Package: BioNet

Version: 1.8.0

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings BioNet_1.8.0.tar.gz

StartedAt: 2011-03-31 04:43:38 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 04:46:09 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 150.7 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/BioNet.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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 ‘1.8.0’
* 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
  'openVignette()'. 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	0.700	0.044	1.275
bumOptim	1.084	0.008	1.094
compareNetworks	2.312	0.032	2.384
fbum	0	0	0
fbumLL	1.292	0.000	1.294
fdrThreshold	0.960	0.000	0.961
fitBumModel	1.460	0.000	1.461
getCompScores	2.880	0.024	2.924
getEdgeList	1.116	0.008	1.123
hist.bum	1.180	0.000	1.178
largestComp	10.017	0.004	10.020
largestScoreComp	10.945	0.604	11.844
loadNetwork.sif	0.000	0.000	0.001
makeNetwork	0.008	0.000	0.010
mapByVar	0	0	0
permutateNodes	13.625	0.036	13.677
piUpper	1.148	0.020	1.166
plot.bum	1.720	0.008	1.732
plot3dModule	3.396	0.016	3.416
plotLLSurface	1.388	0.000	1.387
plotModule	3.648	0.000	3.650
print.bum	1.292	0.004	1.295
pvaluesExample	0.008	0.000	0.009
readHeinzGraph	0.268	0.004	0.270
readHeinzTree	0.272	0.000	0.271
rmSelfLoops	0.008	0.000	0.008
runFastHeinz	9.493	0.008	9.499
save3dModule	2.336	0.004	2.343
saveNetwork	1.992	0.012	2.005
scanFDR	1.156	0.000	1.156
scoreFunction	1.040	0.044	1.083
scoreNodes	3.937	0.012	3.948
scoreOffset	1.596	0.000	1.595
subNetwork	0.040	0.000	0.041
summary.bum	1.592	0.000	1.593
writeHeinz	2.460	0.004	2.466
writeHeinzEdges	7.052	0.004	7.055
writeHeinzNodes	2.697	0.004	2.705