BioC 2.12: CHECK report for plgem on petty

Package: plgem

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch plgem_1.32.0.tar.gz

StartedAt: 2013-10-08 23:28:47 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:30:44 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 116.5 seconds

RetCode: 0

Status:  OK

CheckDir: plgem.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/plgem.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'plgem/DESCRIPTION' ... OK
* this is package 'plgem' version '1.32.0'
* 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 ... [5s/5s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 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 examples ... [57s/58s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plgem.deg          13.327  1.297  14.781
run.plgem          12.267  1.285  13.692
plgem.pValue       12.417  0.976  13.546
plgem.resampledStn  7.240  1.319   8.606
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* 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)

name	user	system	elapsed
LPSeset	0.106	0.015	0.120
plgem.deg	13.327	1.297	14.781
plgem.fit	2.455	0.237	2.736
plgem.obsStn	1.876	0.038	1.931
plgem.pValue	12.417	0.976	13.546
plgem.resampledStn	7.240	1.319	8.606
plgem.write.summary	0.097	0.111	0.208
run.plgem	12.267	1.285	13.692
setGpar	0.003	0.004	0.006