BioC 3.4: CHECK report for chromstaR on malbec1

Package: chromstaR

Version: 1.0.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings chromstaR_1.0.0.tar.gz

StartedAt: 2017-04-14 21:34:46 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 21:40:12 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 325.8 seconds

RetCode: 0

Status:  OK

CheckDir: chromstaR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings chromstaR_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/chromstaR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.0.0’
* 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
readCustomBedFile     12.204  0.012  12.232
combineMultivariates  10.668  0.024  10.702
enrichment_analysis    9.620  0.056  14.182
transitionFrequencies  6.184  0.308  38.276
callPeaksMultivariate  6.008  0.008   6.021
readBedFileAsGRanges   5.336  0.020   5.372
Chromstar              4.384  0.268  28.666
plotExpression         1.240  0.008   6.654
* 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-3.4-bioc/meat/chromstaR.Rcheck/00check.log’
for details.

* installing *source* package ‘chromstaR’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c densities.cpp -o densities.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c init.cpp -o init.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -Wall -c scalehmm.cpp -o scalehmm.o
g++ -I/home/biocbuild/bbs-3.4-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-3.4-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-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-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	4.384	0.268	28.666
binReads	0.236	0.000	0.236
callPeaksMultivariate	6.008	0.008	6.021
callPeaksReplicates	3.084	0.008	3.094
callPeaksUnivariate	1.472	0.004	1.477
changePostCutoff	2.096	0.000	2.099
collapseBins	0.496	0.000	0.500
combinatorialStates	3.684	0.008	3.697
combineMultivariates	10.668	0.024	10.702
combined_model	0.180	0.000	0.179
conversion	0.000	0.000	0.001
enrichment_analysis	9.620	0.056	14.182
experiment.table	0.004	0.000	0.004
exportBinnedData	0.272	0.004	0.275
exportCombinedMultivariate	1.068	0.004	1.074
exportGRangesAsBedFile	1.004	0.004	1.008
exportMultivariate	0.524	0.004	0.530
exportUnivariates	1	0	1
fixedWidthBins	0.116	0.036	4.715
genomicFrequencies	0.156	0.000	0.156
getDistinctColors	0.020	0.000	0.021
getStateColors	0.004	0.000	0.004
heatmapCombinations	0.560	0.000	0.564
loadHmmsFromFiles	1.320	0.004	1.348
multiHMM	0.104	0.004	0.108
multivariate_model	0.116	0.004	0.119
plotExpression	1.240	0.008	6.654
readBamFileAsGRanges	1.008	0.016	1.029
readBedFileAsGRanges	5.336	0.020	5.372
readCustomBedFile	12.204	0.012	12.232
state.brewer	0.008	0.000	0.011
stateBrewer	0.032	0.000	0.032
transitionFrequencies	6.184	0.308	38.276
unis2pseudomulti	2.684	0.008	2.694
variableWidthBins	2.244	0.024	2.272