(v1.1.0.9008) lose dependencies

.gitlab-ci.yml

@@ -62,7 +62,6 @@ R-release:
   allow_failure: false
   script:
     - Rscript -e 'sessionInfo()'
-    - Rscript -e 'AMR::eucast_rules(AMR::example_isolates_unclean, info = TRUE)'
     # install missing and outdated packages
     - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE,  install_lintr = TRUE)'
     - Rscript -e 'devtools::test(stop_on_failure = FALSE)'
@@ -78,7 +77,6 @@ R-devel:
   allow_failure: false
   script:
     - Rscriptdevel -e 'sessionInfo()'
-    - Rscriptdevel -e 'AMR::eucast_rules(AMR::example_isolates_unclean, info = TRUE)'
     # install missing and outdated packages
     - Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE,  install_lintr = TRUE)'
     - Rscriptdevel -e 'devtools::test(stop_on_failure = FALSE)'
@@ -95,6 +93,7 @@ R-release:
   allow_failure: true
   script:
     - Rscript -e 'sessionInfo()'
+    - Rscript -e 'AMR::eucast_rules(AMR::example_isolates_unclean, info = TRUE)'
     # install missing and outdated packages
     - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE,  install_lintr = TRUE)'
     # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
@@ -122,6 +121,7 @@ R-devel:
   allow_failure: true
   script:
     - Rscriptdevel -e 'sessionInfo()'
+    - Rscriptdevel -e 'AMR::eucast_rules(AMR::example_isolates_unclean, info = TRUE)'
     # install missing and outdated packages
     - Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE)'
     # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.1.0.9007
+Version: 1.1.0.9008
-Date: 2020-05-16
+Date: 2020-05-17
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 
@@ -36,8 +36,6 @@ Description: Functions to simplify the analysis and prediction of Antimicrobial
     Standards Institute (2014) <isbn: 1-56238-899-1>.
 Depends:
     R (>= 3.1.0)
-Enhances:
-    ggplot2
 Imports:
     backports,
     cleaner,
@@ -47,6 +45,7 @@ Imports:
 Suggests:
     covr,
     dplyr,
+    ggplot2,
     knitr,
     microbenchmark,
     rmarkdown,

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 1.1.0.9007
+# AMR 1.1.0.9008
-## <small>Last updated: 16-May-2020</small>
+## <small>Last updated: 17-May-2020</small>
 
 ### Breaking 
 * Removed previously deprecated function `p.symbol()` - it was replaced with `p_symbol()`

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9008</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9008</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9008</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9008</span>
       </span>
     </div>
 

docs/index.html

@@ -43,7 +43,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9008</span>
       </span>
     </div>
 

docs/pkgdown.yml

@@ -10,7 +10,7 @@ articles:
   WHONET: WHONET.html
   benchmarks: benchmarks.html
   resistance_predict: resistance_predict.html
-last_built: 2020-05-16T19:39Z
+last_built: 2020-05-17T09:54Z
 urls:
   reference: https://msberends.gitlab.io/AMR/reference
   article: https://msberends.gitlab.io/AMR/articles

docs/reference/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9008</span>
       </span>
     </div>
 

tests/appveyor/appveyor_tool.ps1

@@ -1,3 +1,5 @@
+# from https://github.com/krlmlr/r-appveyor/tree/master/scripts
+
 if ( -not(Test-Path Env:\CRAN) ) {
   $CRAN = "https://cran.rstudio.com"
 }
@@ -44,7 +46,7 @@ Function TravisTool
       [string[]]$Params
   )
 
-  Exec { bash.exe ../travis_tool.sh $Params }
+  Exec { bash.exe ../travis-tool.sh $Params }
 }
 
 Function InstallR {
@@ -100,6 +102,7 @@ Function InstallR {
   Progress ("URL path: " + $url_path)
 
   $rurl = $CRAN + "/bin/windows/base/" + $url_path + "R-" + $version + "-win.exe"
+  $global:rversion = $version
 
