Package: attract

Version: 1.11.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch attract_1.11.1.tar.gz

StartedAt: 2013-03-25 01:16:53 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:21:16 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 263.9 seconds

RetCode: 0

Status:  OK

CheckDir: attract.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/attract.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'attract/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'attract' version '1.11.1'
* 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 ... [18s/18s] 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 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 ... [57s/58s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
findAttractors   16.237  0.242  16.545
findCorrPartners 15.245  0.890  16.220
findSynexprs     12.955  0.225  13.189
* 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
  '/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: replacing previous import 'makeGOGraph' when loading 'AnnotationDbi'
** help
*** installing help indices
** building package indices
** installing vignettes
   'attract.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'makeGOGraph' when loading 'AnnotationDbi'
* DONE (attract)

name	user	system	elapsed
AttractorModuleSet-class	0.006	0.005	0.011
SynExpressionSet-class	0.007	0.005	0.012
attract-package	0.008	0.007	0.016
buildCorMatrix	0.008	0.010	0.032
buildKeggIncidenceMatrix	0.007	0.007	0.014
calcFuncSynexprs	0.007	0.006	0.013
calcInform	0.006	0.007	0.015
calcModfstat	0.007	0.007	0.015
calcRss	0.007	0.008	0.015
exprs.dat	0.393	0.026	0.421
findAttractors	16.237	0.242	16.545
findCorrPartners	15.245	0.890	16.220
findOnepwaySynexprs	0.015	0.008	0.023
findSynexprs	12.955	0.225	13.189
flagPwayExists	0.003	0.005	0.008
loring.eset	0.296	0.032	0.331
plotsynexprs	0.005	0.007	0.012
removeFlatGenes	0.637	0.124	0.769
samp.info	0.004	0.005	0.010
subset.loring.eset	0.127	0.014	0.141