Package: plgem

Version: 1.30.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings plgem_1.30.0.tar.gz

StartedAt: 2013-03-25 03:51:23 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:53:07 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 104.0 seconds

RetCode: 0

Status:  OK

CheckDir: plgem.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/plgem.Rcheck’
* using R version 2.15.3 (2013-03-01)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plgem/DESCRIPTION’ ... OK
* this is package ‘plgem’ version ‘1.30.0’
* 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 whether package ‘plgem’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 ... NOTE
plgem.fit: warning in png(file = "fittingEval.png", width = 600, height
  = 600): partial argument match of 'file' to 'filename'
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plgem.deg          10.508  3.280  21.007
plgem.pValue       10.165  1.648  15.608
run.plgem           9.901  0.584  11.347
plgem.resampledStn  6.212  0.176   6.845
* 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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/plgem.Rcheck/00check.log’
for details.

* installing *source* package ‘plgem’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘plgem.Rnw’ 
** testing if installed package can be loaded

* DONE (plgem)

name	user	system	elapsed
LPSeset	0.044	0.012	0.069
plgem.deg	10.508	3.280	21.007
plgem.fit	1.704	0.104	2.340
plgem.obsStn	1.216	0.024	1.547
plgem.pValue	10.165	1.648	15.608
plgem.resampledStn	6.212	0.176	6.845
plgem.write.summary	0.000	0.000	0.001
run.plgem	9.901	0.584	11.347