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CHECK report for affyContam on riesling1

This page was generated on 2020-10-28 13:27:30 -0400 (Wed, 28 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 27/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affyContam 1.48.0
V. Carey
Snapshot Date: 2020-10-27 13:12:07 -0400 (Tue, 27 Oct 2020)
URL: https://git.bioconductor.org/packages/affyContam
Branch: RELEASE_3_12
Last Commit: 88387a2
Last Changed Date: 2020-10-27 10:34:42 -0400 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK YES, new version is higher than 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 YES, new version is higher than in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK YES, new version is higher than in internal repository

Summary

Package: affyContam
Version: 1.48.0
Command: D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affyContam.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings affyContam_1.48.0.tar.gz
StartedAt: 2020-10-27 20:01:07 -0400 (Tue, 27 Oct 2020)
EndedAt: 2020-10-27 20:02:06 -0400 (Tue, 27 Oct 2020)
EllapsedTime: 59.8 seconds
RetCode: 0
Status:  OK  
CheckDir: affyContam.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affyContam.install-out.txt --library=D:\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings affyContam_1.48.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.12-bioc/meat/affyContam.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.48.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* 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 11.06    0.6   11.69
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
setRectRegion 12.2   0.59   12.79
* 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: 4 NOTEs
See
  'D:/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 http://172.29.0.3/BBS/3.12/bioc/src/contrib/affyContam_1.48.0.tar.gz && rm -rf affyContam.buildbin-libdir && mkdir affyContam.buildbin-libdir && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affyContam.buildbin-libdir affyContam_1.48.0.tar.gz && D:\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL affyContam_1.48.0.zip && rm affyContam_1.48.0.tar.gz affyContam_1.48.0.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  3539k      0 --:--:-- --:--:-- --:--:-- 3539k

install for i386

* installing *source* package 'affyContam' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
     Package    LibPath                                Item      
[1,] "affydata" "D:/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" "D:/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" "D:/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" "D:/biocbuild/bbs-3.12-bioc/R/library" "Dilution"
     Title                        
[1,] "AffyBatch instance Dilution"
* MD5 sums
packaged installation of 'affyContam' as affyContam_1.48.0.zip
* DONE (affyContam)
* installing to library 'D:/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
setRectRegion11.06 0.6011.69

affyContam.Rcheck/examples_x64/affyContam-Ex.timings

nameusersystemelapsed
setRectRegion12.20 0.5912.79