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: 2011-02-24 15:12:19 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 15:14:41 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 142.3 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) (2011-01-10 r53950)
* 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 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 data for non-ASCII characters ... 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	0.740	0.046	0.854
bumOptim	0.787	0.005	0.791
compareNetworks	1.744	0.031	1.792
fbum	0.001	0.000	0.000
fbumLL	0.960	0.043	1.002
fdrThreshold	0.848	0.014	0.862
fitBumModel	1.308	0.050	1.358
getCompScores	2.785	0.023	2.821
getEdgeList	1.001	0.016	1.018
hist.bum	0.799	0.063	0.862
largestComp	8.672	0.946	9.619
largestScoreComp	10.547	1.045	11.592
loadNetwork.sif	0	0	0
makeNetwork	0.01	0.00	0.01
mapByVar	0	0	0
permutateNodes	10.855	1.132	11.988
piUpper	0.874	0.092	0.966
plot.bum	1.251	0.064	1.315
plot3dModule	3.284	0.100	3.385
plotLLSurface	0.815	0.048	0.863
plotModule	3.606	0.194	3.800
print.bum	1.082	0.042	1.124
pvaluesExample	0.012	0.001	0.012
readHeinzGraph	0.381	0.003	0.385
readHeinzTree	0.399	0.005	0.405
rmSelfLoops	0.008	0.001	0.009
runFastHeinz	9.154	0.088	9.242
save3dModule	2.527	0.119	2.646
saveNetwork	1.642	0.040	1.682
scanFDR	0.933	0.014	0.945
scoreFunction	0.958	0.110	1.067
scoreNodes	3.848	0.053	3.902
scoreOffset	0.875	0.057	0.933
subNetwork	0.043	0.001	0.045
summary.bum	0.885	0.048	0.933
writeHeinz	2.589	0.101	2.691
writeHeinzEdges	5.188	0.173	5.362
writeHeinzNodes	3.103	0.132	3.234