Back to Multiple platform build/check report for BioC 3.12
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for ArrayTools on tokay1

This page was generated on 2020-08-13 11:35:07 -0400 (Thu, 13 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ArrayTools PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 80/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayTools 1.49.0
Arthur Li
Snapshot Date: 2020-08-12 14:52:00 -0400 (Wed, 12 Aug 2020)
URL: https://git.bioconductor.org/packages/ArrayTools
Branch: master
Last Commit: e7b0baa
Last Changed Date: 2020-04-27 14:18:01 -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: ArrayTools
Version: 1.49.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ArrayTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ArrayTools_1.49.0.tar.gz
StartedAt: 2020-08-13 00:25:45 -0400 (Thu, 13 Aug 2020)
EndedAt: 2020-08-13 00:27:34 -0400 (Thu, 13 Aug 2020)
EllapsedTime: 108.7 seconds
RetCode: 0
Status:  OK  
CheckDir: ArrayTools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ArrayTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ArrayTools_1.49.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ArrayTools.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 'ArrayTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ArrayTools' 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 'ArrayTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'affy' 'Biobase' 'methods'
A package should be listed in only one of these fields.
* 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
'library' or 'require' calls in package code:
  'R2HTML' 'affyPLM' 'annaffy' 'gcrma' 'simpleaffy'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createIndex: no visible global function definition for 'HTMLStart'
createIndex: no visible global function definition for 'as.title'
createIndex: no visible global function definition for 'HTML'
createIndex: no visible global function definition for 'HTMLStop'
geneFilter: no visible global function definition for 'getText'
geneFilter: no visible global function definition for 'aafSymbol'
geneFilter: no visible global function definition for 'aafDescription'
geneFilter: no visible global function definition for 'aafChromosome'
geneFilter: no visible global function definition for 'aafGenBank'
geneFilter: no visible global function definition for 'aafCytoband'
geneFilter: no visible global function definition for 'aafUniGene'
geneFilter: no visible global function definition for 'aafPubMed'
geneFilter: no visible global function definition for 'aafLocusLink'
output.ing: no visible global function definition for 'getText'
output.ing: no visible global function definition for 'aafSymbol'
output.ing: no visible global function definition for 'aafDescription'
output.ing: no visible global function definition for 'aafChromosome'
output.ing: no visible global function definition for 'aafGenBank'
output.ing: no visible global function definition for 'aafCytoband'
output.ing: no visible global function definition for 'aafUniGene'
output.ing: no visible global function definition for 'aafPubMed'
output.ing: no visible global function definition for 'aafLocusLink'
preProcess3prime: no visible global function definition for 'gcrma'
preProcess3prime: no visible global function definition for 'getText'
preProcess3prime: no visible global function definition for 'aafSymbol'
preProcess3prime: no visible global function definition for
  'aafDescription'
preProcess3prime: no visible global function definition for
  'aafChromosome'
preProcess3prime: no visible global function definition for
  'aafGenBank'
preProcess3prime: no visible global function definition for
  'aafCytoband'
preProcess3prime: no visible global function definition for
  'aafUniGene'
preProcess3prime: no visible global function definition for 'aafPubMed'
preProcess3prime: no visible global function definition for
  'aafLocusLink'
preProcessGeneST: no visible binding for global variable
  'hugene10stCONTROL'
preProcessGeneST: no visible binding for global variable
  'mogene10stCONTROL'
preProcessGeneST: no visible global function definition for 'getText'
preProcessGeneST: no visible global function definition for 'aafSymbol'
preProcessGeneST: no visible global function definition for
  'aafDescription'
preProcessGeneST: no visible global function definition for
  'aafChromosome'
preProcessGeneST: no visible global function definition for
  'aafGenBank'
preProcessGeneST: no visible global function definition for
  'aafCytoband'
preProcessGeneST: no visible global function definition for
  'aafUniGene'
preProcessGeneST: no visible global function definition for 'aafPubMed'
preProcessGeneST: no visible global function definition for
  'aafLocusLink'
qa3prime: no visible global function definition for 'setQCEnvironment'
qa3prime: no visible global function definition for 'qc.get.alpha1'
qa3prime: no visible global function definition for 'HTMLStart'
qa3prime: no visible global function definition for 'as.title'
qa3prime: no visible global function definition for 'HTML'
qa3prime: no visible global function definition for 'HTMLInsertGraph'
qa3prime: no visible global function definition for 'call.exprs'
qa3prime: no visible global function definition for 'avbg'
qa3prime: no visible global function definition for 'percent.present'
qa3prime: no visible global function definition for 'sfs'
qa3prime: no visible global function definition for 'spikeInProbes'
qa3prime: no visible global function definition for 'ratios'
qa3prime: no visible global function definition for 'fitPLM'
qa3prime: no visible global function definition for 'HTMLStop'
qaGeneST: no visible global function definition for 'HTMLStart'
qaGeneST: no visible global function definition for 'as.title'
qaGeneST: no visible global function definition for 'HTML'
qaGeneST: no visible global function definition for 'HTMLInsertGraph'
qaGeneST: no visible global function definition for 'HTMLStop'
regress: no visible global function definition for 'permute.1'
regress: no visible binding for global variable 'design'
Output2HTML,interactionResult: no visible global function definition
  for 'aaf.handler'
Output2HTML,interactionResult: no visible global function definition
  for 'aafTableAnn'
Output2HTML,interactionResult: no visible global function definition
  for 'aafTable'
Output2HTML,interactionResult: no visible global function definition
  for 'saveHTML'
Output2HTML,regressResult: no visible global function definition for
  'aaf.handler'
Output2HTML,regressResult: no visible global function definition for
  'aafTableAnn'
Output2HTML,regressResult: no visible global function definition for
  'aafTable'
Output2HTML,regressResult: no visible global function definition for
  'saveHTML'
Undefined global functions or variables:
  HTML HTMLInsertGraph HTMLStart HTMLStop aaf.handler aafChromosome
  aafCytoband aafDescription aafGenBank aafLocusLink aafPubMed
  aafSymbol aafTable aafTableAnn aafUniGene as.title avbg call.exprs
  design fitPLM gcrma getText hugene10stCONTROL mogene10stCONTROL
  percent.present permute.1 qc.get.alpha1 ratios saveHTML
  setQCEnvironment sfs spikeInProbes
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/ArrayTools.Rcheck/00check.log'
for details.



