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CHECK report for AffyCompatible on tokay1

This page was generated on 2020-08-09 11:57:56 -0400 (Sun, 09 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE AffyCompatible PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 25/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffyCompatible 1.49.0
Martin Morgan
Snapshot Date: 2020-08-08 14:51:01 -0400 (Sat, 08 Aug 2020)
URL: https://git.bioconductor.org/packages/AffyCompatible
Branch: master
Last Commit: cae1554
Last Changed Date: 2020-04-27 14:17:06 -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: AffyCompatible
Version: 1.49.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:AffyCompatible.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AffyCompatible_1.49.0.tar.gz
StartedAt: 2020-08-08 23:52:33 -0400 (Sat, 08 Aug 2020)
EndedAt: 2020-08-08 23:55:42 -0400 (Sat, 08 Aug 2020)
EllapsedTime: 188.9 seconds
RetCode: 0
Status:  OK  
CheckDir: AffyCompatible.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:AffyCompatible.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings AffyCompatible_1.49.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/AffyCompatible.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 'AffyCompatible/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AffyCompatible' version '1.49.0'
* 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 'AffyCompatible' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 R/sysdata.rda ... 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
NetAffxResource-class 5.79   0.36    8.73
readArr               0.22   0.00   26.56
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
NetAffxResource-class 4.83   0.14    7.57
* 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: OK


Installation output

AffyCompatible.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/AffyCompatible_1.49.0.tar.gz && rm -rf AffyCompatible.buildbin-libdir && mkdir AffyCompatible.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AffyCompatible.buildbin-libdir AffyCompatible_1.49.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL AffyCompatible_1.49.0.zip && rm AffyCompatible_1.49.0.tar.gz AffyCompatible_1.49.0.zip
###
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  % 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 74431  100 74431    0     0   761k      0 --:--:-- --:--:-- --:--:--  790k

install for i386

* installing *source* package 'AffyCompatible' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'AffyCompatible'
    finding HTML links ... done
    AffyCompatible-class                    html  
    AffyCompatible-package                  html  
    NetAffxResource-class                   html  
    NetAffxResource                         html  
    accessors-NetAffxResource               html  
    readArr                                 html  
    readMage                                html  
    readNetAffx                             html  
    readXml                                 html  
    xclass                                  html  
    zzz-.TypedAssociation-class             html  
    zzz-ARRCompatibility-class              html  
    zzz-DTTCompatibility-class              html  
    zzz-NetAffxCompatibility-class          html  
    zzz                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'AffyCompatible' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AffyCompatible' as AffyCompatible_1.49.0.zip
* DONE (AffyCompatible)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'AffyCompatible' successfully unpacked and MD5 sums checked

Tests output


Example timings

AffyCompatible.Rcheck/examples_i386/AffyCompatible-Ex.timings

nameusersystemelapsed
AffyCompatible-class000
NetAffxResource-class5.790.368.73
readArr 0.22 0.0026.56
readMage1.030.061.09
readNetAffx000
readXml0.050.000.05
xclass0.060.010.09
zzz-ARRCompatibility-class000
zzz-DTTCompatibility-class0.020.000.02
zzz-NetAffxCompatibility-class000

AffyCompatible.Rcheck/examples_x64/AffyCompatible-Ex.timings

nameusersystemelapsed
AffyCompatible-class000
NetAffxResource-class4.830.147.57
readArr0.260.000.27
readMage1.050.031.07
readNetAffx000
readXml0.060.000.07
xclass0.060.000.29
zzz-ARRCompatibility-class000
zzz-DTTCompatibility-class0.000.020.02
zzz-NetAffxCompatibility-class000