BioC 3.5: CHECK report for chromstaR on toluca2

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: 2017-04-23 01:48:54 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 01:56:37 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 462.5 seconds

RetCode: 0

Status:  OK

CheckDir: chromstaR.Rcheck

Warnings: 0

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


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/chromstaR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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   14.569  0.464  18.294
readCustomBedFile     13.427  0.142  13.699
combineMultivariates  11.259  0.555  11.907
Chromstar              9.371  0.270  50.967
callPeaksMultivariate  6.650  0.253   7.102
transitionFrequencies  6.500  0.320  57.103
readBedFileAsGRanges   6.388  0.157   6.586
plotExpression         2.948  0.051   6.304
* 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	9.371	0.270	50.967
binReads	0.918	0.025	1.123
callPeaksMultivariate	6.650	0.253	7.102
callPeaksReplicates	3.563	0.196	3.804
callPeaksUnivariate	1.573	0.062	1.640
changeFDR	3.387	0.126	3.552
changePostCutoff	2.557	0.133	2.741
collapseBins	1.084	0.027	1.121
combinatorialStates	3.147	0.126	3.307
combineMultivariates	11.259	0.555	11.907
combined_model	0.209	0.021	0.234
conversion	0.001	0.000	0.001
enrichment_analysis	14.569	0.464	18.294
experiment.table	0.005	0.001	0.006
exportFiles	0.675	0.017	0.698
exportGRangesAsBedFile	0.772	0.039	0.822
fixedWidthBins	0.067	0.002	0.069
genes_rn4	0.128	0.007	0.137
genomicFrequencies	0.143	0.012	0.157
getCombinations	0.190	0.008	0.199
getDistinctColors	0.032	0.003	0.037
getStateColors	0.024	0.001	0.026
heatmapCombinations	0.561	0.009	0.575
heatmapCountCorrelation	0.368	0.011	0.383
heatmapTransitionProbs	0.368	0.009	0.386
loadHmmsFromFiles	0.868	0.043	0.919
multiHMM	0.156	0.019	0.175
multivariate_model	0.114	0.007	0.124
plotExpression	2.948	0.051	6.304
plotHistogram	1.702	0.088	1.802
readBamFileAsGRanges	1.120	0.064	1.188
readBedFileAsGRanges	6.388	0.157	6.586
readCustomBedFile	13.427	0.142	13.699
removeCondition	1.195	0.086	1.291
state.brewer	0.014	0.000	0.014
stateBrewer	0.040	0.001	0.041
transitionFrequencies	6.500	0.320	57.103
unis2pseudomulti	2.715	0.179	2.951
variableWidthBins	3.768	0.397	4.200