BioC 3.2: CHECK report for regioneR on oaxaca

Package: regioneR

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regioneR_1.2.0.tar.gz

StartedAt: 2015-10-27 07:07:43 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:18:15 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 632.5 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-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 ‘1.2.0’
* 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 ‘regioneR’ can be installed ... [16s/16s] 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 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
copySeqLevels: no visible global function definition for ‘seqlevels<-’
copySeqLevels: no visible global function definition for ‘seqlevels’
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 ‘IRanges’
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’ ... OK
* checking examples ... [345s/376s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
maskFromBSGenome         50.883  4.598  55.607
filterChromosomes        50.187  4.616  54.849
getMask                  49.791  4.470  54.299
randomizeRegions         49.516  3.935  60.387
createRandomRegions      43.171  2.867  46.038
circularRandomizeRegions 42.611  3.313  61.072
localZScore               4.426  0.431   6.766
characterToBSGenome       0.378  0.060   9.490
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [127s/135s]
 [127s/135s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/regioneR.Rcheck/00check.log’
for details.

* installing *source* package ‘regioneR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (regioneR)

name	user	system	elapsed
characterToBSGenome	0.378	0.060	9.490
circularRandomizeRegions	42.611	3.313	61.072
commonRegions	0.143	0.012	0.155
createFunctionsList	0.689	0.149	0.839
createRandomRegions	43.171	2.867	46.038
emptyCacheRegioneR	0.000	0.000	0.001
extendRegions	0.081	0.000	0.082
filterChromosomes	50.187	4.616	54.849
getChromosomesByOrganism	0.001	0.001	0.001
getGenome	0.055	0.000	0.056
getGenomeAndMask	0.320	0.096	0.416
getMask	49.791	4.470	54.299
joinRegions	0.193	0.001	0.194
listChrTypes	0.022	0.000	0.022
localZScore	4.426	0.431	6.766
maskFromBSGenome	50.883	4.598	55.607
meanDistance	0.117	0.001	0.118
meanInRegions	0.182	0.000	0.183
mergeRegions	0.163	0.001	0.165
numOverlaps	0.219	0.000	0.221
overlapGraphicalSummary	0.213	0.001	0.229
overlapPermTest	1.065	0.003	1.070
overlapRegions	0.064	0.000	0.065
permTest	1.866	0.047	1.916
plot.localZScoreResults	1.663	0.003	1.668
plot.localZScoreResultsList	3.671	0.006	3.685
plot.permTestResults	3.039	0.194	3.238
plot.permTestResultsList	3.043	0.007	3.072
plotRegions	0.058	0.001	0.075
print.permTestResults	1.958	0.003	1.963
randomizeRegions	49.516	3.935	60.387
recomputePermTest	1.194	0.016	1.217
resampleRegions	0.084	0.000	0.085
splitRegions	0.127	0.001	0.131
subtractRegions	0.218	0.001	0.220
toDataframe	0.019	0.000	0.020
toGRanges	0.029	0.001	0.030
uniqueRegions	0.360	0.001	0.362