BioC 2.12: CHECK report for PCpheno on petty

Package: PCpheno

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PCpheno_1.22.0.tar.gz

StartedAt: 2013-10-08 23:24:09 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:29:54 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 344.3 seconds

RetCode: 0

Status:  OK

CheckDir: PCpheno.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/PCpheno.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'PCpheno/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PCpheno' version '1.22.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'PCpheno' can be installed ... [29s/30s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [70s/71s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
graphTheory    14.837  0.337  15.269
gtResult-class 12.291  1.250  13.645
ppiInteraction  9.566  0.885  10.568
* 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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: plot
* DONE (PCpheno)

name	user	system	elapsed
CoHyperGResult-class	1.921	0.058	2.082
Dudley	0.337	0.021	0.360
Giaever	0.251	0.045	0.297
HI	0.005	0.004	0.009
KEGG2SCISI	0.838	0.061	0.967
Kastenmayer	0.029	0.005	0.035
Lesage	0.013	0.004	0.016
Osterberg	0.047	0.014	0.062
SGDphenoL	0.056	0.008	0.064
YEASTOHNOLOG	0.021	0.004	0.025
buildFDMat	0.711	0.054	0.768
categoryToEntrezBuilder	0.530	0.062	0.613
complexStatus	2.584	0.129	2.764
deResult-class	0.169	0.046	0.216
densityEstimate	3.431	0.176	3.627
getDescr	1.452	0.105	1.593
getFDgene	0.273	0.024	0.299
graphTheory	14.837	0.337	15.269
gtResult-class	12.291	1.250	13.645
overlap	0.011	0.070	0.082
plot	3.115	0.255	3.399
ppiInteraction	9.566	0.885	10.568
reduceM	0.003	0.005	0.008
truncName	0.002	0.005	0.008