diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index b7127048..8f840204 100644 --- a/.gitlab-ci.yml +++ b/.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-e 'sessionInfo()' - - Rscript -e 'AMR::eucast_rules(AMR::example_isolates_unclean, info = TRUE)' # install missing and outdated packages - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr =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- - Rscriptdevel -e 'AMR::eucast_rules(AMR::example_isolates_unclean, info = TRUE)' # install missing and outdated packages - Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr =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-e 'sessionInfo()' + - Rscript -e 'AMR::eucast_rules(AMR::example_isolates_unclean, info = TRUE)' # install missing and outdated packages - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr =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+ - Rscriptdevel -e 'AMR::eucast_rules(AMR::example_isolates_unclean, info = TRUE)' # install missing and outdated packages - Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE)' # remove vignettes folder and get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 diff --git a/DESCRIPTION b/DESCRIPTION index 935943e7..9ec90077 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.1.0.9007 -Date: 2020-05-16 +Version: 1.1.0.9008 +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) . Depends: R (>= 3.1.0) -Enhances: - ggplot2 Imports: backports, cleaner, @@ -47,6 +45,7 @@ Imports: Suggests: covr, dplyr, + ggplot2, knitr, microbenchmark, rmarkdown, diff --git a/NEWS.md b/NEWS.md index c432f1dc..57a65e32 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 1.1.0.9007 -## Last updated: 16-May-2020 +# AMR 1.1.0.9008 +## Last updated: 17-May-2020 ### Breaking * Removed previously deprecated function `p.symbol()` - it was replaced with `p_symbol()` diff --git a/docs/404.html b/docs/404.html index ec79042f..34dd5f5b 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9007 + 1.1.0.9008 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index d45e92a8..410fa440 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9007 + 1.1.0.9008 diff --git a/docs/articles/index.html b/docs/articles/index.html index 1ee6d8f2..1128d471 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9007 + 1.1.0.9008 diff --git a/docs/authors.html b/docs/authors.html index d885217b..0f730c88 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9007 + 1.1.0.9008 diff --git a/docs/index.html b/docs/index.html index 7b9ea364..9a0757ad 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.1.0.9007 + 1.1.0.9008 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 69be2641..c46a3056 100644 --- a/docs/pkgdown.yml +++ b/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 diff --git a/docs/reference/index.html b/docs/reference/index.html index 588d7cec..299c6400 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9007 + 1.1.0.9008 diff --git a/tests/appveyor/appveyor_tool.ps1 b/tests/appveyor/appveyor_tool.ps1 index 859b458f..6912c0f4 100644 --- a/tests/appveyor/appveyor_tool.ps1 +++ b/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 = $(Invoke-WebRequest ($CRAN + "/bin/windows/Rtools/VERSION.txt")).Content.Split(' ')[2].Split('.')[0..1] -Join '' + $rtoolsver = '35' } 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 ($env:USE_RTOOLS -eq "yes")) { - InstallRtools + if ($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 - cat .\travis_tool.sh.cmd - bash -c "( echo; echo '^travis_tool\.sh\.cmd$' ) >> .Rbuildignore" + # Invoke-WebRequest https://raw.githubusercontent.com/krlmlr/r-appveyor/master/r-travis/scripts/travis-tool.sh -OutFile "..\travis-tool.sh" + echo '@bash.exe ../travis-tool.sh %*' | Out-File -Encoding ASCII .\travis-tool.sh.cmd + cat .\travis-tool.sh.cmd + bash -c "( echo; echo '^travis-tool\.sh\.cmd$' ) >> .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 }