Package: iterativeBMAsurv

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch iterativeBMAsurv_1.18.0.tar.gz

StartedAt: 2013-05-01 07:14:40 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 07:16:27 -0700 (Wed, 01 May 2013)

EllapsedTime: 107.6 seconds

RetCode: 0

Status:  OK

CheckDir: iterativeBMAsurv.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/iterativeBMAsurv.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'iterativeBMAsurv/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iterativeBMAsurv' version '1.18.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'iterativeBMAsurv' can be installed ... [2s/2s] OK
* checking installed package size ... OK
* 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 ... NOTE
prepare_Rd: predictBicSurv.Rd:46: Dropping empty section \note
prepare_Rd: predictiveAssessCategory.Rd:52: Dropping empty section \note
prepare_Rd: printTopGenes.Rd:49: Dropping empty section \note
prepare_Rd: singleGeneCoxph.Rd:54: Dropping empty section \note
prepare_Rd: testCens.Rd:13-14: Dropping empty section \details
prepare_Rd: testSurv.Rd:13-14: Dropping empty section \details
prepare_Rd: trainCens.Rd:13-14: Dropping empty section \details
prepare_Rd: trainSurv.Rd:13-14: Dropping empty section \details
* 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 ... [73s/77s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
imageplot.iterate.bma.surv   19.939  0.247  20.665
predictiveAssessCategory     11.215  0.185  11.746
predictBicSurv               10.806  0.150  11.956
iterateBMAsurv.train.wrapper 10.188  0.128  10.845
iterateBMAsurv.train         10.153  0.123  10.498
iterativeBMAsurv-package      3.605  0.079   5.070
* 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/iterativeBMAsurv.Rcheck/00check.log'
for details.

* installing *source* package 'iterativeBMAsurv' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (iterativeBMAsurv)

name	user	system	elapsed
crossVal	2.564	0.066	2.730
imageplot.iterate.bma.surv	19.939	0.247	20.665
iterateBMAsurv.train	10.153	0.123	10.498
iterateBMAsurv.train.predict.assess	1.063	0.028	1.121
iterateBMAsurv.train.wrapper	10.188	0.128	10.845
iterativeBMAsurv-package	3.605	0.079	5.070
predictBicSurv	10.806	0.150	11.956
predictiveAssessCategory	11.215	0.185	11.746
printTopGenes	0.541	0.009	0.561
singleGeneCoxph	0.521	0.010	0.553