Package: BioNet

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BioNet_1.18.0.tar.gz

StartedAt: 2013-05-01 02:54:34 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 02:59:33 -0700 (Wed, 01 May 2013)

EllapsedTime: 299.5 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BioNet.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BioNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioNet' version '1.18.0'
* 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 ... [14s/15s] 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 ... [148s/150s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
permutateNodes    15.336  2.102  17.670
largestScoreComp  15.170  1.670  17.092
largestComp       13.458  1.326  14.885
runFastHeinz      12.097  0.636  12.863
resamplingPvalues  8.344  0.351   8.810
writeHeinzEdges    6.724  0.360   7.164
sortedEdgeList     5.444  0.091   5.596
plot3dModule       5.039  0.200   5.305
plotModule         4.709  0.314   5.068
* 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
** testing if installed package can be loaded
* DONE (BioNet)

name	user	system	elapsed
aggrPvals	0.684	0.085	0.784
bumOptim	1.524	0.015	1.554
compareNetworks	2.588	0.090	2.758
consensusScores	0.875	0.008	0.885
fbum	0.016	0.004	0.020
fbumLL	1.308	0.025	1.353
fdrThreshold	1.318	0.105	1.453
fitBumModel	1.562	0.111	1.693
getCompScores	3.327	0.068	3.496
getEdgeList	1.875	0.033	1.941
hist.bum	1.371	0.078	1.473
largestComp	13.458	1.326	14.885
largestScoreComp	15.170	1.670	17.092
loadNetwork.sif	0.087	0.007	0.096
makeNetwork	0.044	0.004	0.048
mapByVar	0.047	0.006	0.054
permutateNodes	15.336	2.102	17.670
piUpper	1.550	0.093	1.664
plot.bum	2.087	0.119	2.224
plot3dModule	5.039	0.200	5.305
plotLLSurface	1.107	0.077	1.208
plotModule	4.709	0.314	5.068
print.bum	1.933	0.093	2.059
pvaluesExample	0.012	0.006	0.018
readHeinzGraph	0.517	0.014	0.540
readHeinzTree	0.496	0.013	0.517
resamplingPvalues	8.344	0.351	8.810
rmSelfLoops	0.120	0.062	0.184
runFastHeinz	12.097	0.636	12.863
save3dModule	2.769	0.222	3.010
saveNetwork	1.911	0.093	2.029
scanFDR	1.268	0.102	1.384
scoreFunction	1.329	0.192	1.527
scoreNodes	4.168	0.202	4.469
scoreOffset	1.176	0.158	1.355
sortedEdgeList	5.444	0.091	5.596
subNetwork	0.114	0.016	0.131
summary.bum	1.251	0.026	1.285
writeHeinz	2.930	0.108	3.086
writeHeinzEdges	6.724	0.360	7.164
writeHeinzNodes	3.374	0.241	3.660