Package: BioNet

Version: 1.17.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BioNet_1.17.1.tar.gz

StartedAt: 2013-03-25 01:25:41 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:30:24 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 282.9 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BioNet.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BioNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioNet' version '1.17.1'
* 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 ... [11s/11s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [147s/148s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
permutateNodes    12.637  2.111  14.828
runFastHeinz      12.853  1.567  14.523
largestScoreComp  10.633  1.964  12.659
largestComp        9.126  1.898  11.100
resamplingPvalues  8.365  0.181   8.553
writeHeinzEdges    6.998  1.059   8.079
sortedEdgeList     7.159  0.064   7.224
scoreNodes         4.942  1.122   6.122
plot3dModule       4.895  0.867   5.788
plotModule         4.152  0.881   5.084
* 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
  '/Users/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	0.952	0.080	1.040
bumOptim	1.200	0.338	1.538
compareNetworks	2.045	0.135	2.191
consensusScores	0.544	0.017	0.561
fbum	0.014	0.006	0.019
fbumLL	1.253	0.357	1.613
fdrThreshold	1.262	0.323	1.587
fitBumModel	1.751	0.337	2.105
getCompScores	3.115	0.183	3.303
getEdgeList	1.658	0.047	1.705
hist.bum	1.332	0.311	1.654
largestComp	9.126	1.898	11.100
largestScoreComp	10.633	1.964	12.659
loadNetwork.sif	0.027	0.007	0.034
makeNetwork	0.038	0.007	0.046
mapByVar	0.026	0.008	0.033
permutateNodes	12.637	2.111	14.828
piUpper	1.034	0.315	1.367
plot.bum	2.032	0.362	2.431
plot3dModule	4.895	0.867	5.788
plotLLSurface	0.863	0.184	1.053
plotModule	4.152	0.881	5.084
print.bum	1.094	0.314	1.418
pvaluesExample	0.029	0.007	0.037
readHeinzGraph	0.546	0.017	0.565
readHeinzTree	0.604	0.019	0.624
resamplingPvalues	8.365	0.181	8.553
rmSelfLoops	0.019	0.009	0.028
runFastHeinz	12.853	1.567	14.523
save3dModule	3.545	0.890	4.511
saveNetwork	2.174	0.120	2.305
scanFDR	1.079	0.410	1.505
scoreFunction	1.150	0.486	1.650
scoreNodes	4.942	1.122	6.122
scoreOffset	1.101	0.404	1.515
sortedEdgeList	7.159	0.064	7.224
subNetwork	0.089	0.021	0.110
summary.bum	1.047	0.368	1.422
writeHeinz	3.731	0.852	4.601
writeHeinzEdges	6.998	1.059	8.079
writeHeinzNodes	3.912	0.759	4.695