BioC 2.14: CHECK report for BioNet on zin2

Package: BioNet

Version: 1.24.1

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings BioNet_1.24.1.tar.gz

StartedAt: 2014-10-07 22:06:28 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:08:51 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 143.0 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings BioNet_1.24.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/BioNet.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (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 ... [8s/8s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [65s/65s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
runFastHeinz     10.393  0.012  10.499
permutateNodes    6.160  0.004   6.179
largestScoreComp  6.061  0.012   6.080
* 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
  ‘/home/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	0.588	0.044	0.633
bumOptim	0.584	0.008	0.593
compareNetworks	1.148	0.012	1.186
consensusScores	0.244	0.000	0.244
fbum	0.000	0.000	0.001
fbumLL	0.544	0.008	0.599
fdrThreshold	0.548	0.004	0.553
fitBumModel	1.460	0.000	1.464
getCompScores	1.584	0.016	1.600
getEdgeList	0.652	0.008	0.661
hist.bum	0.728	0.000	0.760
largestComp	1.660	0.008	1.671
largestScoreComp	6.061	0.012	6.080
loadNetwork.sif	0.004	0.000	0.001
makeNetwork	0.008	0.000	0.009
mapByVar	0.000	0.000	0.001
permutateNodes	6.160	0.004	6.179
piUpper	0.556	0.000	0.558
plot.bum	1.404	0.000	1.405
plot3dModule	2.072	0.008	2.113
plotLLSurface	0.576	0.004	0.584
plotModule	2.317	0.004	2.364
print.bum	0.600	0.000	0.626
pvaluesExample	0.008	0.000	0.007
readHeinzGraph	0.264	0.000	0.265
readHeinzTree	0.236	0.000	0.236
resamplingPvalues	4.732	0.044	4.786
rmSelfLoops	0.004	0.000	0.006
runFastHeinz	10.393	0.012	10.499
save3dModule	1.240	0.004	1.248
saveNetwork	0.832	0.000	0.833
scanFDR	0.552	0.000	0.552
scoreFunction	0.616	0.016	0.631
scoreNodes	2.180	0.012	2.198
scoreOffset	0.576	0.000	0.616
sortedEdgeList	3.536	0.000	3.541
subNetwork	0.028	0.004	0.029
summary.bum	0.524	0.000	0.523
writeHeinz	1.344	0.000	1.346
writeHeinzEdges	2.704	0.012	2.723
writeHeinzNodes	1.777	0.008	1.787