BioC 2.13: CHECK report for attract on perceval

Package: attract

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch attract_1.14.0.tar.gz

StartedAt: 2014-04-04 23:34:30 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:40:58 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 387.7 seconds

RetCode: 0

Status:  OK

CheckDir: attract.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/attract.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.14.0’
* 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 ... [32s/33s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘AnnotationDbi’ ‘KEGG.db’ ‘limma’ ‘cluster’ ‘GOstats’ ‘graphics’ ‘methods’ ‘stats’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
‘library’ or ‘require’ calls to packages already attached by Depends:
  ‘cluster’ ‘GOstats’ ‘KEGG.db’ ‘limma’
  Please remove these calls from your code.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘attract.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [71s/72s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
findCorrPartners 18.783  0.364  19.340
findAttractors   16.838  0.411  17.833
findSynexprs     14.545  0.248  15.071
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/attract.Rcheck/00check.log’
for details.

* installing *source* package ‘attract’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘AnnotationDbi::makeGOGraph’ when loading ‘attract’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘AnnotationDbi::makeGOGraph’ when loading ‘attract’
* DONE (attract)

name	user	system	elapsed
AttractorModuleSet-class	0.008	0.003	0.011
SynExpressionSet-class	0.008	0.003	0.011
attract-package	0.487	0.005	0.507
buildCorMatrix	0.011	0.006	0.017
buildKeggIncidenceMatrix	0.007	0.004	0.012
calcFuncSynexprs	0.008	0.004	0.012
calcInform	0.008	0.006	0.014
calcModfstat	0.008	0.004	0.012
calcRss	0.008	0.005	0.014
exprs.dat	0.176	0.030	0.210
findAttractors	16.838	0.411	17.833
findCorrPartners	18.783	0.364	19.340
findOnepwaySynexprs	0.003	0.005	0.008
findSynexprs	14.545	0.248	15.071
flagPwayExists	0.027	0.007	0.036
loring.eset	0.202	0.041	0.244
plotsynexprs	0.027	0.008	0.036
removeFlatGenes	0.929	0.074	1.026
samp.info	0.025	0.004	0.029
subset.loring.eset	0.110	0.021	0.133