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BioC 2.12: CHECK report for MCRestimate on petty

This page was generated on 2013-10-09 09:39:44 -0700 (Wed, 09 Oct 2013).

Package 396/671HostnameOS / ArchBUILDCHECKBUILD BIN
MCRestimate 2.16.0
Marc Johannes
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/MCRestimate
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: MCRestimate
Version: 2.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch MCRestimate_2.16.0.tar.gz
StartedAt: 2013-10-08 23:00:47 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 23:02:41 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 114.2 seconds
RetCode: 0
Status:  OK 
CheckDir: MCRestimate.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/MCRestimate.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'MCRestimate/DESCRIPTION' ... OK
* this is package 'MCRestimate' version '2.16.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'MCRestimate' can be installed ... [5s/5s] 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 ... NOTE
MCRestimate.default : my.balanced.folds: warning in
  get("balanced.folds", en = asNamespace("pamr")): partial argument
  match of 'en' to 'envir'
important.variable.names : <anonymous>: warning in median(x, na =
  TRUE): partial argument match of 'na' to 'na.rm'
important.variable.names : <anonymous>: warning in var(x, na = TRUE):
  partial argument match of 'na' to 'na.rm'
plot.MCRestimate: warning in layout(c(1, 2), height = c(5, 1)): partial
  argument match of 'height' to 'heights'
* checking Rd files ... NOTE
prepare_Rd: PLR.Rd:19: 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [44s/44s] OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
ClassifierBuild          10.621  0.178  10.901
wrapper.fkt               8.651  0.799   9.506
important.variable.names  8.492  0.772   9.454
* 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 were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/MCRestimate.Rcheck/00check.log'
for details.

MCRestimate.Rcheck/00install.out:

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

MCRestimate.Rcheck/MCRestimate-Ex.timings:

nameusersystemelapsed
ClassifierBuild10.621 0.17810.901
MCRconfusion2.6800.0672.754
MCRestimate3.3400.0873.467
PLR3.0710.1613.262
SVM.OVA.wrap0.0100.0090.018
class.factor.format0.1520.0200.180
geneReduction0.0080.0030.012
important.variable.names8.4920.7729.454
indVotes2.1650.0322.216
intersectList0.0060.0040.010
plot.MCRestimate0.0460.0090.056
wrapper.fkt8.6510.7999.506