BioC 3.4: CHECK report for chromstaR on zin1

Package: chromstaR

Version: 0.99.7

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings chromstaR_0.99.7.tar.gz

StartedAt: 2016-09-20 04:30:50 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 04:35:50 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 300.0 seconds

RetCode: 0

Status:  OK

CheckDir: chromstaR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings chromstaR_0.99.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/chromstaR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘0.99.7’
* 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  13.692  0.056  13.769
readCustomBedFile     10.140  0.024  10.163
enrichment_analysis    9.020  0.044  13.608
transitionFrequencies  6.036  0.276  35.757
callPeaksMultivariate  6.156  0.020   6.183
Chromstar              4.288  0.172  25.063
plotExpression         1.072  0.028   5.559
* 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	4.288	0.172	25.063
binReads	0.232	0.000	0.235
callPeaksMultivariate	6.156	0.020	6.183
callPeaksReplicates	4.248	0.004	4.261
callPeaksUnivariate	1.452	0.004	1.456
changePostCutoff	2.864	0.012	2.875
collapseBins	0.580	0.008	0.590
combinatorialStates	4.532	0.024	4.558
combineMultivariates	13.692	0.056	13.769
combined_model	0.172	0.020	0.192
conversion	0.000	0.000	0.001
enrichment_analysis	9.020	0.044	13.608
experiment.table	0.004	0.000	0.004
exportBinnedData	0.288	0.008	0.297
exportCombinedMultivariate	1.452	0.020	1.472
exportGRangesAsBedFile	0.568	0.008	0.579
exportMultivariate	0.572	0.052	0.624
exportUnivariates	1.188	0.008	1.197
fixedWidthBins	0.076	0.000	0.625
genomicFrequencies	0.100	0.004	0.106
getDistinctColors	0.016	0.000	0.015
getStateColors	0.004	0.000	0.003
heatmapCombinations	0.340	0.004	0.344
loadHmmsFromFiles	1.496	0.008	1.505
multiHMM	0.100	0.008	0.109
multivariate_model	0.108	0.004	0.112
plotExpression	1.072	0.028	5.559
readBamFileAsGRanges	1.448	0.004	1.451
readBedFileAsGRanges	4.452	0.016	4.535
readCustomBedFile	10.140	0.024	10.163
state.brewer	0.012	0.000	0.011
stateBrewer	0.036	0.000	0.034
transitionFrequencies	6.036	0.276	35.757
unis2pseudomulti	3.292	0.016	3.308
variableWidthBins	2.788	0.028	2.817