BioC 2.12: CHECK report for BioNet on george2

Package: BioNet

Version: 1.17.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings BioNet_1.17.1.tar.gz

StartedAt: 2013-03-25 00:21:07 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:26:52 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 344.1 seconds

RetCode: 0

Status: OK

CheckDir: BioNet.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/BioNet.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘1.17.1’
* 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 ... [17s/17s] OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  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 installed files from ‘inst/doc’ ... OK
* checking examples ... [168s/175s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
permutateNodes    21.245  0.096  22.249
largestScoreComp  16.349  0.032  16.692
largestComp       13.925  0.024  14.262
runFastHeinz      13.429  0.024  13.637
resamplingPvalues  9.560  0.164  10.781
writeHeinzEdges    9.053  0.016   9.621
plotModule         6.461  0.000   6.944
sortedEdgeList     6.345  0.036   7.361
scoreNodes         5.392  0.036   5.605
plot3dModule       5.364  0.008   5.414
writeHeinzNodes    5.292  0.004   5.589
* 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
  ‘/home/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
   ‘Tutorial.Rnw’ 
** testing if installed package can be loaded
* DONE (BioNet)

name	user	system	elapsed
aggrPvals	0.724	0.060	0.784
bumOptim	1.868	0.004	1.874
compareNetworks	3.436	0.060	3.836
consensusScores	0.964	0.004	1.033
fbum	0.024	0.000	0.027
fbumLL	1.901	0.032	2.126
fdrThreshold	1.000	0.004	1.003
fitBumModel	1.756	0.028	1.787
getCompScores	4.172	0.052	4.244
getEdgeList	2.220	0.020	2.305
hist.bum	2.040	0.000	2.038
largestComp	13.925	0.024	14.262
largestScoreComp	16.349	0.032	16.692
loadNetwork.sif	0.060	0.000	0.062
makeNetwork	0.084	0.000	0.085
mapByVar	0.048	0.000	0.047
permutateNodes	21.245	0.096	22.249
piUpper	1.805	0.008	1.910
plot.bum	2.428	0.000	2.431
plot3dModule	5.364	0.008	5.414
plotLLSurface	1.584	0.008	1.594
plotModule	6.461	0.000	6.944
print.bum	1.036	0.004	1.041
pvaluesExample	0.016	0.000	0.015
readHeinzGraph	0.428	0.008	0.439
readHeinzTree	0.360	0.000	0.361
resamplingPvalues	9.560	0.164	10.781
rmSelfLoops	0.012	0.004	0.017
runFastHeinz	13.429	0.024	13.637
save3dModule	3.188	0.016	3.466
saveNetwork	2.241	0.016	2.578
scanFDR	1.760	0.004	1.997
scoreFunction	1.084	0.036	1.335
scoreNodes	5.392	0.036	5.605
scoreOffset	1.324	0.000	1.326
sortedEdgeList	6.345	0.036	7.361
subNetwork	0.124	0.008	0.132
summary.bum	1.828	0.004	1.832
writeHeinz	4.920	0.004	4.944
writeHeinzEdges	9.053	0.016	9.621
writeHeinzNodes	5.292	0.004	5.589

Summary

Command output