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: 2015-11-10 08:45:53 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 08:57:23 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 690.0 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 ... [361s/377s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
createRandomRegions      49.251  6.523  55.782
randomizeRegions         49.365  5.536  57.805
filterChromosomes        48.033  6.023  54.060
circularRandomizeRegions 47.794  5.986  63.773
maskFromBSGenome         46.499  6.153  52.665
getMask                  45.768  5.924  51.695
localZScore               3.972  0.370   5.926
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [126s/130s]
 [126s/130s] 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	0.674	0.184	4.861
circularRandomizeRegions	47.794	5.986	63.773
commonRegions	0.255	0.019	0.274
createFunctionsList	1.021	0.383	1.404
createRandomRegions	49.251	6.523	55.782
emptyCacheRegioneR	0.001	0.000	0.001
extendRegions	0.131	0.001	0.132
filterChromosomes	48.033	6.023	54.060
getChromosomesByOrganism	0.002	0.000	0.002
getGenome	0.056	0.000	0.056
getGenomeAndMask	0.407	0.133	0.540
getMask	45.768	5.924	51.695
joinRegions	0.160	0.001	0.161
listChrTypes	0.019	0.000	0.019
localZScore	3.972	0.370	5.926
maskFromBSGenome	46.499	6.153	52.665
meanDistance	0.116	0.000	0.116
meanInRegions	0.165	0.001	0.165
mergeRegions	0.134	0.001	0.135
numOverlaps	0.197	0.000	0.198
overlapGraphicalSummary	0.180	0.001	0.181
overlapPermTest	0.982	0.003	0.992
overlapRegions	0.072	0.000	0.072
permTest	1.783	0.004	1.787
plot.localZScoreResults	1.465	0.192	1.659
plot.localZScoreResultsList	3.240	0.005	3.245
plot.permTestResults	2.554	0.005	2.565
plot.permTestResultsList	3.101	0.239	3.425
plotRegions	0.057	0.001	0.058
print.permTestResults	1.720	0.002	1.721
randomizeRegions	49.365	5.536	57.805
recomputePermTest	1.051	0.025	1.169
resampleRegions	0.079	0.001	0.079
splitRegions	0.117	0.001	0.118
subtractRegions	0.184	0.001	0.185
toDataframe	0.018	0.001	0.018
toGRanges	0.027	0.000	0.026
uniqueRegions	0.362	0.002	0.364