BioC 2.14: CHECK report for BioNet on morelia

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 21:29:57 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 21:32:55 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 178.2 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-darwin13.1.0 (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 ... [10s/10s] 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’ ‘RBGL’ ‘graph’
  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 ... [77s/77s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
runFastHeinz      12.281  0.241  12.531
largestScoreComp   8.549  0.655   9.211
permutateNodes     8.206  0.640   8.851
resamplingPvalues  5.478  0.138   5.619
* 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	0.585	0.047	0.636
bumOptim	0.329	0.010	0.340
compareNetworks	1.463	0.026	1.508
consensusScores	0.320	0.012	0.332
fbum	0.001	0.000	0.000
fbumLL	0.340	0.008	0.347
fdrThreshold	0.340	0.000	0.341
fitBumModel	1.422	0.010	1.434
getCompScores	2.207	0.028	2.252
getEdgeList	0.849	0.010	0.860
hist.bum	0.470	0.009	0.480
largestComp	1.966	0.028	1.994
largestScoreComp	8.549	0.655	9.211
loadNetwork.sif	0.001	0.001	0.001
makeNetwork	0.013	0.000	0.013
mapByVar	0.001	0.000	0.001
permutateNodes	8.206	0.640	8.851
piUpper	0.506	0.012	0.519
plot.bum	1.226	0.026	1.253
plot3dModule	2.501	0.061	2.565
plotLLSurface	0.333	0.008	0.342
plotModule	2.573	0.053	2.628
print.bum	0.365	0.002	0.368
pvaluesExample	0.009	0.001	0.010
readHeinzGraph	0.345	0.002	0.347
readHeinzTree	0.328	0.003	0.332
resamplingPvalues	5.478	0.138	5.619
rmSelfLoops	0.007	0.000	0.008
runFastHeinz	12.281	0.241	12.531
save3dModule	1.593	0.096	1.692
saveNetwork	1.201	0.044	1.246
scanFDR	0.333	0.010	0.343
scoreFunction	0.388	0.048	0.439
scoreNodes	2.278	0.148	2.428
scoreOffset	0.328	0.006	0.334
sortedEdgeList	3.745	0.022	3.769
subNetwork	0.060	0.001	0.061
summary.bum	0.337	0.013	0.351
writeHeinz	1.313	0.145	1.458
writeHeinzEdges	3.570	0.165	3.739
writeHeinzNodes	1.906	0.099	2.007