Installation output

ArrayTools.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/ArrayTools_1.49.0.tar.gz && rm -rf ArrayTools.buildbin-libdir && mkdir ArrayTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ArrayTools.buildbin-libdir ArrayTools_1.49.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ArrayTools_1.49.0.zip && rm ArrayTools_1.49.0.tar.gz ArrayTools_1.49.0.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  172k  100  172k    0     0  4451k      0 --:--:-- --:--:-- --:--:-- 4928k

install for i386

* installing *source* package 'ArrayTools' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ArrayTools'
    finding HTML links ... done
    Output2HTML                             html  
    QC                                      html  
    Sort                                    html  
    adjustment                              html  
    contrastMatrix-class                    html  
    createExpressionSet                     html  
    createGSEAFiles                         html  
    createIndex                             html  
    createIngenuityFile                     html  
    designMatrix-class                      html  
    eSetExample                             html  
    exprsExample                            html  
    geneFilter                              html  
    getAdjP                                 html  
    getAnnotation                           html  
    getCompare1                             html  
    getCompare2                             html  
    getContrast                             html  
    getCovariates                           html  
    getDesign                               html  
    getF                                    html  
    getFC                                   html  
    getFCCutoff                             html  
    getFilterMethod                         html  
    getID                                   html  
    getIndex                                html  
    getIntIndex                             html  
    getInteraction                          html  
    getLength                               html  
    getLevel                                html  
    getNormalizationMethod                  html  
    getP                                    html  
    getPCutoff                              html  
    getTarget                               html  
    hugene10stCONTROL                       html  
    interactionResult-class                 html  
    mogene10stCONTROL                       html  
    output.cls                              html  
    output.gct                              html  
    output.ing                              html  
    pDataExample                            html  
    postInteraction                         html  
    preProcess3prime                        html  
    preProcessGeneST                        html  
    qa3prime                                html  
    qaGeneST                                html  
    regress                                 html  
    regressResult-class                     html  
    regressionMethod                        html  
    selectSigGene                           html  
    selectSigGeneInt                        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 'ArrayTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ArrayTools' as ArrayTools_1.49.0.zip
* DONE (ArrayTools)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ArrayTools' successfully unpacked and MD5 sums checked

Tests output


Example timings

ArrayTools.Rcheck/examples_i386/ArrayTools-Ex.timings

nameusersystemelapsed
Output2HTML0.090.000.09
QC000
Sort0.060.000.06
contrastMatrix-class0.010.010.03
createExpressionSet0.050.000.05
createGSEAFiles000
createIndex0.090.000.10
createIngenuityFile0.020.000.01
designMatrix-class0.010.000.02
eSetExample000
exprsExample000
geneFilter3.950.164.11
interactionResult-class0.070.010.08
pDataExample000
postInteraction0.080.000.08
preProcess3prime3.160.133.29
preProcessGeneST0.030.000.03
qa3prime000
qaGeneST0.030.010.05
regress0.030.000.03
regressResult-class0.020.000.02
selectSigGene0.070.000.08
selectSigGeneInt0.070.000.06

ArrayTools.Rcheck/examples_x64/ArrayTools-Ex.timings

nameusersystemelapsed
Output2HTML0.090.020.11
QC000
Sort0.060.000.06
contrastMatrix-class0.020.010.03
createExpressionSet0.060.000.06
createGSEAFiles000
createIndex0.090.000.10
createIngenuityFile0.020.000.01
designMatrix-class0.010.000.02
eSetExample000
exprsExample000
geneFilter3.890.114.00
interactionResult-class0.080.000.08
pDataExample000
postInteraction0.080.000.08
preProcess3prime3.160.083.23
preProcessGeneST0.020.000.02
qa3prime000
qaGeneST0.030.000.03
regress0.020.000.01
regressResult-class0.010.000.02
selectSigGene0.050.000.04
selectSigGeneInt0.060.000.07