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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).

Package 134/750HostnameOS / ArchBUILDCHECKBUILD BIN
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:

nameusersystemelapsed
ChIPsim-package0.0070.0030.010
bindDens2readDens4.4300.1574.611
decodeQuality0.3380.0070.346
defaultControl0.0060.0050.011
defaultErrorProb0.0020.0040.006
defaultFunctions0.0070.0050.012
defaultGenerator0.1040.0080.113
extractQuality0.0060.0050.011
feat2dens1.8280.2842.112
featureDensity0.0150.0040.019
makeFeatures0.1150.0050.120
placeFeatures0.1800.0050.186
pos2fastq0.0820.0100.092
readError0.0090.0080.017
reconcileFeatures0.1950.0090.204
sampleReads3.3670.3613.769
simChIP0.0030.0060.009
simpleNames0.0110.0050.016
stableFeature0.0140.0050.019
writeFASTQ0.0140.0070.020