BioC 3.4: CHECK report for chromstaR on morelia

Package: chromstaR

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chromstaR_1.0.0.tar.gz

StartedAt: 2017-04-14 23:55:49 -0700 (Fri, 14 Apr 2017)

EndedAt: 2017-04-15 00:02:26 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 396.5 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_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/chromstaR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.0.0’
* 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 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
readCustomBedFile     12.850  0.168  13.071
combineMultivariates  12.359  0.447  13.684
enrichment_analysis   12.306  0.422  19.696
transitionFrequencies  7.303  0.404  47.992
readBedFileAsGRanges   6.111  0.229   6.393
callPeaksMultivariate  5.487  0.196   5.782
Chromstar              5.090  0.224  36.126
plotExpression         2.142  0.071   7.257
* 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	5.090	0.224	36.126
binReads	0.282	0.023	0.424
callPeaksMultivariate	5.487	0.196	5.782
callPeaksReplicates	3.602	0.143	3.800
callPeaksUnivariate	1.776	0.070	1.849
changePostCutoff	2.827	0.114	2.946
collapseBins	0.688	0.016	0.705
combinatorialStates	3.718	0.106	3.960
combineMultivariates	12.359	0.447	13.684
combined_model	0.208	0.016	0.225
conversion	0.001	0.000	0.001
enrichment_analysis	12.306	0.422	19.696
experiment.table	0.004	0.001	0.004
exportBinnedData	0.369	0.027	0.468
exportCombinedMultivariate	1.730	0.078	2.101
exportGRangesAsBedFile	0.752	0.042	0.930
exportMultivariate	0.773	0.044	0.865
exportUnivariates	1.175	0.051	1.237
fixedWidthBins	0.134	0.059	3.467
genomicFrequencies	0.128	0.015	0.142
getDistinctColors	0.036	0.006	0.485
getStateColors	0.003	0.001	0.164
heatmapCombinations	0.640	0.011	0.814
loadHmmsFromFiles	1.722	0.054	1.819
multiHMM	0.122	0.013	0.137
multivariate_model	0.122	0.012	0.135
plotExpression	2.142	0.071	7.257
readBamFileAsGRanges	1.406	0.085	1.492
readBedFileAsGRanges	6.111	0.229	6.393
readCustomBedFile	12.850	0.168	13.071
state.brewer	0.018	0.001	0.018
stateBrewer	0.050	0.002	0.052
transitionFrequencies	7.303	0.404	47.992
unis2pseudomulti	3.270	0.137	3.431
variableWidthBins	3.408	0.499	3.912