BioC 2.12: CHECK report for attract on petty

Package: attract

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch attract_1.12.0.tar.gz

StartedAt: 2013-10-08 21:37:47 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:43:08 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 320.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: attract.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/attract.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 'attract/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'attract' version '1.12.0'
* 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 'attract' can be installed ... [23s/24s] 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/attract.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
plotsynexprs: warning in axis(1, at = tickMarks, lab = tickLabels):
  partial argument match of 'lab' to 'labels'
removeFlatGenes: warning in topTable(fit2, coef =
  (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
  partial argument match of 'n' to 'number'
removeFlatGenes: warning in topTable(fit2, coef =
  (1:(length(my.contrasts))), adjust = "fdr", n = nrow(dat.fr)):
  partial argument match of 'adjust' to 'adjust.method'
* 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' ... NOTE
The following files should probably not be installed:
  'fancyvrb.sty'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [80s/82s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
findCorrPartners 22.711  0.450  23.462
findAttractors   21.440  0.384  22.016
findSynexprs     20.015  0.272  20.582
* 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 were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/attract.Rcheck/00check.log'
for details.

* installing *source* package 'attract' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: package 'KEGG.db' was built under R version 3.1.0
Warning: replacing previous import 'makeGOGraph' when loading 'AnnotationDbi'
** 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
Warning: replacing previous import 'makeGOGraph' when loading 'AnnotationDbi'
* DONE (attract)

name	user	system	elapsed
AttractorModuleSet-class	0.007	0.001	0.008
SynExpressionSet-class	0.013	0.002	0.014
attract-package	0.011	0.002	0.012
buildCorMatrix	0.008	0.002	0.009
buildKeggIncidenceMatrix	0.008	0.002	0.011
calcFuncSynexprs	0.010	0.003	0.014
calcInform	0.014	0.004	0.018
calcModfstat	0.009	0.002	0.011
calcRss	0.007	0.003	0.010
exprs.dat	0.554	0.029	0.583
findAttractors	21.440	0.384	22.016
findCorrPartners	22.711	0.450	23.462
findOnepwaySynexprs	0.003	0.004	0.007
findSynexprs	20.015	0.272	20.582
flagPwayExists	0.002	0.005	0.007
loring.eset	0.279	0.042	0.329
plotsynexprs	0.004	0.006	0.011
removeFlatGenes	0.822	0.096	0.926
samp.info	0.030	0.005	0.036
subset.loring.eset	0.172	0.025	0.204