BioC 2.12: CHECK report for BioNet on petty

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: 2013-10-08 21:44:44 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 21:50:05 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 320.5 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 3.0.1 (2013-05-16)
* 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 ... [16s/16s] 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 ... [148s/152s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
permutateNodes    17.968  1.450  20.185
largestScoreComp  14.847  1.361  16.588
runFastHeinz      13.336  0.631  14.036
resamplingPvalues  9.903  0.349  10.298
sortedEdgeList     6.869  0.066   6.990
writeHeinzEdges    6.409  0.416   6.880
largestComp        5.903  0.065   6.238
plot3dModule       4.781  0.171   5.077
* 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	0.948	0.079	1.099
bumOptim	1.415	0.079	1.618
compareNetworks	2.430	0.036	2.691
consensusScores	0.950	0.012	1.020
fbum	0.015	0.002	0.019
fbumLL	1.332	0.043	1.486
fdrThreshold	1.235	0.032	1.347
fitBumModel	1.756	0.042	1.960
getCompScores	4.265	0.079	4.725
getEdgeList	1.975	0.037	2.200
hist.bum	1.547	0.061	1.685
largestComp	5.903	0.065	6.238
largestScoreComp	14.847	1.361	16.588
loadNetwork.sif	0.039	0.003	0.042
makeNetwork	0.060	0.003	0.063
mapByVar	0.021	0.003	0.025
permutateNodes	17.968	1.450	20.185
piUpper	1.191	0.087	1.326
plot.bum	1.982	0.084	2.171
plot3dModule	4.781	0.171	5.077
plotLLSurface	1.421	0.031	1.564
plotModule	4.398	0.213	4.777
print.bum	1.153	0.073	1.238
pvaluesExample	0.014	0.005	0.020
readHeinzGraph	0.522	0.011	0.534
readHeinzTree	0.590	0.012	0.611
resamplingPvalues	9.903	0.349	10.298
rmSelfLoops	0.030	0.015	0.045
runFastHeinz	13.336	0.631	14.036
save3dModule	2.737	0.293	3.046
saveNetwork	2.135	0.076	2.223
scanFDR	1.262	0.132	1.397
scoreFunction	1.753	0.185	1.941
scoreNodes	4.031	0.476	4.569
scoreOffset	1.048	0.141	1.202
sortedEdgeList	6.869	0.066	6.990
subNetwork	0.121	0.019	0.140
summary.bum	1.333	0.150	1.499
writeHeinz	3.924	0.230	4.220
writeHeinzEdges	6.409	0.416	6.880
writeHeinzNodes	4.121	0.272	4.414