Package: eisa

Version: 1.3.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings eisa_1.3.0.tar.gz

StartedAt: 2011-02-24 19:18:00 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 19:21:54 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 234.0 seconds

RetCode: 0

Status:  OK

CheckDir: eisa.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/eisa.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘eisa/DESCRIPTION’ ... OK
* this is package ‘eisa’ version ‘1.3.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘eisa’ can be installed ... 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 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... NOTE
'library' or 'require' calls not declared from:
  org.Hs.eg.db targetscan.Hs.eg.db
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘eisa’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

in method for ‘coerce’ with signature ‘"Biclust","ISAModules"’: no definition for class "Biclust"
in method for ‘coerce’ with signature ‘"ISAModules","Biclust"’: no definition for class "Biclust"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (eisa)

name	user	system	elapsed
ALLModules	0.032	0.008	0.042
ISA.CHR	1.880	0.040	1.968
ISA.GO	6.116	0.124	9.073
ISA.KEGG	2.572	0.040	3.061
ISA	34.203	0.188	34.996
ISA.html	15.08	0.27	15.58
ISA.iterate	8.3	0.1	8.4
ISA.miRNA	0.012	0.000	0.011
ISA.normalize	5.492	0.076	5.572
ISA.sweep	15.549	0.064	15.647
ISA.unique	7.6	0.1	7.7
ISA2heatmap	1.424	0.032	1.455
ISAExpressionSet	5.776	0.072	7.282
ISAModules-class	0.016	0.000	0.015
ListHyperGParams-class	3.588	0.056	3.650
ListHyperGResult-class	4.089	0.056	4.152
cond.plot	2.356	0.024	2.397
eisa.biclust	4.54	0.04	4.60
enrichment	0.536	0.024	0.577
exp.plot	2.420	0.044	2.739
gograph	4.69	0.15	5.05
mnplot	2.232	0.052	2.296
overlap	0.56	0.47	1.09
profilePlot	1.672	0.056	1.730
robustness	3.616	0.048	3.667