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CHECK report for affycoretools on tokay1

This page was generated on 2020-08-12 11:37:28 -0400 (Wed, 12 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE affycoretools PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 27/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affycoretools 1.61.2
James W. MacDonald
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 Aug 2020)
URL: https://git.bioconductor.org/packages/affycoretools
Branch: master
Last Commit: 2f77a7b
Last Changed Date: 2020-05-26 15:52:12 -0400 (Tue, 26 May 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 [ WARNINGS ] 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: affycoretools
Version: 1.61.2
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affycoretools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings affycoretools_1.61.2.tar.gz
StartedAt: 2020-08-11 23:56:06 -0400 (Tue, 11 Aug 2020)
EndedAt: 2020-08-12 00:04:14 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 487.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: affycoretools.Rcheck
Warnings: 1

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:affycoretools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings affycoretools_1.61.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/affycoretools.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 'affycoretools/DESCRIPTION' ... OK
* this is package 'affycoretools' version '1.61.2'
* 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:
  .travis.yml
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 'affycoretools' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpATQA5L/R.INSTALL248818f1564e/affycoretools/man/annotateEset.Rd:44: file link 'columns' in package 'AnnotationDbi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpATQA5L/R.INSTALL248818f1564e/affycoretools/man/annotateEset.Rd:47: file link 'mapIds' in package 'AnnotationDbi' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpATQA5L/R.INSTALL248818f1564e/affycoretools/man/annotateEset.Rd:52: file link 'rma' in package 'oligo' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpATQA5L/R.INSTALL248818f1564e/affycoretools/man/makeVenn.Rd:91: file link 'glmQLFit' in package 'edgeR' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpATQA5L/R.INSTALL248818f1564e/affycoretools/man/writeFit.Rd:39: file link 'write.fit' in package 'limma' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/affycoretools.Rcheck/00install.out' for details.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/affycoretools.Rcheck/00check.log'
for details.



Installation output

affycoretools.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/affycoretools_1.61.2.tar.gz && rm -rf affycoretools.buildbin-libdir && mkdir affycoretools.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affycoretools.buildbin-libdir affycoretools_1.61.2.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL affycoretools_1.61.2.zip && rm affycoretools_1.61.2.tar.gz affycoretools_1.61.2.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 6444k  100 6444k    0     0  53.8M      0 --:--:-- --:--:-- --:--:-- 56.1M

install for i386

* installing *source* package 'affycoretools' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'affycoretools'
    finding HTML links ... done
    affycoretools-defunct                   html  
    affycoretools                           html  
    affystart                               html  
    annotateEset                            html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpATQA5L/R.INSTALL248818f1564e/affycoretools/man/annotateEset.Rd:44: file link 'columns' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpATQA5L/R.INSTALL248818f1564e/affycoretools/man/annotateEset.Rd:47: file link 'mapIds' in package 'AnnotationDbi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpATQA5L/R.INSTALL248818f1564e/affycoretools/man/annotateEset.Rd:52: file link 'rma' in package 'oligo' does not exist and so has been treated as a topic
    dataAndHeatmapPage                      html  
    doGlimma                                html  
    entrezLinks                             html  
    fixHeaderAndGo                          html  
    geneSetPage                             html  
    finding level-2 HTML links ... done

    getCols                                 html  
    getMainProbes                           html  
    gsHeatmap                               html  
    intNames                                html  
    make.cl                                 html  
    makeGoGeneTable                         html  
    makeGoTable                             html  
    makeHmap                                html  
    makeImages                              html  
    makeIndices                             html  
    makeVenn                                html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpATQA5L/R.INSTALL248818f1564e/affycoretools/man/makeVenn.Rd:91: file link 'glmQLFit' in package 'edgeR' does not exist and so has been treated as a topic
    maplot                                  html  
    mirna2mrna                              html  
    outputRomer                             html  
    pca.legend                              html  
    plotDeg                                 html  
    plotPCA                                 html  
    runRomer                                html  
    tableFilt                               html  
    venn4Way                                html  
    vennCounts2                             html  
    vennInLine                              html  
    vennPage                                html  
    vennSelect2                             html  
    writeFit                                html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpATQA5L/R.INSTALL248818f1564e/affycoretools/man/writeFit.Rd:39: file link 'write.fit' in package 'limma' does not exist and so has been treated as a topic
** 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 'affycoretools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affycoretools' as affycoretools_1.61.2.zip
* DONE (affycoretools)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'affycoretools' successfully unpacked and MD5 sums checked

Tests output


Example timings

affycoretools.Rcheck/examples_i386/affycoretools-Ex.timings

nameusersystemelapsed
annotateEset000
doGlimma000
entrezLinks000
makeVenn000
plotDeg4.300.344.64
plotPCA0.030.020.04
vennCounts20.050.000.05
vennPage000

affycoretools.Rcheck/examples_x64/affycoretools-Ex.timings

nameusersystemelapsed
annotateEset000
doGlimma000
entrezLinks000
makeVenn000
plotDeg3.200.113.32
plotPCA0.050.000.04
vennCounts21.120.011.14
vennPage000