   Progress ("Downloading R from: " + $rurl)
   & "C:\Program Files\Git\mingw64\bin\curl.exe" -s -o ../R-win.exe -L $rurl
@@ -117,16 +120,28 @@ Function InstallR {
   Rscript -e "sessionInfo()"
 }
 
+Function InstallRtools40 {
+  $rtoolsurl = $CRAN + "/bin/windows/Rtools/rtools40-x86_64.exe"
+
+  Progress ("Downloading Rtools40 from: " + $rtoolsurl)
+  & "C:\Program Files\Git\mingw64\bin\curl.exe" -s -o ../rtools40-x86_64.exe -L $rtoolsurl
+
+  Progress "Running Rtools40 installer"
+  Start-Process -FilePath ..\rtools40-x86_64.exe -ArgumentList /VERYSILENT -NoNewWindow -Wait
+
+  Progress "Setting PATH"
+  $env:PATH = 'c:\rtools40\usr\bin;c:\rtools40\mingw64\bin;' + $env:PATH
+}
+
 Function InstallRtools {
   if ( -not(Test-Path Env:\RTOOLS_VERSION) ) {
-    Progress "Determining Rtools version"
+    $rtoolsver = '35'
-    $rtoolsver = $(Invoke-WebRequest ($CRAN + "/bin/windows/Rtools/VERSION.txt")).Content.Split(' ')[2].Split('.')[0..1] -Join ''
   }
   Else {
     $rtoolsver = $env:RTOOLS_VERSION
   }
 
-  $rtoolsurl = $CRAN + "/bin/windows/Rtools/Rtools$rtoolsver-x86_64.exe"
+  $rtoolsurl = $CRAN + "/bin/windows/Rtools/Rtools$rtoolsver.exe"
 
   Progress ("Downloading Rtools from: " + $rtoolsurl)
   & "C:\Program Files\Git\mingw64\bin\curl.exe" -s -o ../Rtools-current.exe -L $rtoolsurl
@@ -165,24 +180,28 @@ Function Bootstrap {
   InstallR
 
   if ((Test-Path "src") -or ($env:USE_RTOOLS -eq "true") -or ($env:USE_RTOOLS -eq "yes")) {
+    if ($rversion.StartsWith("3")) {
       InstallRtools
+    } Else {
+      InstallRtools40
+    }
   }
   Else {
     Progress "Skipping download of Rtools because src/ directory is missing."
   }
 
-  Progress "Downloading and installing travis_tool.sh"
+  Progress "Downloading and installing travis-tool.sh"
-  
   cp "tests\appveyor\travis_tool.sh" "..\travis_tool.sh"
-  echo '@bash.exe ../travis_tool.sh %*' | Out-File -Encoding ASCII .\travis_tool.sh.cmd
+  # Invoke-WebRequest https://raw.githubusercontent.com/krlmlr/r-appveyor/master/r-travis/scripts/travis-tool.sh -OutFile "..\travis-tool.sh"
-  cat .\travis_tool.sh.cmd
+  echo '@bash.exe ../travis-tool.sh %*' | Out-File -Encoding ASCII .\travis-tool.sh.cmd
-  bash -c "( echo; echo '^travis_tool\.sh\.cmd$' ) >> .Rbuildignore"
+  cat .\travis-tool.sh.cmd
+  bash -c "( echo; echo '^travis-tool\.sh\.cmd$' ) >> .Rbuildignore"
   cat .\.Rbuildignore
 
   $env:PATH.Split(";")
 
   Progress "Setting R_LIBS_USER"
-  $env:R_LIBS_USER = 'c:\RLibrary'
+  $env:R_LIBS_USER = 'c:\RLibrary\' + $rversion.Substring(0,3)
   if ( -not(Test-Path $env:R_LIBS_USER) ) {
     mkdir $env:R_LIBS_USER
   }