BioC 3.2: CHECK report for regioneR on linux1.bioconductor.org

Package: regioneR

Version: 1.2.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings regioneR_1.2.0.tar.gz

StartedAt: 2015-10-27 07:20:43 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:26:54 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 371.1 seconds

RetCode: 0

Status:  OK

CheckDir: regioneR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings regioneR_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/regioneR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [164s/166s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
circularRandomizeRegions 20.253  4.640  25.054
createRandomRegions      21.180  3.584  24.858
filterChromosomes        18.547  3.683  22.299
getMask                  18.968  2.783  21.816
maskFromBSGenome         17.902  2.485  20.435
randomizeRegions         17.292  2.966  20.297
localZScore               3.525  0.152   5.176
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [60s/61s]
 [61s/61s] 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
  ‘/home/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	0.435	0.040	0.482
circularRandomizeRegions	20.253	4.640	25.054
commonRegions	0.173	0.008	0.180
createFunctionsList	0.895	0.365	1.260
createRandomRegions	21.180	3.584	24.858
emptyCacheRegioneR	0.001	0.000	0.001
extendRegions	0.135	0.000	0.136
filterChromosomes	18.547	3.683	22.299
getChromosomesByOrganism	0.001	0.001	0.001
getGenome	0.034	0.000	0.034
getGenomeAndMask	0.254	0.259	0.514
getMask	18.968	2.783	21.816
joinRegions	0.103	0.000	0.103
listChrTypes	0.012	0.000	0.013
localZScore	3.525	0.152	5.176
maskFromBSGenome	17.902	2.485	20.435
meanDistance	0.084	0.005	0.088
meanInRegions	0.131	0.000	0.131
mergeRegions	0.083	0.000	0.083
numOverlaps	0.128	0.000	0.127
overlapGraphicalSummary	0.182	0.000	0.182
overlapPermTest	0.656	0.000	0.655
overlapRegions	0.076	0.000	0.075
permTest	1.498	0.000	1.498
plot.localZScoreResults	1.159	0.000	1.160
plot.localZScoreResultsList	2.697	0.004	2.702
plot.permTestResults	3.009	0.060	3.070
plot.permTestResultsList	2.764	0.001	2.770
plotRegions	0.061	0.000	0.061
print.permTestResults	1.300	0.000	1.299
randomizeRegions	17.292	2.966	20.297
recomputePermTest	0.923	0.004	0.927
resampleRegions	0.077	0.000	0.079
splitRegions	0.119	0.000	0.122
subtractRegions	0.192	0.000	0.194
toDataframe	0.019	0.000	0.019
toGRanges	0.025	0.000	0.025
uniqueRegions	0.360	0.000	0.363