BioC 2.13: CHECK report for PCpheno on perceval

Package: PCpheno

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PCpheno_1.24.0.tar.gz

StartedAt: 2014-04-05 03:17:56 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:24:54 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 417.9 seconds

RetCode: 0

Status:  OK

CheckDir: PCpheno.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/PCpheno.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.24.0’
* 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 ... [31s/34s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Category’ ‘ScISI’ ‘KEGG.db’ ‘GO.db’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘annotate’ ‘ppiData’ ‘ppiStats’ ‘SLGI’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘PCpheno.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [86s/90s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
graphTheory    21.307  0.432  22.426
gtResult-class 19.140  1.312  21.070
ppiInteraction  7.388  0.718   8.463
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/PCpheno.Rcheck/00check.log’
for details.

* 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	2.644	0.065	2.858
Dudley	0.011	0.007	0.020
Giaever	0.156	0.025	0.193
HI	0.006	0.004	0.010
KEGG2SCISI	0.971	0.058	1.149
Kastenmayer	0.022	0.007	0.034
Lesage	0.021	0.007	0.028
Osterberg	0.029	0.008	0.038
SGDphenoL	0.038	0.010	0.049
YEASTOHNOLOG	0.011	0.004	0.016
buildFDMat	0.244	0.052	0.306
categoryToEntrezBuilder	0.240	0.046	0.310
complexStatus	3.987	0.104	4.251
deResult-class	0.129	0.041	0.176
densityEstimate	4.087	0.162	4.367
getDescr	1.002	0.028	1.310
getFDgene	0.166	0.021	0.187
graphTheory	21.307	0.432	22.426
gtResult-class	19.140	1.312	21.070
overlap	0.005	0.005	0.011
plot	2.881	0.300	3.374
ppiInteraction	7.388	0.718	8.463
reduceM	0.004	0.006	0.009
truncName	0.003	0.004	0.007