Package: PCpheno

Version: 1.15.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings PCpheno_1.15.0.tar.gz

StartedAt: 2011-07-07 01:46:46 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 01:49:28 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 161.6 seconds

RetCode: 0

Status:  OK

CheckDir: PCpheno.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/PCpheno.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PCpheno/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PCpheno’ version ‘1.15.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘PCpheno’ 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 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 ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* 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 ‘PCpheno’ ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: AnnotationDbi
Loading required package: Biobase

Welcome to Bioconductor

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

Loading required package: GO.db
Loading required package: DBI

Loading required package: RpsiXML
Loading required package: annotate
Loading required package: graph
Loading required package: RBGL
Loading required package: XML

Attaching package: ‘XML’

The following object(s) are masked from ‘package:graph’:

    addNode

Loading required package: hypergraph

Attaching package: ‘hypergraph’

The following object(s) are masked from ‘package:AnnotationDbi’:

    head, tail

The following object(s) are masked from ‘package:utils’:

    head, tail

Loading required package: apComplex

Loading required package: lattice
Loading required package: ppiData

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘PCpheno.Rnw’ 
** testing if installed package can be loaded

* DONE (PCpheno)

name	user	system	elapsed
CoHyperGResult-class	0.980	0.020	1.002
Dudley	0.012	0.000	0.012
Giaever	0.080	0.000	0.084
HI	0.004	0.004	0.003
KEGG2SCISI	0.520	0.024	0.580
Kastenmayer	0.008	0.000	0.013
Lesage	0.008	0.000	0.008
Osterberg	0.016	0.004	0.020
SGDphenoL	0.020	0.000	0.018
YEASTOHNOLOG	0.004	0.004	0.008
buildFDMat	0.392	0.004	0.399
categoryToEntrezBuilder	0.568	0.012	0.591
complexStatus	1.260	0.036	1.301
deResult-class	0.196	0.004	0.200
densityEstimate	2.428	0.012	2.441
getDescr	0.832	0.024	0.857
getFDgene	0.080	0.008	0.087
graphTheory	12.753	0.264	13.115
gtResult-class	10.137	0.724	10.933
overlap	0.004	0.000	0.002
plot	2.236	0.004	2.241
ppiInteraction	6.188	0.092	6.285
reduceM	0.004	0.000	0.001
truncName	0	0	0