BioC 2.13: CHECK report for BioNet on zin1

Package: BioNet

Version: 1.23.2

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings BioNet_1.23.2.tar.gz

StartedAt: 2014-04-04 23:52:21 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:54:50 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 149.2 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/BioNet.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.23.2’
* 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 ... [8s/8s] 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 ‘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 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 ... [70s/71s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
runFastHeinz     9.213  0.016   9.269
permutateNodes   7.716  0.020   7.811
largestScoreComp 6.597  0.016   6.628
* 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
  ‘/home/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	0.460	0.028	0.490
bumOptim	0.648	0.000	0.648
compareNetworks	1.492	0.016	1.545
consensusScores	0.292	0.000	0.293
fbum	0.004	0.000	0.002
fbumLL	0.684	0.000	0.689
fdrThreshold	0.580	0.000	0.579
fitBumModel	0.992	0.000	0.995
getCompScores	1.736	0.008	1.749
getEdgeList	0.880	0.008	0.889
hist.bum	0.876	0.000	0.881
largestComp	2.664	0.004	2.672
largestScoreComp	6.597	0.016	6.628
loadNetwork.sif	0.016	0.000	0.017
makeNetwork	0.020	0.000	0.021
mapByVar	0.008	0.000	0.009
permutateNodes	7.716	0.020	7.811
piUpper	0.768	0.004	0.772
plot.bum	1.128	0.004	1.134
plot3dModule	2.261	0.012	2.276
plotLLSurface	0.664	0.004	0.670
plotModule	2.212	0.004	2.220
print.bum	0.756	0.000	0.759
pvaluesExample	0.008	0.000	0.007
readHeinzGraph	0.288	0.000	0.306
readHeinzTree	0.304	0.000	0.306
resamplingPvalues	4.736	0.056	4.809
rmSelfLoops	0.008	0.000	0.010
runFastHeinz	9.213	0.016	9.269
save3dModule	1.368	0.004	1.376
saveNetwork	1.000	0.008	1.028
scanFDR	0.920	0.004	0.930
scoreFunction	0.664	0.036	0.704
scoreNodes	2.088	0.012	2.106
scoreOffset	0.668	0.000	0.667
sortedEdgeList	3.508	0.004	3.550
subNetwork	0.060	0.000	0.059
summary.bum	0.784	0.000	0.787
writeHeinz	1.589	0.000	1.593
writeHeinzEdges	3.240	0.000	3.247
writeHeinzNodes	2.004	0.004	2.012