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CHECK report for affyContam on celaya2

This page was generated on 2019-10-16 12:47:17 -0400 (Wed, 16 Oct 2019).

Package 26/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyContam 1.42.0
V. Carey
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/affyContam
Branch: RELEASE_3_9
Last Commit: 8a5e94a
Last Changed Date: 2019-05-02 11:53:11 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: affyContam
Version: 1.42.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:affyContam.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings affyContam_1.42.0.tar.gz
StartedAt: 2019-10-16 00:25:21 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:26:33 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 71.8 seconds
RetCode: 0
Status:  OK 
CheckDir: affyContam.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:affyContam.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings affyContam_1.42.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/affyContam.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyContam/DESCRIPTION’ ... OK
* this is package ‘affyContam’ version ‘1.42.0’
* 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 ... 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 : : no visible global function definition for
  ‘xy2indices’
getCircRegion: no visible global function definition for ‘exprs’
getRectRegion: no visible global function definition for ‘annotation’
getRectRegion : : no visible global function definition for
  ‘xy2indices’
getRectRegion: no visible global function definition for ‘exprs’
setCircRegion: no visible global function definition for ‘annotation’
setCircRegion : : 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 : : no visible global function definition for
  ‘xy2indices’
setRectRegion: no visible global function definition for ‘exprs’
setRectRegion: no visible global function definition for ‘exprs<-’
Undefined global functions or variables:
  annotation exprs exprs<- xy2indices
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
setRectRegion 24.062  1.373  25.679
* 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-3.9-bioc/meat/affyContam.Rcheck/00check.log’
for details.



Installation output

affyContam.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL affyContam
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘affyContam’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
     Package   
[1,] "affydata"
     LibPath                                                         
[1,] "/Library/Frameworks/R.framework/Versions/3.6/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 from temporary location
     Package   
[1,] "affydata"
     LibPath                                                         
[1,] "/Library/Frameworks/R.framework/Versions/3.6/Resources/library"
     Item       Title                        
[1,] "Dilution" "AffyBatch instance Dilution"
** testing if installed package can be loaded from final location
     Package   
[1,] "affydata"
     LibPath                                                         
[1,] "/Library/Frameworks/R.framework/Versions/3.6/Resources/library"
     Item       Title                        
[1,] "Dilution" "AffyBatch instance Dilution"
** testing if installed package keeps a record of temporary installation path
* DONE (affyContam)

Tests output


Example timings

affyContam.Rcheck/affyContam-Ex.timings

nameusersystemelapsed
setRectRegion24.062 1.37325.679