Package: BioNet

Version: 1.17.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings BioNet_1.17.0.tar.gz

StartedAt: 2013-01-16 01:01:24 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 01:05:23 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 238.3 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/BioNet.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.17.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BioNet’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   3.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
Examples with CPU or elapsed time > 5s
                    user system elapsed
permutateNodes    14.909  0.016  14.928
largestScoreComp  13.336  0.036  13.379
largestComp       11.777  0.020  11.800
runFastHeinz      10.392  0.020  10.412
resamplingPvalues  7.061  0.108   7.172
writeHeinzEdges    5.132  0.012   5.145
* 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/biocbuild/bbs-2.12-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	0.552	0.020	0.574
bumOptim	1.444	0.000	1.441
compareNetworks	2.356	0.036	2.413
consensusScores	0.744	0.008	0.749
fbum	0.016	0.004	0.018
fbumLL	1.652	0.004	1.654
fdrThreshold	1.676	0.004	1.680
fitBumModel	1.648	0.004	1.649
getCompScores	3.029	0.020	3.079
getEdgeList	1.240	0.008	1.246
hist.bum	2.048	0.004	2.052
largestComp	11.777	0.020	11.800
largestScoreComp	13.336	0.036	13.379
loadNetwork.sif	0.024	0.000	0.025
makeNetwork	0.052	0.000	0.055
mapByVar	0.048	0.000	0.049
permutateNodes	14.909	0.016	14.928
piUpper	1.536	0.004	1.541
plot.bum	1.921	0.004	1.926
plot3dModule	4.344	0.000	4.348
plotLLSurface	1.672	0.008	1.680
plotModule	3.552	0.000	3.549
print.bum	1.680	0.000	1.684
pvaluesExample	0.040	0.000	0.041
readHeinzGraph	0.380	0.004	0.384
readHeinzTree	0.408	0.004	0.413
resamplingPvalues	7.061	0.108	7.172
rmSelfLoops	0.020	0.004	0.023
runFastHeinz	10.392	0.020	10.412
save3dModule	2.021	0.004	2.029
saveNetwork	1.448	0.012	1.459
scanFDR	1.344	0.000	1.344
scoreFunction	1.368	0.036	1.405
scoreNodes	3.544	0.008	3.555
scoreOffset	1.424	0.004	1.426
sortedEdgeList	4.796	0.008	4.803
subNetwork	0.140	0.004	0.146
summary.bum	1.769	0.012	1.779
writeHeinz	2.188	0.004	2.198
writeHeinzEdges	5.132	0.012	5.145
writeHeinzNodes	2.948	0.000	2.953