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BioC 3.5: CHECK report for iterativeBMAsurv on oaxaca

This page was generated on 2017-03-04 16:36:37 -0500 (Sat, 04 Mar 2017).

Package 667/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
iterativeBMAsurv 1.33.0
Ka Yee Yeung
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/iterativeBMAsurv
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: iterativeBMAsurv
Version: 1.33.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings iterativeBMAsurv_1.33.0.tar.gz
StartedAt: 2017-03-04 04:46:55 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 04:48:56 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 120.8 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 iterativeBMAsurv_1.33.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/iterativeBMAsurv.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.33.0’
* 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 ... 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’
Undefined global functions or variables:
  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 ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
imageplot.iterate.bma.surv   12.240  0.087  12.329
predictiveAssessCategory      5.638  0.064   5.702
iterateBMAsurv.train          5.185  0.054   5.240
iterateBMAsurv.train.wrapper  4.965  0.041   5.007
* 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

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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
crossVal2.5500.0512.602
imageplot.iterate.bma.surv12.240 0.08712.329
iterateBMAsurv.train5.1850.0545.240
iterateBMAsurv.train.predict.assess0.7930.0200.836
iterateBMAsurv.train.wrapper4.9650.0415.007
iterativeBMAsurv-package2.3270.0432.370
predictBicSurv4.5770.0364.612
predictiveAssessCategory5.6380.0645.702
printTopGenes0.2630.0030.267
singleGeneCoxph0.5360.0060.543