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: 2017-10-17 22:01:26 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 22:07:27 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 360.4 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 3.4.2 (2017-09-28)
* 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  12.344  0.036  12.521
enrichment_analysis    9.876  0.020  15.084
readCustomBedFile      9.556  0.016   9.580
Chromstar              7.844  0.380  36.321
callPeaksMultivariate  7.584  0.024   7.702
transitionFrequencies  5.796  0.300  46.226
readBedFileAsGRanges   5.448  0.012   5.481
plotExpression         1.920  0.012   5.596
* 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	7.844	0.380	36.321
binReads	0.412	0.016	0.577
callPeaksMultivariate	7.584	0.024	7.702
callPeaksReplicates	3.740	0.016	3.827
callPeaksUnivariate	1.288	0.004	1.292
changeFDR	2.640	0.024	2.667
changePostCutoff	2.696	0.004	2.702
collapseBins	0.436	0.000	0.435
combinatorialStates	4.148	0.012	4.165
combineMultivariates	12.344	0.036	12.521
combined_model	0.184	0.004	0.190
conversion	0.004	0.000	0.001
enrichment_analysis	9.876	0.020	15.084
experiment.table	0.004	0.000	0.005
exportFiles	0.548	0.008	0.557
exportGRangesAsBedFile	0.54	0.00	0.54
fixedWidthBins	0.044	0.004	0.048
genes_rn4	0.108	0.000	0.107
genomicFrequencies	0.124	0.000	0.124
getCombinations	0.152	0.000	0.149
getDistinctColors	0.016	0.000	0.017
getStateColors	0.016	0.000	0.014
heatmapCombinations	0.396	0.004	0.400
heatmapCountCorrelation	0.256	0.000	0.255
heatmapTransitionProbs	0.268	0.000	0.269
loadHmmsFromFiles	0.988	0.008	0.997
multiHMM	0.640	0.000	0.642
multivariate_model	0.104	0.000	0.105
plotExpression	1.920	0.012	5.596
plotHistogram	1.468	0.000	1.468
readBamFileAsGRanges	0.732	0.008	0.744
readBedFileAsGRanges	5.448	0.012	5.481
readCustomBedFile	9.556	0.016	9.580
removeCondition	1.180	0.000	1.185
state.brewer	0.012	0.000	0.011
stateBrewer	0.028	0.004	0.031
transitionFrequencies	5.796	0.300	46.226
unis2pseudomulti	3.180	0.064	3.248
variableWidthBins	2.224	0.008	2.231