BioC 3.4: CHECK report for chromstaR on morelia

Package: chromstaR

Version: 0.99.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromstaR_0.99.7.tar.gz

StartedAt: 2016-09-20 04:29:34 -0700 (Tue, 20 Sep 2016)

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

EllapsedTime: 330.0 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_0.99.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/chromstaR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘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
enrichment_analysis   10.598  0.299  15.835
readCustomBedFile     10.530  0.150  10.683
combineMultivariates   9.849  0.361  10.619
transitionFrequencies  5.739  0.311  40.065
readBedFileAsGRanges   5.071  0.155   5.249
callPeaksMultivariate  4.675  0.180   5.023
Chromstar              4.253  0.165  27.280
plotExpression         1.126  0.045   6.064
* 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-3.4-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 -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c R_interface.cpp -o R_interface.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c densities.cpp -o densities.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c init.cpp -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c scalehmm.cpp -o scalehmm.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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	4.253	0.165	27.280
binReads	0.232	0.019	1.104
callPeaksMultivariate	4.675	0.180	5.023
callPeaksReplicates	2.840	0.124	2.999
callPeaksUnivariate	1.347	0.049	1.396
changePostCutoff	2.080	0.098	2.179
collapseBins	0.592	0.032	0.624
combinatorialStates	3.168	0.089	3.258
combineMultivariates	9.849	0.361	10.619
combined_model	0.164	0.009	0.174
conversion	0.001	0.000	0.000
enrichment_analysis	10.598	0.299	15.835
experiment.table	0.004	0.001	0.005
exportBinnedData	0.262	0.019	0.281
exportCombinedMultivariate	1.516	0.062	1.578
exportGRangesAsBedFile	0.578	0.029	0.607
exportMultivariate	1.044	0.049	1.093
exportUnivariates	1.093	0.043	1.137
fixedWidthBins	0.092	0.002	1.062
genomicFrequencies	0.135	0.011	0.146
getDistinctColors	0.016	0.003	0.020
getStateColors	0.003	0.000	0.003
heatmapCombinations	0.426	0.010	0.437
loadHmmsFromFiles	0.909	0.038	0.951
multiHMM	0.092	0.011	0.104
multivariate_model	0.093	0.010	0.102
plotExpression	1.126	0.045	6.064
readBamFileAsGRanges	1.461	0.049	1.510
readBedFileAsGRanges	5.071	0.155	5.249
readCustomBedFile	10.530	0.150	10.683
state.brewer	0.017	0.000	0.017
stateBrewer	0.043	0.001	0.045
transitionFrequencies	5.739	0.311	40.065
unis2pseudomulti	2.291	0.119	2.410
variableWidthBins	3.328	0.336	3.665