Package: iterativeBMAsurv

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch iterativeBMAsurv_1.16.0.tar.gz

StartedAt: 2013-03-25 00:09:52 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:11:10 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 78.8 seconds

RetCode: 0

Status:  OK

CheckDir: iterativeBMAsurv.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/iterativeBMAsurv.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 'iterativeBMAsurv/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iterativeBMAsurv' 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 'iterativeBMAsurv' can be installed ... OK
* checking installed package size ... 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 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 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
imageplot.iterate.bma.surv   15.627  0.101  15.806
predictiveAssessCategory      8.240  0.065   8.408
predictBicSurv                7.743  0.048   7.885
iterateBMAsurv.train          7.704  0.050   7.859
iterateBMAsurv.train.wrapper  7.496  0.038   7.664
* 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/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
   'iterativeBMAsurv.Rnw' 
** testing if installed package can be loaded

* DONE (iterativeBMAsurv)

name	user	system	elapsed
crossVal	2.123	0.055	2.208
imageplot.iterate.bma.surv	15.627	0.101	15.806
iterateBMAsurv.train	7.704	0.050	7.859
iterateBMAsurv.train.predict.assess	0.855	0.020	0.885
iterateBMAsurv.train.wrapper	7.496	0.038	7.664
iterativeBMAsurv-package	2.527	0.046	2.603
predictBicSurv	7.743	0.048	7.885
predictiveAssessCategory	8.240	0.065	8.408
printTopGenes	0.370	0.004	0.378
singleGeneCoxph	0.362	0.004	0.367