BioC 2.12: CHECK report for BioNet on george2

Package: BioNet

Version: 1.18.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings BioNet_1.18.0.tar.gz

StartedAt: 2013-10-09 00:28:09 -0700 (Wed, 09 Oct 2013)

EndedAt: 2013-10-09 00:33:42 -0700 (Wed, 09 Oct 2013)

EllapsedTime: 333.1 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 3.0.1 (2013-05-16)
* 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 ‘1.18.0’
* 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 ... [156s/159s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
permutateNodes    22.689  0.052  23.413
largestScoreComp  16.425  0.056  16.881
runFastHeinz      13.773  0.048  13.990
resamplingPvalues  9.545  0.096  10.188
largestComp        6.873  0.032   6.905
writeHeinzEdges    6.773  0.004   6.775
sortedEdgeList     6.356  0.004   6.518
plot3dModule       6.081  0.072   6.156
* 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
** testing if installed package can be loaded
* DONE (BioNet)

name	user	system	elapsed
aggrPvals	0.696	0.048	0.743
bumOptim	1.412	0.016	1.472
compareNetworks	3.572	0.112	3.951
consensusScores	0.476	0.004	0.479
fbum	0.028	0.000	0.027
fbumLL	1.536	0.004	1.540
fdrThreshold	1.713	0.000	1.713
fitBumModel	1.548	0.028	1.574
getCompScores	3.552	0.032	3.620
getEdgeList	2.376	0.008	2.514
hist.bum	2.656	0.016	2.674
largestComp	6.873	0.032	6.905
largestScoreComp	16.425	0.056	16.881
loadNetwork.sif	0.068	0.000	0.070
makeNetwork	0.088	0.000	0.091
mapByVar	0.040	0.000	0.039
permutateNodes	22.689	0.052	23.413
piUpper	1.580	0.012	1.593
plot.bum	2.448	0.004	2.459
plot3dModule	6.081	0.072	6.156
plotLLSurface	2.300	0.012	2.649
plotModule	4.808	0.000	4.811
print.bum	2.132	0.000	2.132
pvaluesExample	0.060	0.004	0.066
readHeinzGraph	0.560	0.008	0.565
readHeinzTree	1.308	0.000	1.312
resamplingPvalues	9.545	0.096	10.188
rmSelfLoops	0.008	0.008	0.016
runFastHeinz	13.773	0.048	13.990
save3dModule	3.212	0.008	3.585
saveNetwork	1.772	0.008	1.785
scanFDR	1.212	0.000	1.214
scoreFunction	1.244	0.056	1.299
scoreNodes	3.969	0.016	3.984
scoreOffset	1.488	0.000	1.489
sortedEdgeList	6.356	0.004	6.518
subNetwork	0.240	0.004	0.249
summary.bum	1.736	0.000	1.920
writeHeinz	3.496	0.004	3.555
writeHeinzEdges	6.773	0.004	6.775
writeHeinzNodes	3.764	0.000	3.766