BioC 2.13: CHECK report for ChIPsim on perceval
This page was generated on 2014-04-05 09:52:19 -0700 (Sat, 05 Apr 2014).
ChIPsim 1.16.0 Peter Humburg
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/ChIPsim | Last Changed Rev: 81642 / Revision: 88450 | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| 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: ChIPsim |
Version: 1.16.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ChIPsim_1.16.0.tar.gz |
StartedAt: 2014-04-05 00:17:51 -0700 (Sat, 05 Apr 2014) |
EndedAt: 2014-04-05 00:22:05 -0700 (Sat, 05 Apr 2014) |
EllapsedTime: 253.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ChIPsim.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ChIPsim.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPsim/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPsim’ version ‘1.16.0’
* 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 ‘ChIPsim’ can be installed ... [24s/24s] 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:
‘Biostrings’
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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘ChIPsimIntro.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [23s/24s] 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
NOTE: There were 2 notes.
See
‘/Users/biocbuild/bbs-2.13-bioc/meat/ChIPsim.Rcheck/00check.log’
for details.
ChIPsim.Rcheck/00install.out:
* installing *source* package ‘ChIPsim’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ChIPsim)
ChIPsim.Rcheck/ChIPsim-Ex.timings:
name | user | system | elapsed
|
ChIPsim-package | 0.007 | 0.003 | 0.010 |
|
bindDens2readDens | 4.430 | 0.157 | 4.611 |
|
decodeQuality | 0.338 | 0.007 | 0.346 |
|
defaultControl | 0.006 | 0.005 | 0.011 |
|
defaultErrorProb | 0.002 | 0.004 | 0.006 |
|
defaultFunctions | 0.007 | 0.005 | 0.012 |
|
defaultGenerator | 0.104 | 0.008 | 0.113 |
|
extractQuality | 0.006 | 0.005 | 0.011 |
|
feat2dens | 1.828 | 0.284 | 2.112 |
|
featureDensity | 0.015 | 0.004 | 0.019 |
|
makeFeatures | 0.115 | 0.005 | 0.120 |
|
placeFeatures | 0.180 | 0.005 | 0.186 |
|
pos2fastq | 0.082 | 0.010 | 0.092 |
|
readError | 0.009 | 0.008 | 0.017 |
|
reconcileFeatures | 0.195 | 0.009 | 0.204 |
|
sampleReads | 3.367 | 0.361 | 3.769 |
|
simChIP | 0.003 | 0.006 | 0.009 |
|
simpleNames | 0.011 | 0.005 | 0.016 |
|
stableFeature | 0.014 | 0.005 | 0.019 |
|
writeFASTQ | 0.014 | 0.007 | 0.020 |
|