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BioC 3.0: CHECK report for iterativeBMAsurv on oaxaca

This page was generated on 2015-04-10 10:03:09 -0700 (Fri, 10 Apr 2015).

Package 471/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iterativeBMAsurv 1.24.0
Ka Yee Yeung
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/iterativeBMAsurv
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: iterativeBMAsurv
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch iterativeBMAsurv_1.24.0.tar.gz
StartedAt: 2015-04-10 00:45:09 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:46:34 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 85.0 seconds
RetCode: 0
Status:  OK 
CheckDir: iterativeBMAsurv.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch iterativeBMAsurv_1.24.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/iterativeBMAsurv.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘iterativeBMAsurv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iterativeBMAsurv’ version ‘1.24.0’
* 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 ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘survival’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘BMA’ ‘leaps’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
iterateBMAsurv.train: no visible global function definition for
  ‘bic.surv’
iterateBMAsurv.train.wrapper: no visible global function definition for
  ‘bic.surv’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [51s/52s] OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
imageplot.iterate.bma.surv   14.394  0.046  14.737
predictiveAssessCategory      7.671  0.042   8.055
predictBicSurv                7.279  0.027   7.451
iterateBMAsurv.train          7.186  0.036   7.332
iterateBMAsurv.train.wrapper  6.729  0.021   6.956
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/iterativeBMAsurv.Rcheck/00check.log’
for details.

iterativeBMAsurv.Rcheck/00install.out:

* 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)

iterativeBMAsurv.Rcheck/iterativeBMAsurv-Ex.timings:

nameusersystemelapsed
crossVal2.0270.0342.092
imageplot.iterate.bma.surv14.394 0.04614.737
iterateBMAsurv.train7.1860.0367.332
iterateBMAsurv.train.predict.assess0.9350.0130.974
iterateBMAsurv.train.wrapper6.7290.0216.956
iterativeBMAsurv-package2.7480.0352.789
predictBicSurv7.2790.0277.451
predictiveAssessCategory7.6710.0428.055
printTopGenes0.3930.0030.397
singleGeneCoxph0.3850.0020.389