BioC 2.12: CHECK report for apComplex on george2

Package: apComplex

Version: 2.26.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings apComplex_2.26.0.tar.gz

StartedAt: 2013-10-09 00:09:29 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:12:27 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 178.0 seconds

RetCode: 0

Status:  OK

CheckDir: apComplex.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/apComplex.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘apComplex/DESCRIPTION’ ... OK
* this is package ‘apComplex’ version ‘2.26.0’
* 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 ‘apComplex’ can be installed ... [19s/20s] 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 ... NOTE
plotComplex: warning in mget(complexMembers, env = org.Sc.sgdGENENAME,
  ifnotfound = NA): partial argument match of 'env' to 'envir'
* 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 ... [13s/13s] 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/apComplex.Rcheck/00check.log’
for details.

* installing *source* package ‘apComplex’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (apComplex)

name	user	system	elapsed
FilteredEstimates	0.080	0.004	0.081
HMSPCI	0.816	0.024	0.892
Krogan	0.344	0.000	0.346
LCjoin	0.476	0.000	0.478
MBMEcHMSPCI	0.012	0.008	0.017
MBMEcKrogan	0.008	0.004	0.012
MBMEcTAP	0.004	0.020	0.022
TAP	0.040	0.016	0.053
apEX	0.004	0.008	0.012
bhmaxSubgraph	0.712	0.012	0.722
findComplexes	0.048	0.000	0.049
gavinBP2006	0.120	0.080	0.199
kroganBPMat2006	0.664	0.264	0.947
mergeComplexes	0.816	0.028	0.847
plotComplex	0.432	0.016	0.449
sortComplexes	0.404	0.004	0.411
yNameTAP	0.016	0.016	0.033
yTAP	0.012	0.000	0.016