Package: GSEAlm

Version: 1.12.0

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch GSEAlm_1.12.0.tar.gz

StartedAt: 2011-10-20 14:50:38 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 14:51:13 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 34.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GSEAlm.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/GSEAlm.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GSEAlm/DESCRIPTION' ... OK
* this is package 'GSEAlm' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GSEAlm' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... 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 examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  graph lattice
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   GSEAlm.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-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 ...
** testing if installed package can be loaded

* DONE (GSEAlm)

name	user	system	elapsed
GSNormalize	0.16	0.00	0.16
dfbetasPerGene	0.40	0.01	0.42
getResidPerGene	0.27	0.02	0.28
gsealmPerm	5.97	0.00	5.97
lmPerGene	0.07	0.00	0.08
resplot	0.29	0.00	0.28