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BioC 3.2: CHECK report for PWMEnrich on perceval

This page was generated on 2015-11-10 14:47:35 -0800 (Tue, 10 Nov 2015).

Package 817/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PWMEnrich 4.6.0
Robert Stojnic
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/PWMEnrich
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 UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PWMEnrich
Version: 4.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PWMEnrich_4.6.0.tar.gz
StartedAt: 2015-11-10 08:24:40 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 08:27:16 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 155.4 seconds
RetCode: 0
Status:  OK 
CheckDir: PWMEnrich.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PWMEnrich_4.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/PWMEnrich.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 ‘PWMEnrich/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PWMEnrich’ version ‘4.6.0’
* 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 ‘PWMEnrich’ can be installed ... [10s/10s] OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   3.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
'library' or 'require' calls in package code:
  ‘parallel’ ‘PWMEnrich.Dmelanogaster.background’
  ‘PWMEnrich.Hsapiens.background’ ‘PWMEnrich.Mmusculus.background’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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 ... NOTE
getPromoters: no visible global function definition for
  ‘providerVersion’
motifScores: no visible global function definition for ‘mclapply’
motifScoresBigMemory: no visible global function definition for
  ‘mclapply’
registerCoresPWMEnrich: no visible global function definition for
  ‘detectCores’
* 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 ... [49s/49s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
motifScores     5.854  0.029   5.883
motifEnrichment 5.227  0.008   5.252
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’ [6s/6s]
 [6s/6s] 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/PWMEnrich.Rcheck/00check.log’
for details.


PWMEnrich.Rcheck/00install.out:

* installing *source* package ‘PWMEnrich’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PWMEnrich)

PWMEnrich.Rcheck/PWMEnrich-Ex.timings:

nameusersystemelapsed
PFMtoPWM3.2320.4093.704
PWMUnscaled0.5610.0070.569
getBackgroundFrequencies000
groupReport-commaMotifEnrichmentResults-method3.5590.0403.615
makeBackground0.0050.0010.005
makePWMCutoffBackground0.0010.0000.000
makePWMEmpiricalBackground0.0000.0000.001
makePWMGEVBackground0.0000.0000.001
makePWMLognBackground0.0010.0000.000
makePWMPvalCutoffBackground0.0010.0010.001
makePWMPvalCutoffBackgroundFromSeq0.0010.0000.000
makePriors0.0030.0000.003
motifDiffEnrichment3.8670.0043.872
motifEnrichment5.2270.0085.252
motifIC0.0910.0020.120
motifRankingForGroup-commaMotifEnrichmentResults-method2.8980.0042.902
motifRankingForSequence-commaMotifEnrichmentResults-method3.0040.0063.010
motifScores5.8540.0295.883
motifSimilarity0.1270.0010.129
plot0.2660.0060.277
plotMotifScores0.1190.0030.123
plotTopMotifsGroup-commaMotifEnrichmentResults-method3.1670.0083.177
plotTopMotifsSequence-commaMotifEnrichmentResults-method3.1480.0113.226
readMotifs0.1060.0160.122
registerCoresPWMEnrich0.0010.0010.001
reverseComplement0.0550.0010.056
scanWithPWM0.0810.0020.083
sequenceReport-commaMotifEnrichmentResults-method4.0770.0854.218
toPWM3.3690.3813.750
useBigMemoryPWMEnrich0.0000.0000.001