Package: PCpheno

Version: 1.18.0

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings PCpheno_1.18.0.tar.gz

StartedAt: 2012-09-24 02:47:14 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 02:51:20 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 246.3 seconds

RetCode: 0

Status:  OK

CheckDir: PCpheno.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/PCpheno.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘1.18.0’
* 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 ‘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 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 ... 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
* 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
No methods found in "BiocGenerics" for requests: plot

*** Deprecation warning ***:
The package 'ppiData' is deprecated and will not be supported after Bioconductor release 2.11


** help
*** installing help indices
** building package indices
** installing vignettes
   ‘PCpheno.Rnw’ 
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: plot

*** Deprecation warning ***:
The package 'ppiData' is deprecated and will not be supported after Bioconductor release 2.11



* DONE (PCpheno)

name	user	system	elapsed
CoHyperGResult-class	1.544	0.036	1.607
Dudley	0.004	0.004	0.009
Giaever	0.144	0.004	0.147
HI	0.000	0.000	0.003
KEGG2SCISI	0.628	0.036	0.712
Kastenmayer	0.012	0.000	0.015
Lesage	0.004	0.000	0.008
Osterberg	0.016	0.000	0.022
SGDphenoL	0.024	0.000	0.027
YEASTOHNOLOG	0.008	0.000	0.009
buildFDMat	0.58	0.02	0.60
categoryToEntrezBuilder	0.508	0.008	0.527
complexStatus	1.792	0.016	1.823
deResult-class	0.104	0.024	0.131
densityEstimate	3.097	0.020	3.117
getDescr	0.780	0.008	0.830
getFDgene	0.140	0.004	0.141
graphTheory	15.365	0.160	15.524
gtResult-class	12.604	0.844	13.455
overlap	0.000	0.000	0.002
plot	2.537	0.068	2.603
ppiInteraction	6.024	0.016	6.075
reduceM	0.004	0.000	0.001
truncName	0	0	0