Package: BioNet

Version: 1.14.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings BioNet_1.14.0.tar.gz

StartedAt: 2012-03-31 23:55:43 -0700 (Sat, 31 Mar 2012)

EndedAt: 2012-03-31 23:58:21 -0700 (Sat, 31 Mar 2012)

EllapsedTime: 158.2 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/BioNet.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BioNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioNet' 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 whether package 'BioNet' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   3.7Mb
* 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 installed files from 'inst/doc' ... 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

NOTE: There was 1 note.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/BioNet.Rcheck/00check.log'
for details.

* installing *source* package 'BioNet' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'Tutorial.Rnw' 
** testing if installed package can be loaded

* DONE (BioNet)

name	user	system	elapsed
aggrPvals	0.652	0.020	0.686
bumOptim	0.776	0.004	0.792
compareNetworks	1.336	0.016	1.377
consensusScores	0.284	0.004	0.304
fbum	0	0	0
fbumLL	0.824	0.000	0.829
fdrThreshold	0.608	0.000	0.615
fitBumModel	0.968	0.012	0.989
getCompScores	1.876	0.020	1.923
getEdgeList	0.848	0.008	0.877
hist.bum	0.980	0.000	0.989
largestComp	5.953	0.004	5.976
largestScoreComp	6.556	0.028	6.613
loadNetwork.sif	0	0	0
makeNetwork	0.012	0.000	0.010
mapByVar	0	0	0
permutateNodes	7.773	0.040	7.832
piUpper	0.664	0.004	0.673
plot.bum	1.080	0.000	1.089
plot3dModule	3.028	0.004	3.065
plotLLSurface	0.600	0.004	0.624
plotModule	2.220	0.000	2.245
print.bum	0.652	0.000	0.658
pvaluesExample	0.008	0.000	0.017
readHeinzGraph	0.240	0.000	0.255
readHeinzTree	0.232	0.004	0.259
resamplingPvalues	4.616	0.036	4.674
rmSelfLoops	0.008	0.000	0.006
runFastHeinz	8.209	0.004	8.243
save3dModule	1.548	0.004	1.584
saveNetwork	0.924	0.008	0.955
scanFDR	0.720	0.000	0.731
scoreFunction	0.620	0.020	0.652
scoreNodes	2.272	0.016	2.311
scoreOffset	0.632	0.000	0.647
sortedEdgeList	4.301	0.012	4.337
subNetwork	0.032	0.000	0.040
summary.bum	0.656	0.012	0.678
writeHeinz	1.528	0.004	1.555
writeHeinzEdges	3.160	0.000	3.219
writeHeinzNodes	1.972	0.004	2.019