Package: BioNet

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BioNet_1.9.0.tar.gz

StartedAt: 2011-02-24 18:26:38 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 18:30:17 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 218.2 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/BioNet.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-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 ‘1.9.0’
* 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 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... 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 ...
** testing if installed package can be loaded

* DONE (BioNet)

name	user	system	elapsed
aggrPvals	1.093	0.072	1.168
bumOptim	1.166	0.336	1.550
compareNetworks	2.562	0.140	2.771
fbum	0.000	0.000	0.001
fbumLL	1.422	0.362	1.798
fdrThreshold	1.237	0.354	1.606
fitBumModel	1.793	0.363	2.189
getCompScores	3.740	0.209	3.994
getEdgeList	1.579	0.047	1.634
hist.bum	1.183	0.363	1.564
largestComp	13.177	2.505	15.810
largestScoreComp	15.851	2.714	18.693
loadNetwork.sif	0	0	0
makeNetwork	0.014	0.001	0.013
mapByVar	0	0	0
permutateNodes	16.689	2.709	19.550
piUpper	1.265	0.356	1.628
plot.bum	1.777	0.380	2.172
plot3dModule	4.862	0.945	5.840
plotLLSurface	1.219	0.216	1.450
plotModule	5.372	0.931	6.420
print.bum	1.687	0.376	2.079
pvaluesExample	0.018	0.002	0.019
readHeinzGraph	0.543	0.008	0.552
readHeinzTree	0.581	0.011	0.600
rmSelfLoops	0.012	0.000	0.013
runFastHeinz	13.382	1.486	14.975
save3dModule	3.749	0.802	4.575
saveNetwork	2.302	0.086	2.397
scanFDR	1.394	0.377	1.786
scoreFunction	1.522	0.445	2.077
scoreNodes	5.593	0.969	6.619
scoreOffset	1.268	0.356	1.642
subNetwork	0.059	0.002	0.062
summary.bum	1.281	0.358	1.651
writeHeinz	3.820	0.784	4.635
writeHeinzEdges	7.697	1.030	8.777
writeHeinzNodes	4.532	0.782	5.340