Package: BioNet

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BioNet_1.16.0.tar.gz

StartedAt: 2013-03-24 22:44:40 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 22:48:55 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 254.7 seconds

RetCode: 0

Status:  OK

CheckDir: BioNet.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/BioNet.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.16.0'
* 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 whether package 'BioNet' can be installed ... 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 for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
permutateNodes    14.337  2.626  17.287
largestScoreComp  12.606  2.760  15.728
largestComp       11.151  2.501  13.980
runFastHeinz       9.841  1.515  11.685
resamplingPvalues  6.599  0.213   6.925
writeHeinzEdges    4.890  1.037   6.009
plotModule         4.804  0.896   5.757
* 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-2.11-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	0.710	0.061	0.774
bumOptim	0.912	0.382	1.413
compareNetworks	2.111	0.139	2.362
consensusScores	0.402	0.008	0.425
fbum	0	0	0
fbumLL	0.956	0.296	1.272
fdrThreshold	1.062	0.358	1.454
fitBumModel	1.422	0.398	1.847
getCompScores	2.715	0.200	2.956
getEdgeList	1.344	0.041	1.389
hist.bum	1.002	0.386	1.453
largestComp	11.151	2.501	13.980
largestScoreComp	12.606	2.760	15.728
loadNetwork.sif	0.000	0.001	0.000
makeNetwork	0.013	0.000	0.014
mapByVar	0	0	0
permutateNodes	14.337	2.626	17.287
piUpper	0.949	0.350	1.341
plot.bum	1.184	0.338	1.568
plot3dModule	3.833	0.869	4.806
plotLLSurface	1.001	0.207	1.226
plotModule	4.804	0.896	5.757
print.bum	1.185	0.353	1.611
pvaluesExample	0.011	0.001	0.012
readHeinzGraph	0.393	0.008	0.410
readHeinzTree	0.421	0.013	0.444
resamplingPvalues	6.599	0.213	6.925
rmSelfLoops	0.008	0.000	0.009
runFastHeinz	9.841	1.515	11.685
save3dModule	2.795	0.837	3.834
saveNetwork	1.322	0.086	1.421
scanFDR	1.095	0.374	1.574
scoreFunction	0.872	0.416	1.367
scoreNodes	3.443	0.980	4.676
scoreOffset	0.829	0.347	1.210
sortedEdgeList	4.835	0.062	4.934
subNetwork	0.039	0.005	0.056
summary.bum	1.384	0.398	1.860
writeHeinz	2.470	0.842	3.420
writeHeinzEdges	4.890	1.037	6.009
writeHeinzNodes	3.440	0.704	4.175