Package: BioNet

Version: 1.10.1

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings BioNet_1.10.1.tar.gz

StartedAt: 2011-10-20 11:57:28 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 12:00:15 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 166.8 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/BioNet.Rcheck’
* using R version 2.13.2 (2011-09-30)
* 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 namespace 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 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 ... 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
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (BioNet)

name	user	system	elapsed
aggrPvals	0.728	0.024	0.753
bumOptim	1.432	0.016	1.447
compareNetworks	2.584	0.036	2.620
fbum	0	0	0
fbumLL	1.668	0.000	1.668
fdrThreshold	1.624	0.004	1.634
fitBumModel	1.616	0.000	1.620
getCompScores	3.440	0.040	3.479
getEdgeList	1.277	0.024	1.314
hist.bum	1.780	0.000	1.782
largestComp	12.652	0.020	12.686
largestScoreComp	11.905	0.040	12.082
loadNetwork.sif	0	0	0
makeNetwork	0.012	0.000	0.014
mapByVar	0	0	0
permutateNodes	15.365	0.056	15.473
piUpper	1.428	0.000	1.432
plot.bum	1.616	0.004	1.631
plot3dModule	3.529	0.016	3.550
plotLLSurface	1.496	0.000	1.523
plotModule	4.252	0.004	4.297
print.bum	1.380	0.004	1.423
pvaluesExample	0.008	0.000	0.022
readHeinzGraph	0.300	0.004	0.323
readHeinzTree	0.288	0.004	0.294
rmSelfLoops	0.008	0.000	0.009
runFastHeinz	11.081	0.020	11.164
save3dModule	3.244	0.004	3.251
saveNetwork	2.480	0.008	2.491
scanFDR	1.472	0.004	1.477
scoreFunction	1.616	0.040	1.727
scoreNodes	4.257	0.004	4.262
scoreOffset	1.976	0.000	2.443
subNetwork	0.032	0.000	0.042
summary.bum	1.156	0.000	1.158
writeHeinz	3.540	0.004	3.546
writeHeinzEdges	8.764	0.012	8.880
writeHeinzNodes	2.773	0.004	2.781