BioC 3.1: CHECK report for regioneR on petty

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 01:30:58 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:42:14 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 676.7 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 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [22s/23s] 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 ... [424s/443s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
circularRandomizeRegions 59.386  8.302  81.978
filterChromosomes        59.058  7.689  71.956
createRandomRegions      58.331  8.130  66.525
randomizeRegions         57.310  8.447  65.989
maskFromBSGenome         55.873  7.491  63.418
getMask                  54.611  6.707  61.361
* 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	0.872	0.105	1.005
circularRandomizeRegions	59.386	8.302	81.978
commonRegions	0.320	0.002	0.322
createRandomRegions	58.331	8.130	66.525
emptyCacheRegioneR	0.001	0.000	0.002
extendRegions	0.137	0.000	0.138
filterChromosomes	59.058	7.689	71.956
getChromosomesByOrganism	0.001	0.000	0.002
getGenome	0.057	0.001	0.059
getGenomeAndMask	0.430	0.132	0.562
getMask	54.611	6.707	61.361
joinRegions	0.220	0.288	0.509
listChrTypes	0.034	0.000	0.034
localZScore	1.137	0.379	1.557
maskFromBSGenome	55.873	7.491	63.418
meanDistance	0.241	0.001	0.242
meanInRegions	0.243	0.001	0.245
mergeRegions	0.148	0.001	0.149
numOverlaps	0.16	0.00	0.16
overlapGraphicalSummary	0.287	0.001	0.288
overlapPermTest	0.628	0.219	0.850
overlapRegions	0.116	0.000	0.117
permTest	1.959	0.003	1.967
plot.localZScoreResults	1.678	0.705	1.788
plot.permTestResults	2.724	0.118	2.858
plotRegions	0.093	0.001	0.101
print.permTestResults	1.894	0.003	1.898
randomizeRegions	57.310	8.447	65.989
recomputePermTest	2.900	0.075	2.977
resampleRegions	0.115	0.000	0.115
splitRegions	0.160	0.001	0.163
subtractRegions	0.290	0.001	0.295
toDataframe	0.028	0.000	0.029
toGRanges	0.036	0.000	0.037
uniqueRegions	0.528	0.002	0.531