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: 2013-05-01 09:11:37 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 09:16:43 -0700 (Wed, 01 May 2013)

EllapsedTime: 305.4 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 3.0.0 Patched (2013-04-08 r62531)
* 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 ... [24s/26s] 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 installed files from 'inst/doc' ... OK
* checking examples ... [67s/68s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
graphTheory    15.589  0.369  16.265
gtResult-class 13.542  1.133  14.760
ppiInteraction  8.114  0.863   9.063
* 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	2.292	0.064	2.406
Dudley	0.017	0.008	0.026
Giaever	0.213	0.022	0.237
HI	0.009	0.004	0.014
KEGG2SCISI	0.754	0.056	0.842
Kastenmayer	0.019	0.006	0.025
Lesage	0.011	0.007	0.016
Osterberg	0.032	0.011	0.044
SGDphenoL	0.042	0.007	0.050
YEASTOHNOLOG	0.019	0.006	0.025
buildFDMat	0.293	0.050	0.344
categoryToEntrezBuilder	0.214	0.058	0.287
complexStatus	2.502	0.118	2.694
deResult-class	0.152	0.041	0.211
densityEstimate	3.005	0.174	3.240
getDescr	1.098	0.075	1.204
getFDgene	0.208	0.019	0.232
graphTheory	15.589	0.369	16.265
gtResult-class	13.542	1.133	14.760
overlap	0.015	0.079	0.094
plot	2.662	0.279	3.007
ppiInteraction	8.114	0.863	9.063
reduceM	0.004	0.005	0.009
truncName	0.003	0.005	0.008