Package: GSEAlm

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GSEAlm_1.20.0.tar.gz

StartedAt: 2013-05-01 06:37:36 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 06:38:36 -0700 (Wed, 01 May 2013)

EllapsedTime: 60.2 seconds

RetCode: 0

Status:  OK

CheckDir: GSEAlm.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GSEAlm.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GSEAlm/DESCRIPTION' ... OK
* this is package 'GSEAlm' version '1.20.0'
* 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 'GSEAlm' can be installed ... [4s/4s] 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 ... NOTE
pvalFromPermMat: warning in matrix(as.double(NA), nr = nrow(perms),
  ncol = 2): partial argument match of 'nr' to 'nrow'
* checking Rd files ... NOTE
prepare_Rd: gsealmPerm.Rd:62: Dropping empty section \references
* 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 installed files from 'inst/doc' ... NOTE
The following files contain a license that requires
distribution of original sources:
  'crop.sty'
Please ensure that you have complied with it.
The following files should probably not be installed:
  'alltt.sty', 'array.sty', 'chngpage.sty', 'color.sty', 'crop.sty',
  'float.sty', 'flushend.sty', 'graphicx.sty', 'landscap.sty',
  'natbib.bst', 'natbib.sty', 'rmgreek.sty', 'stfloats.sty',
  'times.sty', 'url.sty'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [10s/10s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
gsealmPerm 6.508  0.099   6.712
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  'graph' 'lattice'
* 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 were 4 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/GSEAlm.Rcheck/00check.log'
for details.

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

name	user	system	elapsed
GSNormalize	0.245	0.018	0.273
dfbetasPerGene	0.596	0.036	0.639
getResidPerGene	0.297	0.014	0.322
gsealmPerm	6.508	0.099	6.712
lmPerGene	0.101	0.013	0.123
resplot	0.341	0.018	0.363