BioC 2.13: CHECK report for plgem on perceval
This page was generated on 2014-04-05 09:51:45 -0700 (Sat, 05 Apr 2014).
plgem 1.34.0 Norman Pavelka
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/plgem | 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: plgem |
Version: 1.34.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch plgem_1.34.0.tar.gz |
StartedAt: 2014-04-05 03:24:57 -0700 (Sat, 05 Apr 2014) |
EndedAt: 2014-04-05 03:26:45 -0700 (Sat, 05 Apr 2014) |
EllapsedTime: 108.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: plgem.Rcheck |
Warnings: 0 |
Command output
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/plgem.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 ‘plgem/DESCRIPTION’ ... OK
* this is package ‘plgem’ version ‘1.34.0’
* 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 ‘plgem’ can be installed ... [4s/5s] 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
Packages in Depends field not imported from:
‘Biobase’ ‘MASS’
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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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/51s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plgem.deg 11.193 1.260 12.863
run.plgem 10.613 1.369 12.285
plgem.pValue 10.442 1.161 11.977
plgem.resampledStn 5.925 1.516 7.749
* 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 was 1 note.
See
‘/Users/biocbuild/bbs-2.13-bioc/meat/plgem.Rcheck/00check.log’
for details.
plgem.Rcheck/00install.out:
* installing *source* package ‘plgem’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (plgem)
plgem.Rcheck/plgem-Ex.timings:
name | user | system | elapsed
|
LPSeset | 0.087 | 0.009 | 0.097 |
|
plgem.deg | 11.193 | 1.260 | 12.863 |
|
plgem.fit | 1.865 | 0.272 | 2.633 |
|
plgem.obsStn | 1.268 | 0.043 | 1.332 |
|
plgem.pValue | 10.442 | 1.161 | 11.977 |
|
plgem.resampledStn | 5.925 | 1.516 | 7.749 |
|
plgem.write.summary | 0.007 | 0.004 | 0.012 |
|
run.plgem | 10.613 | 1.369 | 12.285 |
|
setGpar | 0.002 | 0.003 | 0.005 |
|