BioC 2.14: CHECK report for BioNet on petty

Package: BioNet

Version: 1.24.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BioNet_1.24.1.tar.gz

StartedAt: 2014-10-07 20:57:20 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:02:43 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 323.9 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BioNet_1.24.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/BioNet.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.24.1’
* 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 ... [16s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘graph’ ‘RBGL’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [140s/143s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
runFastHeinz      22.485  0.560  23.593
largestScoreComp  13.833  1.213  15.165
permutateNodes    13.563  1.249  14.877
resamplingPvalues 10.053  0.293  11.230
sortedEdgeList     7.390  0.047   7.512
writeHeinzEdges    5.815  0.261   6.088
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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	1.108	0.084	1.213
bumOptim	0.727	0.007	0.734
compareNetworks	2.369	0.037	2.424
consensusScores	0.604	0.016	0.623
fbum	0.001	0.000	0.001
fbumLL	0.826	0.008	0.835
fdrThreshold	1.023	0.006	1.029
fitBumModel	2.480	0.009	2.622
getCompScores	4.169	0.052	4.364
getEdgeList	1.407	0.015	1.432
hist.bum	1.070	0.018	1.093
largestComp	3.962	0.030	4.047
largestScoreComp	13.833	1.213	15.165
loadNetwork.sif	0.001	0.000	0.002
makeNetwork	0.02	0.00	0.02
mapByVar	0.001	0.000	0.002
permutateNodes	13.563	1.249	14.877
piUpper	0.896	0.003	0.912
plot.bum	2.726	0.019	2.772
plot3dModule	4.459	0.048	4.561
plotLLSurface	1.054	0.012	1.087
plotModule	4.186	0.029	4.513
print.bum	0.860	0.005	0.954
pvaluesExample	0.014	0.001	0.015
readHeinzGraph	0.573	0.007	0.625
readHeinzTree	0.618	0.009	0.683
resamplingPvalues	10.053	0.293	11.230
rmSelfLoops	0.011	0.001	0.013
runFastHeinz	22.485	0.560	23.593
save3dModule	2.659	0.018	2.721
saveNetwork	1.867	0.051	1.943
scanFDR	0.792	0.002	0.798
scoreFunction	0.936	0.072	1.012
scoreNodes	4.523	0.176	4.839
scoreOffset	0.768	0.003	0.771
sortedEdgeList	7.390	0.047	7.512
subNetwork	0.132	0.003	0.136
summary.bum	0.758	0.009	0.770
writeHeinz	2.898	0.210	3.118
writeHeinzEdges	5.815	0.261	6.088
writeHeinzNodes	3.365	0.023	3.454