BioC 3.5: CHECK report for chromstaR on oaxaca

Package: chromstaR

Version: 1.1.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromstaR_1.1.4.tar.gz

StartedAt: 2017-03-04 00:36:04 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 00:43:35 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 450.7 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_1.1.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/chromstaR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.1.4’
* 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   14.988  0.468  21.489
combineMultivariates  11.119  0.571  12.667
readCustomBedFile     10.335  0.137  10.475
Chromstar              8.781  0.264  46.884
transitionFrequencies  7.217  0.349  53.388
callPeaksMultivariate  6.941  0.246   8.179
readBedFileAsGRanges   5.508  0.210   5.733
plotExpression         3.069  0.074   8.210
* 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-3.5-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-3.5-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	8.781	0.264	46.884
binReads	0.414	0.021	1.727
callPeaksMultivariate	6.941	0.246	8.179
callPeaksReplicates	3.663	0.207	3.996
callPeaksUnivariate	1.568	0.071	1.684
changeFDR	3.732	0.140	3.939
changePostCutoff	2.515	0.148	2.667
collapseBins	0.63	0.03	0.66
combinatorialStates	3.299	0.132	3.647
combineMultivariates	11.119	0.571	12.667
combined_model	0.219	0.019	0.237
conversion	0.001	0.000	0.002
enrichment_analysis	14.988	0.468	21.489
experiment.table	0.004	0.001	0.005
exportFiles	0.615	0.014	0.629
exportGRangesAsBedFile	0.745	0.036	0.782
fixedWidthBins	0.081	0.003	0.084
genes_rn4	0.102	0.006	0.108
genomicFrequencies	0.131	0.009	0.141
getCombinations	0.201	0.010	0.210
getDistinctColors	0.048	0.005	0.053
getStateColors	0.023	0.000	0.023
heatmapCombinations	0.565	0.010	0.576
heatmapCountCorrelation	0.378	0.012	0.390
heatmapTransitionProbs	0.366	0.012	0.378
loadHmmsFromFiles	1.372	0.048	1.504
multiHMM	0.135	0.016	0.151
multivariate_model	0.132	0.014	0.146
plotExpression	3.069	0.074	8.210
plotHistogram	1.894	0.095	1.991
readBamFileAsGRanges	1.751	0.123	1.902
readBedFileAsGRanges	5.508	0.210	5.733
readCustomBedFile	10.335	0.137	10.475
removeCondition	0.596	0.063	0.659
state.brewer	0.01	0.00	0.01
stateBrewer	0.046	0.002	0.066
transitionFrequencies	7.217	0.349	53.388
unis2pseudomulti	2.524	0.144	2.672
variableWidthBins	3.053	0.349	3.412