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CHECK report for affyContam on tokay1

This page was generated on 2020-08-12 11:38:25 -0400 (Wed, 12 Aug 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 26/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyContam 1.47.0
V. Carey
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 Aug 2020)
URL: https://git.bioconductor.org/packages/affyContam
Branch: master
Last Commit: 24a5fca
Last Changed Date: 2020-04-27 14:18:21 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affyContam
Version: 1.47.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affyContam.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings affyContam_1.47.0.tar.gz
StartedAt: 2020-08-12 00:11:40 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 00:12:59 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 79.3 seconds
RetCode: 0
Status:  OK  
CheckDir: affyContam.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affyContam.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings affyContam_1.47.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/affyContam.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyContam/DESCRIPTION' ... OK
* this is package 'affyContam' version '1.47.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
setRectRegion 25.44   0.73   26.23
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
setRectRegion 16.35   0.45   16.81
* 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/affyContam.Rcheck/00check.log'
for details.



Installation output

affyContam.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/affyContam_1.47.0.tar.gz && rm -rf affyContam.buildbin-libdir && mkdir affyContam.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affyContam.buildbin-libdir affyContam_1.47.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL affyContam_1.47.0.zip && rm affyContam_1.47.0.tar.gz affyContam_1.47.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  219k  100  219k    0     0  5332k      0 --:--:-- --:--:-- --:--:-- 5774k

install for i386

* installing *source* package 'affyContam' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
     Package    LibPath                                      Item      
[1,] "affydata" "C:/Users/biocbuild/bbs-3.12-bioc/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
** help
*** installing help indices
  converting help for package 'affyContam'
    finding HTML links ... done
    setRectRegion                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
     Package    LibPath                                      Item      
[1,] "affydata" "C:/Users/biocbuild/bbs-3.12-bioc/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
** testing if installed package can be loaded from final location
     Package    LibPath                                      Item      
[1,] "affydata" "C:/Users/biocbuild/bbs-3.12-bioc/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'affyContam' ...
** testing if installed package can be loaded
     Package    LibPath                                      Item      
[1,] "affydata" "C:/Users/biocbuild/bbs-3.12-bioc/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
* MD5 sums
packaged installation of 'affyContam' as affyContam_1.47.0.zip
* DONE (affyContam)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'affyContam' successfully unpacked and MD5 sums checked

Tests output


Example timings

affyContam.Rcheck/examples_i386/affyContam-Ex.timings

nameusersystemelapsed
setRectRegion25.44 0.7326.23

affyContam.Rcheck/examples_x64/affyContam-Ex.timings

nameusersystemelapsed
setRectRegion16.35 0.4516.81