Package: BioNet

Version: 1.16.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings BioNet_1.16.0.tar.gz

StartedAt: 2013-03-24 23:40:30 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:44:30 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 239.7 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/BioNet.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘1.16.0’
* 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  5.4Mb
  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 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    14.921  0.032  15.092
largestScoreComp  12.244  0.024  12.524
largestComp       11.593  0.004  11.602
runFastHeinz      10.360  0.028  10.519
resamplingPvalues  6.245  0.080   6.466
writeHeinzEdges    5.801  0.016   5.939
* 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-2.11-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	0.740	0.032	0.788
bumOptim	1.380	0.012	1.391
compareNetworks	2.556	0.048	2.779
consensusScores	0.312	0.008	0.349
fbum	0	0	0
fbumLL	1.832	0.004	2.163
fdrThreshold	1.068	0.000	1.134
fitBumModel	1.528	0.012	1.656
getCompScores	2.945	0.024	3.151
getEdgeList	1.196	0.012	1.252
hist.bum	2.180	0.012	2.330
largestComp	11.593	0.004	11.602
largestScoreComp	12.244	0.024	12.524
loadNetwork.sif	0	0	0
makeNetwork	0.016	0.000	0.014
mapByVar	0	0	0
permutateNodes	14.921	0.032	15.092
piUpper	1.448	0.008	1.458
plot.bum	1.844	0.000	1.870
plot3dModule	4.153	0.008	4.889
plotLLSurface	1.560	0.008	1.587
plotModule	3.636	0.004	3.653
print.bum	1.500	0.012	1.551
pvaluesExample	0.004	0.004	0.022
readHeinzGraph	0.296	0.004	0.303
readHeinzTree	0.276	0.004	0.291
resamplingPvalues	6.245	0.080	6.466
rmSelfLoops	0.008	0.000	0.007
runFastHeinz	10.360	0.028	10.519
save3dModule	2.264	0.004	2.287
saveNetwork	1.464	0.008	1.495
scanFDR	1.613	0.000	1.639
scoreFunction	1.460	0.032	1.491
scoreNodes	4.016	0.020	4.043
scoreOffset	1.216	0.004	1.250
sortedEdgeList	3.824	0.012	3.866
subNetwork	0.028	0.004	0.065
summary.bum	1.344	0.000	1.369
writeHeinz	2.564	0.008	2.597
writeHeinzEdges	5.801	0.016	5.939
writeHeinzNodes	2.896	0.004	3.034