionFrequencies	6.212	0.244	44.740
unis2pseudomulti	3.436	0.036	3.473
variableWidthBins	2.428	0.016	2.444