Package: BioNet

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BioNet_1.9.0.tar.gz

StartedAt: 2011-03-17 15:45:57 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 15:48:38 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 160.8 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/BioNet.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BioNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioNet' version '1.9.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'BioNet' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'BioNet' ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (BioNet)

name	user	system	elapsed
aggrPvals	0.759	0.049	0.807
bumOptim	0.814	0.003	0.817
compareNetworks	1.794	0.028	1.842
fbum	0.000	0.000	0.001
fbumLL	0.963	0.008	0.970
fdrThreshold	0.724	0.006	0.730
fitBumModel	1.311	0.003	1.314
getCompScores	2.617	0.061	2.684
getEdgeList	1.009	0.013	1.022
hist.bum	0.909	0.052	0.961
largestComp	11.109	0.896	12.006
largestScoreComp	12.063	1.059	13.123
loadNetwork.sif	0	0	0
makeNetwork	0.010	0.000	0.011
mapByVar	0	0	0
permutateNodes	13.687	1.073	14.759
piUpper	0.870	0.017	0.887
plot.bum	1.343	0.064	1.407
plot3dModule	3.549	0.010	3.559
plotLLSurface	0.854	0.074	0.927
plotModule	3.549	0.125	3.674
print.bum	1.035	0.001	1.037
pvaluesExample	0.013	0.001	0.013
readHeinzGraph	0.396	0.003	0.399
readHeinzTree	0.419	0.004	0.422
rmSelfLoops	0.01	0.00	0.01
runFastHeinz	10.412	0.117	10.530
save3dModule	2.569	0.093	2.661
saveNetwork	1.626	0.048	1.674
scanFDR	0.763	0.047	0.811
scoreFunction	0.849	0.094	0.943
scoreNodes	4.318	0.026	4.345
scoreOffset	1.199	0.006	1.206
subNetwork	0.044	0.002	0.046
summary.bum	0.898	0.034	0.932
writeHeinz	3.437	0.005	3.443
writeHeinzEdges	6.269	0.031	6.301
writeHeinzNodes	2.920	0.123	3.043