Back to Multiple platform build/check report for BioC 3.11
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for affyContam on malbec2

This page was generated on 2020-10-17 11:54:21 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE affyContam PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 26/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyContam 1.46.0
V. Carey
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/affyContam
Branch: RELEASE_3_11
Last Commit: 11c4fbd
Last Changed Date: 2020-04-27 14:18:21 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affyContam
Version: 1.46.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:affyContam.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings affyContam_1.46.0.tar.gz
StartedAt: 2020-10-16 22:41:03 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 22:41:50 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 47.4 seconds
RetCode: 0
Status:  OK 
CheckDir: affyContam.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:affyContam.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings affyContam_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/affyContam.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyContam/DESCRIPTION’ ... OK
* this is package ‘affyContam’ version ‘1.46.0’
* 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 : <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<-’
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
setRectRegion 17.986  0.284  18.271
* 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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/affyContam.Rcheck/00check.log’
for details.



Installation output

affyContam.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL affyContam
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘affyContam’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
     Package    LibPath                                   Item      
[1,] "affydata" "/home/biocbuild/bbs-3.11-bioc/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
     Package    LibPath                                   Item      
[1,] "affydata" "/home/biocbuild/bbs-3.11-bioc/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
** testing if installed package can be loaded from final location
     Package    LibPath                                   Item      
[1,] "affydata" "/home/biocbuild/bbs-3.11-bioc/R/library" "Dilution"
     Title                        
[1,] "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
setRectRegion17.986 0.28418.271