Package: BioNet

Version: 1.17.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BioNet_1.17.1.tar.gz

StartedAt: 2013-03-24 02:52:16 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 02:57:24 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 307.4 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BioNet.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BioNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BioNet' version '1.17.1'
* 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 ... [15s/17s] OK
* checking installed package size ... NOTE
  installed size is  5.4Mb
  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 ... [148s/149s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
permutateNodes    15.942  1.869  17.870
largestScoreComp  13.838  1.811  15.719
largestComp       12.842  1.425  14.313
runFastHeinz      12.085  0.406  12.528
resamplingPvalues  8.520  0.329   8.876
writeHeinzEdges    7.053  0.413   7.492
sortedEdgeList     5.454  0.073   5.560
plot3dModule       5.334  0.179   5.529
* 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
  '/Users/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
   'Tutorial.Rnw' 
** testing if installed package can be loaded
* DONE (BioNet)

name	user	system	elapsed
aggrPvals	0.719	0.084	0.808
bumOptim	1.551	0.025	1.583
compareNetworks	2.564	0.071	2.751
consensusScores	0.938	0.012	0.955
fbum	0.016	0.003	0.020
fbumLL	1.309	0.070	1.385
fdrThreshold	0.998	0.069	1.072
fitBumModel	1.605	0.115	1.730
getCompScores	3.646	0.074	3.744
getEdgeList	1.903	0.039	1.953
hist.bum	1.303	0.076	1.385
largestComp	12.842	1.425	14.313
largestScoreComp	13.838	1.811	15.719
loadNetwork.sif	0.049	0.005	0.053
makeNetwork	0.064	0.003	0.068
mapByVar	0.048	0.005	0.052
permutateNodes	15.942	1.869	17.870
piUpper	1.651	0.062	1.719
plot.bum	2.093	0.122	2.223
plot3dModule	5.334	0.179	5.529
plotLLSurface	1.211	0.043	1.260
plotModule	4.532	0.137	4.676
print.bum	1.480	0.010	1.495
pvaluesExample	0.041	0.004	0.045
readHeinzGraph	1.030	0.014	1.043
readHeinzTree	0.491	0.014	0.506
resamplingPvalues	8.520	0.329	8.876
rmSelfLoops	0.020	0.007	0.027
runFastHeinz	12.085	0.406	12.528
save3dModule	2.735	0.144	2.886
saveNetwork	1.885	0.095	1.982
scanFDR	1.253	0.139	1.398
scoreFunction	1.249	0.143	1.398
scoreNodes	4.162	0.233	4.432
scoreOffset	1.512	0.156	1.679
sortedEdgeList	5.454	0.073	5.560
subNetwork	0.137	0.015	0.152
summary.bum	1.256	0.023	1.285
writeHeinz	3.183	0.255	3.454
writeHeinzEdges	7.053	0.413	7.492
writeHeinzNodes	3.920	0.223	4.153