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BioC 3.2: CHECK report for affyContam on oaxaca

This page was generated on 2015-10-27 17:38:50 -0400 (Tue, 27 Oct 2015).

Package 19/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyContam 1.28.0
V. Carey
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/affyContam
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: affyContam
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings affyContam_1.28.0.tar.gz
StartedAt: 2015-10-27 01:09:40 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 01:10:39 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 59.0 seconds
RetCode: 0
Status:  OK 
CheckDir: affyContam.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings affyContam_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/affyContam.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyContam/DESCRIPTION’ ... OK
* this is package ‘affyContam’ version ‘1.28.0’
* 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 ‘affyContam’ can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’ ‘affydata’
  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
getCircRegion: no visible global function definition for ‘annotation’
getCircRegion : <anonymous>: no visible global function definition for
  ‘xy2indices’
getCircRegion: no visible global function definition for ‘exprs’
getRectRegion: no visible global function definition for ‘annotation’
getRectRegion : <anonymous>: no visible global function definition for
  ‘xy2indices’
getRectRegion: no visible global function definition for ‘exprs’
setCircRegion: no visible global function definition for ‘annotation’
setCircRegion : <anonymous>: no visible global function definition for
  ‘xy2indices’
setCircRegion: no visible global function definition for ‘exprs’
setCircRegion: no visible global function definition for ‘exprs<-’
setRectRegion: no visible global function definition for ‘annotation’
setRectRegion : <anonymous>: no visible global function definition for
  ‘xy2indices’
setRectRegion: no visible global function definition for ‘exprs’
setRectRegion: no visible global function definition for ‘exprs<-’
* 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 ... [22s/29s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
setRectRegion 20.051  0.631  26.936
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/affyContam.Rcheck/00check.log’
for details.


affyContam.Rcheck/00install.out:

* installing *source* package ‘affyContam’ ...
** R
** inst
** preparing package for lazy loading
     Package   
[1,] "affydata"
     LibPath                                                         
[1,] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library"
     Item       Title                        
[1,] "Dilution" "AffyBatch instance Dilution"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
     Package   
[1,] "affydata"
     LibPath                                                         
[1,] "/Library/Frameworks/R.framework/Versions/3.2/Resources/library"
     Item       Title                        
[1,] "Dilution" "AffyBatch instance Dilution"
* DONE (affyContam)

affyContam.Rcheck/affyContam-Ex.timings:

nameusersystemelapsed
setRectRegion20.051 0.63126.936