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(v1.1.0.9008) lose dependencies
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071bdc5a9e
@ -62,7 +62,6 @@ R-release:
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allow_failure: false
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script:
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- Rscript -e 'sessionInfo()'
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- Rscript -e 'AMR::eucast_rules(AMR::example_isolates_unclean, info = TRUE)'
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# install missing and outdated packages
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- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)'
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- Rscript -e 'devtools::test(stop_on_failure = FALSE)'
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@ -78,7 +77,6 @@ R-devel:
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allow_failure: false
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script:
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- Rscriptdevel -e 'sessionInfo()'
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- Rscriptdevel -e 'AMR::eucast_rules(AMR::example_isolates_unclean, info = TRUE)'
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# install missing and outdated packages
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- Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)'
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- Rscriptdevel -e 'devtools::test(stop_on_failure = FALSE)'
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@ -95,6 +93,7 @@ R-release:
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allow_failure: true
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script:
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- Rscript -e 'sessionInfo()'
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- Rscript -e 'AMR::eucast_rules(AMR::example_isolates_unclean, info = TRUE)'
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# install missing and outdated packages
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- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)'
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# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
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@ -122,6 +121,7 @@ R-devel:
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allow_failure: true
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script:
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- Rscriptdevel -e 'sessionInfo()'
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- Rscriptdevel -e 'AMR::eucast_rules(AMR::example_isolates_unclean, info = TRUE)'
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# install missing and outdated packages
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- Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE)'
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# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.1.0.9007
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Date: 2020-05-16
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Version: 1.1.0.9008
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Date: 2020-05-17
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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@ -36,8 +36,6 @@ Description: Functions to simplify the analysis and prediction of Antimicrobial
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Standards Institute (2014) <isbn: 1-56238-899-1>.
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Depends:
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R (>= 3.1.0)
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Enhances:
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ggplot2
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Imports:
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backports,
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cleaner,
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@ -47,6 +45,7 @@ Imports:
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Suggests:
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covr,
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dplyr,
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ggplot2,
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knitr,
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microbenchmark,
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rmarkdown,
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4
NEWS.md
4
NEWS.md
@ -1,5 +1,5 @@
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# AMR 1.1.0.9007
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## <small>Last updated: 16-May-2020</small>
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# AMR 1.1.0.9008
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## <small>Last updated: 17-May-2020</small>
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### Breaking
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* Removed previously deprecated function `p.symbol()` - it was replaced with `p_symbol()`
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9008</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9008</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9008</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9008</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9008</span>
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</span>
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</div>
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@ -10,7 +10,7 @@ articles:
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WHONET: WHONET.html
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benchmarks: benchmarks.html
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resistance_predict: resistance_predict.html
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last_built: 2020-05-16T19:39Z
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last_built: 2020-05-17T09:54Z
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urls:
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reference: https://msberends.gitlab.io/AMR/reference
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article: https://msberends.gitlab.io/AMR/articles
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9008</span>
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</span>
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</div>
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@ -1,3 +1,5 @@
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# from https://github.com/krlmlr/r-appveyor/tree/master/scripts
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if ( -not(Test-Path Env:\CRAN) ) {
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$CRAN = "https://cran.rstudio.com"
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}
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@ -44,7 +46,7 @@ Function TravisTool
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[string[]]$Params
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)
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Exec { bash.exe ../travis_tool.sh $Params }
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Exec { bash.exe ../travis-tool.sh $Params }
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}
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Function InstallR {
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@ -100,6 +102,7 @@ Function InstallR {
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Progress ("URL path: " + $url_path)
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$rurl = $CRAN + "/bin/windows/base/" + $url_path + "R-" + $version + "-win.exe"
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$global:rversion = $version
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Progress ("Downloading R from: " + $rurl)
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& "C:\Program Files\Git\mingw64\bin\curl.exe" -s -o ../R-win.exe -L $rurl
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@ -117,16 +120,28 @@ Function InstallR {
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Rscript -e "sessionInfo()"
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}
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Function InstallRtools40 {
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$rtoolsurl = $CRAN + "/bin/windows/Rtools/rtools40-x86_64.exe"
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Progress ("Downloading Rtools40 from: " + $rtoolsurl)
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& "C:\Program Files\Git\mingw64\bin\curl.exe" -s -o ../rtools40-x86_64.exe -L $rtoolsurl
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Progress "Running Rtools40 installer"
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Start-Process -FilePath ..\rtools40-x86_64.exe -ArgumentList /VERYSILENT -NoNewWindow -Wait
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Progress "Setting PATH"
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$env:PATH = 'c:\rtools40\usr\bin;c:\rtools40\mingw64\bin;' + $env:PATH
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}
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Function InstallRtools {
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if ( -not(Test-Path Env:\RTOOLS_VERSION) ) {
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Progress "Determining Rtools version"
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$rtoolsver = $(Invoke-WebRequest ($CRAN + "/bin/windows/Rtools/VERSION.txt")).Content.Split(' ')[2].Split('.')[0..1] -Join ''
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$rtoolsver = '35'
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}
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Else {
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$rtoolsver = $env:RTOOLS_VERSION
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}
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$rtoolsurl = $CRAN + "/bin/windows/Rtools/Rtools$rtoolsver-x86_64.exe"
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$rtoolsurl = $CRAN + "/bin/windows/Rtools/Rtools$rtoolsver.exe"
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Progress ("Downloading Rtools from: " + $rtoolsurl)
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& "C:\Program Files\Git\mingw64\bin\curl.exe" -s -o ../Rtools-current.exe -L $rtoolsurl
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@ -165,24 +180,28 @@ Function Bootstrap {
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InstallR
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if ((Test-Path "src") -or ($env:USE_RTOOLS -eq "true") -or ($env:USE_RTOOLS -eq "yes")) {
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InstallRtools
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if ($rversion.StartsWith("3")) {
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InstallRtools
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} Else {
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InstallRtools40
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}
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}
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Else {
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Progress "Skipping download of Rtools because src/ directory is missing."
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}
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Progress "Downloading and installing travis_tool.sh"
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Progress "Downloading and installing travis-tool.sh"
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cp "tests\appveyor\travis_tool.sh" "..\travis_tool.sh"
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echo '@bash.exe ../travis_tool.sh %*' | Out-File -Encoding ASCII .\travis_tool.sh.cmd
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cat .\travis_tool.sh.cmd
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bash -c "( echo; echo '^travis_tool\.sh\.cmd$' ) >> .Rbuildignore"
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# Invoke-WebRequest https://raw.githubusercontent.com/krlmlr/r-appveyor/master/r-travis/scripts/travis-tool.sh -OutFile "..\travis-tool.sh"
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echo '@bash.exe ../travis-tool.sh %*' | Out-File -Encoding ASCII .\travis-tool.sh.cmd
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cat .\travis-tool.sh.cmd
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bash -c "( echo; echo '^travis-tool\.sh\.cmd$' ) >> .Rbuildignore"
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cat .\.Rbuildignore
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$env:PATH.Split(";")
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Progress "Setting R_LIBS_USER"
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$env:R_LIBS_USER = 'c:\RLibrary'
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$env:R_LIBS_USER = 'c:\RLibrary\' + $rversion.Substring(0,3)
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if ( -not(Test-Path $env:R_LIBS_USER) ) {
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mkdir $env:R_LIBS_USER
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}
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