BioC 2.13: CHECK report for BioNet on perceval

Package: BioNet

Version: 1.23.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BioNet_1.23.2.tar.gz

StartedAt: 2014-04-04 23:47:51 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:52:10 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 258.5 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/BioNet.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.23.2’
* 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 ... [13s/13s] 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 ‘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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘Tutorial.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [124s/125s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
permutateNodes    16.603  1.640  18.275
largestScoreComp  11.531  1.555  13.090
runFastHeinz      12.352  0.538  12.899
resamplingPvalues  7.649  0.249   7.917
largestComp        6.131  0.073   6.206
writeHeinzEdges    5.885  0.109   6.000
* 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 were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.622	0.074	0.697
bumOptim	0.824	0.010	0.833
compareNetworks	3.029	0.062	3.094
consensusScores	0.474	0.007	0.482
fbum	0.013	0.010	0.024
fbumLL	0.722	0.006	0.729
fdrThreshold	1.018	0.007	1.025
fitBumModel	1.294	0.021	1.316
getCompScores	3.156	0.050	3.215
getEdgeList	1.445	0.031	1.477
hist.bum	1.235	0.014	1.250
largestComp	6.131	0.073	6.206
largestScoreComp	11.531	1.555	13.090
loadNetwork.sif	0.044	0.003	0.047
makeNetwork	0.066	0.003	0.069
mapByVar	0.053	0.005	0.058
permutateNodes	16.603	1.640	18.275
piUpper	1.266	0.025	1.292
plot.bum	1.620	0.009	1.644
plot3dModule	4.273	0.033	4.318
plotLLSurface	1.484	0.010	1.494
plotModule	3.547	0.047	3.595
print.bum	1.017	0.009	1.026
pvaluesExample	0.013	0.004	0.017
readHeinzGraph	0.374	0.012	0.386
readHeinzTree	0.395	0.012	0.408
resamplingPvalues	7.649	0.249	7.917
rmSelfLoops	0.008	0.004	0.013
runFastHeinz	12.352	0.538	12.899
save3dModule	2.044	0.048	2.095
saveNetwork	1.558	0.086	1.648
scanFDR	1.106	0.078	1.184
scoreFunction	1.235	0.151	1.386
scoreNodes	4.102	0.095	4.200
scoreOffset	0.973	0.174	1.148
sortedEdgeList	4.777	0.066	4.847
subNetwork	0.178	0.014	0.192
summary.bum	0.926	0.020	0.946
writeHeinz	2.268	0.050	2.322
writeHeinzEdges	5.885	0.109	6.000
writeHeinzNodes	3.130	0.379	3.511