BioC 3.3: CHECK report for regioneR on linux2.bioconductor.org

Package: regioneR

Version: 1.3.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings regioneR_1.3.0.tar.gz

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

EndedAt: 2015-10-27 07:25:41 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 334.7 seconds

RetCode: 0

Status:  OK

CheckDir: regioneR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings regioneR_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/regioneR.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.3.0’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [146s/148s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
createRandomRegions      21.188  1.832  23.063
circularRandomizeRegions 19.689  1.645  21.483
filterChromosomes        18.732  1.471  20.264
randomizeRegions         18.327  1.662  20.034
getMask                  17.816  1.566  19.439
maskFromBSGenome         16.705  1.633  18.414
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [57s/57s]
 [57s/57s] 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-3.3-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	0.515	0.020	0.536
circularRandomizeRegions	19.689	1.645	21.483
commonRegions	0.161	0.003	0.164
createFunctionsList	0.678	0.083	0.762
createRandomRegions	21.188	1.832	23.063
emptyCacheRegioneR	0	0	0
extendRegions	0.089	0.000	0.089
filterChromosomes	18.732	1.471	20.264
getChromosomesByOrganism	0.001	0.000	0.001
getGenome	0.033	0.000	0.036
getGenomeAndMask	0.044	0.000	0.045
getMask	17.816	1.566	19.439
joinRegions	0.16	0.00	0.16
listChrTypes	0.019	0.000	0.018
localZScore	3.325	0.120	4.954
maskFromBSGenome	16.705	1.633	18.414
meanDistance	0.087	0.000	0.087
meanInRegions	0.093	0.000	0.092
mergeRegions	0.097	0.000	0.096
numOverlaps	0.163	0.000	0.164
overlapGraphicalSummary	0.180	0.000	0.181
overlapPermTest	0.606	0.000	0.606
overlapRegions	0.045	0.000	0.044
permTest	1.236	0.001	1.238
plot.localZScoreResults	0.895	0.000	0.895
plot.localZScoreResultsList	2.452	0.000	2.460
plot.permTestResults	2.029	0.007	2.036
plot.permTestResultsList	2.133	0.000	2.133
plotRegions	0.036	0.000	0.036
print.permTestResults	1.569	0.000	1.581
randomizeRegions	18.327	1.662	20.034
recomputePermTest	0.879	0.000	0.885
resampleRegions	0.063	0.000	0.063
splitRegions	0.106	0.000	0.106
subtractRegions	0.175	0.000	0.175
toDataframe	0.017	0.000	0.017
toGRanges	0.021	0.000	0.021
uniqueRegions	0.344	0.000	0.345