BioC 3.2: CHECK report for regioneR on perceval

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 11:34:26 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 11:45:53 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 686.9 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 Patched (2015-10-08 r69496)
* 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 ‘1.2.0’
* 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 ... [19s/19s] 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 ... [360s/374s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
createRandomRegions      49.725  6.724  56.453
filterChromosomes        48.812  6.257  55.087
circularRandomizeRegions 48.591  6.294  64.628
maskFromBSGenome         46.554  6.227  52.795
getMask                  45.942  6.013  51.961
randomizeRegions         45.397  5.233  50.636
localZScore               4.077  0.390   6.042
characterToBSGenome       0.675  0.194   5.353
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [131s/135s]
 [131s/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	0.675	0.194	5.353
circularRandomizeRegions	48.591	6.294	64.628
commonRegions	0.265	0.019	0.284
createFunctionsList	1.027	0.400	1.427
createRandomRegions	49.725	6.724	56.453
emptyCacheRegioneR	0.001	0.000	0.001
extendRegions	0.143	0.001	0.144
filterChromosomes	48.812	6.257	55.087
getChromosomesByOrganism	0.002	0.000	0.001
getGenome	0.058	0.000	0.058
getGenomeAndMask	0.417	0.153	0.571
getMask	45.942	6.013	51.961
joinRegions	0.164	0.001	0.165
listChrTypes	0.02	0.00	0.02
localZScore	4.077	0.390	6.042
maskFromBSGenome	46.554	6.227	52.795
meanDistance	0.109	0.000	0.109
meanInRegions	0.150	0.001	0.151
mergeRegions	0.131	0.001	0.132
numOverlaps	0.208	0.000	0.208
overlapGraphicalSummary	0.187	0.001	0.188
overlapPermTest	1.042	0.003	1.045
overlapRegions	0.07	0.00	0.07
permTest	1.814	0.004	1.820
plot.localZScoreResults	1.528	0.199	1.730
plot.localZScoreResultsList	3.296	0.006	3.302
plot.permTestResults	2.725	0.008	2.739
plot.permTestResultsList	3.190	0.243	3.446
plotRegions	0.063	0.001	0.064
print.permTestResults	1.809	0.002	1.810
randomizeRegions	45.397	5.233	50.636
recomputePermTest	1.055	0.023	1.080
resampleRegions	0.070	0.001	0.071
splitRegions	0.109	0.001	0.111
subtractRegions	0.167	0.000	0.169
toDataframe	0.017	0.000	0.018
toGRanges	0.025	0.001	0.025
uniqueRegions	0.337	0.002	0.340