BioC 3.2: CHECK report for regioneR on perceval
This page was generated on 2015-11-10 14:49:45 -0800 (Tue, 10 Nov 2015).
regioneR 1.2.0 Bernat Gel
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/regioneR | Last Changed Rev: 109589 / Revision: 110496 | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | | |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
Summary
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 |
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings regioneR_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* 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.
regioneR.Rcheck/00install.out:
* 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)
regioneR.Rcheck/regioneR-Ex.timings:
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 |
|