BioC 3.1: CHECK report for regioneR on morelia

Package: regioneR

Version: 1.0.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regioneR_1.0.3.tar.gz

StartedAt: 2015-10-09 05:30:45 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:39:27 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 522.6 seconds

RetCode: 0

Status:  OK

CheckDir: regioneR.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 regioneR_1.0.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/regioneR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘regioneR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘regioneR’ version ‘1.0.3’
* 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 ‘regioneR’ can be installed ... [15s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘memoise’ ‘GenomicRanges’ ‘BSgenome’ ‘rtracklayer’ ‘parallel’
A package should be listed in only one of these fields.
* 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
createRandomRegions: no visible global function definition for
  ‘seqlevels’
filterChromosomes: no visible global function definition for
  ‘keepSeqlevels’
randomizeRegions: no visible global function definition for
  ‘seqlevels<-’
randomizeRegions: no visible global function definition for ‘seqlevels’
resampleRegions: no visible global function definition for ‘seqlevels’
toGRanges: no visible global function definition for ‘IRanges’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
* checking examples ... [357s/378s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
createRandomRegions      50.913  6.494  57.482
randomizeRegions         50.896  6.399  57.696
circularRandomizeRegions 49.737  7.296  69.976
maskFromBSGenome         49.923  6.498  56.505
filterChromosomes        49.711  6.195  55.930
getMask                  47.349  5.583  52.961
characterToBSGenome       0.518  0.106   8.264
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/regioneR.Rcheck/00check.log’
for details.

* installing *source* package ‘regioneR’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (regioneR)

name	user	system	elapsed
characterToBSGenome	0.518	0.106	8.264
circularRandomizeRegions	49.737	7.296	69.976
commonRegions	0.273	0.006	0.279
createRandomRegions	50.913	6.494	57.482
emptyCacheRegioneR	0.001	0.000	0.000
extendRegions	0.091	0.000	0.092
filterChromosomes	49.711	6.195	55.930
getChromosomesByOrganism	0.001	0.001	0.003
getGenome	0.042	0.011	0.054
getGenomeAndMask	0.066	0.013	0.078
getMask	47.349	5.583	52.961
joinRegions	0.120	0.001	0.121
listChrTypes	0.022	0.000	0.023
localZScore	0.798	0.197	1.099
maskFromBSGenome	49.923	6.498	56.505
meanDistance	0.158	0.016	0.174
meanInRegions	0.171	0.009	0.180
mergeRegions	0.098	0.026	0.124
numOverlaps	0.109	0.033	0.142
overlapGraphicalSummary	0.190	0.018	0.208
overlapPermTest	0.516	0.019	0.537
overlapRegions	0.083	0.001	0.083
permTest	1.263	0.050	1.316
plot.localZScoreResults	1.142	0.410	1.071
plot.permTestResults	1.779	0.104	1.893
plotRegions	0.062	0.014	0.077
print.permTestResults	1.276	0.004	1.280
randomizeRegions	50.896	6.399	57.696
recomputePermTest	1.921	0.120	2.049
resampleRegions	0.075	0.002	0.076
splitRegions	0.119	0.016	0.134
subtractRegions	0.163	0.000	0.163
toDataframe	0.014	0.001	0.014
toGRanges	0.026	0.000	0.030
uniqueRegions	0.342	0.037	0.383