BioC 2.12: CHECK report for domainsignatures on petty

Package: domainsignatures

Version: 1.20.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch domainsignatures_1.20.0.tar.gz

StartedAt: 2013-10-08 22:11:57 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:15:19 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 201.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: domainsignatures.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/domainsignatures.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 'domainsignatures/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'domainsignatures' version '1.20.0'
* 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 'domainsignatures' can be installed ... [21s/21s] WARNING
Found the following significant warnings:
  Warning: package 'KEGG.db' was built under R version 3.1.0
  Warning: package 'KEGG.db' was built under R version 3.1.0
See '/Users/biocbuild/bbs-2.12-bioc/meat/domainsignatures.Rcheck/00install.out' for details.
* 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
File 'domainsignatures/R/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

sage.test: warning in dbinom(0:isize, p = (prob[i])[1], size = isize):
  partial argument match of 'p' to 'prob'
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [10s/10s] 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

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/domainsignatures.Rcheck/00check.log'
for details.

* installing *source* package 'domainsignatures' ...
** R
** inst
** preparing package for lazy loading
Warning: package 'KEGG.db' was built under R version 3.1.0
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: package 'KEGG.db' was built under R version 3.1.0
* DONE (domainsignatures)

name	user	system	elapsed
dataSource	0.010	0.003	0.013
getKEGGdata	0.009	0.002	0.012
getKEGGdescription	0.058	0.001	0.063
gseDomain	0.010	0.001	0.011