BioC 3.3: CHECK report for regioneR on morelia

Package: regioneR

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regioneR_1.3.0.tar.gz

StartedAt: 2015-10-22 10:19:14 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 10:29:27 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 613.5 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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/regioneR.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.3.0’
* 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 ... [13s/13s] 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’
Undefined global functions or variables:
  IRanges keepSeqlevels seqlevels seqlevels<-
* 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 ... [336s/365s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
createRandomRegions      48.836  4.320  53.616
circularRandomizeRegions 47.996  4.350  70.652
filterChromosomes        47.648  4.035  52.047
randomizeRegions         47.410  3.671  51.800
getMask                  46.518  3.573  50.515
maskFromBSGenome         46.224  3.814  50.413
characterToBSGenome       0.467  0.077   9.324
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [113s/123s]
 [113s/123s] 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-3.3-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	0.467	0.077	9.324
circularRandomizeRegions	47.996	4.350	70.652
commonRegions	0.201	0.014	0.215
createFunctionsList	0.805	0.236	1.072
createRandomRegions	48.836	4.320	53.616
emptyCacheRegioneR	0.001	0.000	0.000
extendRegions	0.123	0.008	0.132
filterChromosomes	47.648	4.035	52.047
getChromosomesByOrganism	0.001	0.000	0.001
getGenome	0.049	0.000	0.050
getGenomeAndMask	0.361	0.103	0.464
getMask	46.518	3.573	50.515
joinRegions	0.149	0.164	0.321
listChrTypes	0.019	0.000	0.019
localZScore	3.107	0.230	4.417
maskFromBSGenome	46.224	3.814	50.413
meanDistance	0.112	0.000	0.113
meanInRegions	0.124	0.078	0.201
mergeRegions	0.097	0.000	0.098
numOverlaps	0.146	0.000	0.147
overlapGraphicalSummary	0.109	0.001	0.110
overlapPermTest	0.770	0.002	0.881
overlapRegions	0.040	0.000	0.041
permTest	1.549	0.005	1.558
plot.localZScoreResults	1.183	0.003	1.237
plot.localZScoreResultsList	2.670	0.166	2.869
plot.permTestResults	1.981	0.004	2.114
plot.permTestResultsList	1.978	0.005	1.987
plotRegions	0.041	0.001	0.042
print.permTestResults	1.286	0.003	1.290
randomizeRegions	47.410	3.671	51.800
recomputePermTest	0.894	0.002	0.898
resampleRegions	0.045	0.000	0.046
splitRegions	0.102	0.001	0.102
subtractRegions	0.109	0.000	0.110
toDataframe	0.010	0.000	0.011
toGRanges	0.016	0.000	0.015
uniqueRegions	0.290	0.001	0.291