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(v1.1.0.9008) lose dependencies

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dr. M.S. (Matthijs) Berends 2020-05-17 11:56:12 +02:00
parent f68d71a5e0
commit 071bdc5a9e
11 changed files with 44 additions and 26 deletions
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4
.gitlab-ci.yml
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@ -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# install missing and outdated packages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# install missing and outdated packages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# install missing and outdated packages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# install missing and outdated packages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

7
DESCRIPTION
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@ -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) <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,

4
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.1.0.9007
## <small>Last updated: 16-May-2020</small>
# AMR 1.1.0.9008
## <small>Last updated: 17-May-2020</small>
### Breaking
* Removed previously deprecated function `p.symbol()` - it was replaced with `p_symbol()`

2
docs/404.html
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@ -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>

2
docs/LICENSE-text.html
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@ -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>

2
docs/articles/index.html
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@ -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>

2
docs/authors.html
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@ -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>

2
docs/index.html
View File

@ -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>

2
docs/pkgdown.yml
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@ -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

2
docs/reference/index.html
View File

@ -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>

41
tests/appveyor/appveyor_tool.ps1
View File

@ -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
}