BioC 2.12: CHECK report for attract on george2

Package: attract

Version: 1.12.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings attract_1.12.0.tar.gz

StartedAt: 2013-10-09 00:16:51 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:22:27 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 335.4 seconds

RetCode: 0

Status:  OK

CheckDir: attract.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/attract.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 ‘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 ... [27s/27s] 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
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 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/81s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
findCorrPartners 22.921  0.352  23.508
findAttractors   20.694  0.124  20.829
findSynexprs     18.737  0.032  18.921
* 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 were 2 notes.
See
  ‘/home/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: replacing previous import ‘makeGOGraph’ when loading ‘AnnotationDbi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘makeGOGraph’ when loading ‘AnnotationDbi’
* DONE (attract)

name	user	system	elapsed
AttractorModuleSet-class	0.012	0.000	0.015
SynExpressionSet-class	0.012	0.000	0.011
attract-package	0.024	0.000	0.023
buildCorMatrix	0.016	0.000	0.018
buildKeggIncidenceMatrix	0.016	0.000	0.016
calcFuncSynexprs	0.012	0.000	0.012
calcInform	0.012	0.000	0.015
calcModfstat	0.020	0.000	0.018
calcRss	0.012	0.004	0.019
exprs.dat	0.660	0.016	0.693
findAttractors	20.694	0.124	20.829
findCorrPartners	22.921	0.352	23.508
findOnepwaySynexprs	0.036	0.000	0.036
findSynexprs	18.737	0.032	18.921
flagPwayExists	0.008	0.000	0.006
loring.eset	0.172	0.016	0.187
plotsynexprs	0.012	0.000	0.011
removeFlatGenes	1.068	0.012	1.080
samp.info	0.044	0.000	0.043
subset.loring.eset	0.128	0.004	0.132