BioC 2.13: CHECK report for MethylSeekR on zin1
This page was generated on 2014-04-05 09:48:33 -0700 (Sat, 05 Apr 2014).
MethylSeekR 1.2.2 Lukas Burger
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/MethylSeekR | Last Changed Rev: 85304 / Revision: 88450 | Last Changed Date: 2014-01-07 06:54:01 -0800 (Tue, 07 Jan 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | [ OK ] | |
moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
Summary
Package: MethylSeekR |
Version: 1.2.2 |
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings MethylSeekR_1.2.2.tar.gz |
StartedAt: 2014-04-05 02:22:37 -0700 (Sat, 05 Apr 2014) |
EndedAt: 2014-04-05 02:29:44 -0700 (Sat, 05 Apr 2014) |
EllapsedTime: 427.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MethylSeekR.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/MethylSeekR.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MethylSeekR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MethylSeekR’ version ‘1.2.2’
* 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 ‘MethylSeekR’ can be installed ... [13s/13s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘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 ... NOTE
Namespace in Imports field not imported from: ‘geneplotter’
All declared Imports should be used.
Package in Depends field not imported from: ‘rtracklayer’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... [288s/304s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
MethylSeekR-package 84.325 0.476 92.817
plotPMDSegmentation 54.804 0.232 55.132
savePMDSegments 49.727 0.224 50.096
segmentPMDs 48.499 0.228 48.847
calculateFDRs 16.465 0.032 24.379
plotAlphaDistributionOneChr 11.989 0.060 12.077
plotFinalSegmentation 6.460 0.048 6.536
* 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
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-2.13-bioc/meat/MethylSeekR.Rcheck/00check.log’
for details.
MethylSeekR.Rcheck/00install.out:
* installing *source* package ‘MethylSeekR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MethylSeekR)
MethylSeekR.Rcheck/MethylSeekR-Ex.timings:
name | user | system | elapsed
|
MethylSeekR-package | 84.325 | 0.476 | 92.817 |
|
calculateFDRs | 16.465 | 0.032 | 24.379 |
|
plotAlphaDistributionOneChr | 11.989 | 0.060 | 12.077 |
|
plotFinalSegmentation | 6.460 | 0.048 | 6.536 |
|
plotPMDSegmentation | 54.804 | 0.232 | 55.132 |
|
readMethylome | 0.588 | 0.004 | 0.593 |
|
readSNPTable | 0.180 | 0.004 | 0.186 |
|
removeSNPs | 1.164 | 0.008 | 1.172 |
|
savePMDSegments | 49.727 | 0.224 | 50.096 |
|
saveUMRLMRSegments | 2.900 | 0.028 | 2.969 |
|
segmentPMDs | 48.499 | 0.228 | 48.847 |
|
segmentUMRsLMRs | 2.536 | 0.060 | 2.600 |
|