BioC 2.9: CHECK report for BioNet on wilson2

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/BioNet.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioNet’ version ‘1.11.1’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘BioNet’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* 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 examples ... 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

* installing *source* package ‘BioNet’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘Tutorial.Rnw’ 
** testing if installed package can be loaded

* DONE (BioNet)

name	user	system	elapsed
aggrPvals	0.732	0.036	0.772
bumOptim	1.492	0.016	1.508
compareNetworks	2.664	0.084	2.756
fbum	0	0	0
fbumLL	1.560	0.008	1.570
fdrThreshold	1.144	0.000	1.143
fitBumModel	1.668	0.000	1.668
getCompScores	3.348	0.012	3.431
getEdgeList	1.368	0.012	1.382
hist.bum	1.369	0.012	1.380
largestComp	12.584	0.020	12.868
largestScoreComp	11.825	0.036	11.868
loadNetwork.sif	0	0	0
makeNetwork	0.012	0.000	0.010
mapByVar	0	0	0
permutateNodes	15.437	0.048	15.773
piUpper	1.388	0.000	1.405
plot.bum	1.604	0.008	1.671
plot3dModule	3.384	0.028	3.570
plotLLSurface	1.441	0.000	1.491
plotModule	4.424	0.000	4.456
print.bum	1.236	0.000	1.237
pvaluesExample	0.02	0.00	0.02
readHeinzGraph	0.288	0.000	0.288
readHeinzTree	0.276	0.008	0.286
rmSelfLoops	0.012	0.000	0.010
runFastHeinz	10.013	0.004	10.151
save3dModule	2.672	0.004	2.676
saveNetwork	2.276	0.004	2.280
scanFDR	1.568	0.000	1.573
scoreFunction	1.632	0.016	1.649
scoreNodes	3.688	0.008	3.781
scoreOffset	1.524	0.000	1.524
subNetwork	0.060	0.000	0.062
summary.bum	1.545	0.004	1.549
writeHeinz	2.792	0.000	2.793
writeHeinzEdges	6.796	0.004	6.807
writeHeinzNodes	2.960	0.008	2.969

Summary

Command output