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) (2011-04-18 r55504)
* 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 ‘1.10.1’
* 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	0.632	0.048	0.679
bumOptim	1.460	0.012	1.469
compareNetworks	2.584	0.060	2.646
fbum	0.000	0.000	0.001
fbumLL	1.716	0.012	1.728
fdrThreshold	1.304	0.008	1.310
fitBumModel	1.632	0.012	1.645
getCompScores	3.252	0.036	3.292
getEdgeList	1.228	0.016	1.256
hist.bum	1.437	0.008	1.468
largestComp	12.100	0.036	12.241
largestScoreComp	11.461	0.052	11.617
loadNetwork.sif	0	0	0
makeNetwork	0.012	0.000	0.009
mapByVar	0	0	0
permutateNodes	16.185	0.036	16.222
piUpper	1.368	0.016	1.389
plot.bum	1.992	0.000	2.008
plot3dModule	3.528	0.012	3.634
plotLLSurface	1.213	0.000	1.210
plotModule	3.304	0.008	3.315
print.bum	1.548	0.000	1.547
pvaluesExample	0.008	0.004	0.012
readHeinzGraph	0.300	0.000	0.297
readHeinzTree	0.292	0.000	0.291
rmSelfLoops	0.008	0.000	0.010
runFastHeinz	10.153	0.012	10.359
save3dModule	2.408	0.008	2.518
saveNetwork	1.836	0.004	1.847
scanFDR	1.356	0.000	1.354
scoreFunction	1.144	0.032	1.174
scoreNodes	3.992	0.044	4.228
scoreOffset	1.728	0.164	2.723
subNetwork	0.040	0.004	0.043
summary.bum	1.860	0.000	1.907
writeHeinz	2.833	0.000	2.837
writeHeinzEdges	7.768	0.008	7.900
writeHeinzNodes	3.028	0.012	3.042

Summary

Command output