PWMEnrich 4.2.0
Robert Stojnic
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/PWMEnrich | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | 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 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PWMEnrich_4.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/PWMEnrich.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘4.2.0’
* 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 ‘PWMEnrich’ can be installed ... [16s/19s] OK
* checking installed package size ... OK
* 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.
Package in Depends field not imported from: ‘grid’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* 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’
plotMultipleMotifs: no visible global function definition for
‘grid.newpage’
plotMultipleMotifs: no visible global function definition for
‘pushViewport’
plotMultipleMotifs: no visible global function definition for
‘viewport’
plotMultipleMotifs: no visible global function definition for
‘grid.layout’
plotMultipleMotifs: no visible global function definition for
‘popViewport’
registerCoresPWMEnrich: no visible global function definition for
‘detectCores’
seqLogoGrid: no visible global function definition for ‘pushViewport’
seqLogoGrid: no visible global function definition for ‘plotViewport’
seqLogoGrid: no visible global function definition for ‘dataViewport’
seqLogoGrid: no visible global function definition for ‘grid.polygon’
seqLogoGrid: no visible global function definition for ‘unit’
seqLogoGrid: no visible global function definition for ‘gpar’
seqLogoGrid: no visible global function definition for ‘grid.text’
seqLogoGrid: no visible global function definition for ‘grid.xaxis’
seqLogoGrid: no visible global function definition for ‘grid.yaxis’
seqLogoGrid: no visible global function definition for ‘popViewport’
* 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 ... [50s/50s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
motifScores 5.811 0.057 5.874
motifEnrichment 5.334 0.017 5.354
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘test-all.R’ [10s/10s]
[10s/10s] 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
NOTE: There were 2 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/PWMEnrich.Rcheck/00check.log’
for details.
* installing *source* package ‘PWMEnrich’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graphics::plot’ when loading ‘seqLogo’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graphics::plot’ when loading ‘seqLogo’
* DONE (PWMEnrich)