Package: PCpheno

Version: 1.15.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch PCpheno_1.15.0.tar.gz

StartedAt: 2011-07-07 05:41:09 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 05:43:47 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 158.9 seconds

RetCode: 0

Status:  OK

CheckDir: PCpheno.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/PCpheno.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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

Warning in fun(...) :
  Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.
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
Warning message:
In fun(...) : Rgraphviz built with Graphviz version 2.20.3.
Found installed Graphviz version 2.25.20090912.445. This _may_ cause problems.

* DONE (PCpheno)

name	user	system	elapsed
CoHyperGResult-class	0.95	0.02	1.03
Dudley	0.02	0.00	0.01
Giaever	0.07	0.01	0.10
HI	0	0	0
KEGG2SCISI	0.55	0.03	1.07
Kastenmayer	0.02	0.00	0.02
Lesage	0	0	0
Osterberg	0.01	0.01	0.03
SGDphenoL	0.03	0.00	0.03
YEASTOHNOLOG	0.02	0.00	0.01
buildFDMat	0.36	0.05	0.41
categoryToEntrezBuilder	0.62	0.00	0.67
complexStatus	1.36	0.00	1.41
deResult-class	0.21	0.02	0.22
densityEstimate	2.58	0.07	2.66
getDescr	1.09	0.02	1.23
getFDgene	0.10	0.02	0.11
graphTheory	11.17	0.18	11.36
gtResult-class	8.19	1.19	9.39
overlap	0	0	0
plot	1.98	0.13	2.11
ppiInteraction	5.56	0.07	5.64
reduceM	0	0	0
truncName	0	0	0