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BioC 2.14: CHECK report for dyebias on petty

This page was generated on 2014-10-08 08:58:38 -0700 (Wed, 08 Oct 2014).

Package 241/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dyebias 1.22.0
Philip Lijnzaad
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/dyebias
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: dyebias
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch dyebias_1.22.0.tar.gz
StartedAt: 2014-10-07 21:45:40 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:47:52 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 132.3 seconds
RetCode: 0
Status:  OK 
CheckDir: dyebias.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch dyebias_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/dyebias.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dyebias/DESCRIPTION’ ... OK
* this is package ‘dyebias’ version ‘1.22.0’
* 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 ‘dyebias’ can be installed ... [8s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘marray’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
dyebias.apply.correction: no visible global function definition for
  ‘maR<-’
dyebias.apply.correction: no visible global function definition for
  ‘maG<-’
* checking Rd files ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... [51s/52s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
dyebias.rgplot             10.177  0.097  10.380
dyebias.trendplot           8.533  0.067   8.660
dyebias.boxplot             8.384  0.055   8.536
dyebias.application.subset  8.000  0.140   8.316
dyebias.apply.correction    7.287  0.067   7.439
* 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/dyebias.Rcheck/00check.log’
for details.

dyebias.Rcheck/00install.out:

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

dyebias.Rcheck/dyebias-Ex.timings:

nameusersystemelapsed
dyebias.application.subset8.0000.1408.316
dyebias.apply.correction7.2870.0677.439
dyebias.boxplot8.3840.0558.536
dyebias.estimate.iGSDBs4.5660.0354.701
dyebias.monotonicity0.0030.0010.003
dyebias.monotonicityplot0.0030.0000.004
dyebias.rgplot10.177 0.09710.380
dyebias.trendplot8.5330.0678.660