mirror of
https://github.com/msberends/AMR.git
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(v1.1.0.9002) CI fix
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parent
5bdece1f9d
commit
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@ -23,6 +23,7 @@
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# chck <- rhub::check(devtools::build(), platform = rhub::platforms()[!is.na(rhub::platforms()$`cran-name`), 'name'])
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stages:
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- test
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- check
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- lint
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- website
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@ -53,9 +54,25 @@ before_script:
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- echo 'LANG="en_US.utf8"' >> .Renviron
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- echo 'LANGUAGE="en_US.utf8"' > ~/.Renviron
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R-release-test-only:
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stage: test
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when: always
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allow_failure: false
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script:
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- Rscript -e 'sessionInfo()'
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# install missing and outdated packages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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cache:
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key: release_4_0
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paths:
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- installed_deps/
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policy: pull # no uploading after run
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R-release:
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stage: check
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allow_failure: false
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when: on_success
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allow_failure: true
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script:
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- Rscript -e 'sessionInfo()'
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# install missing and outdated packages
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@ -80,6 +97,7 @@ R-release:
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R-devel:
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stage: check
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when: on_success
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image: rocker/r-devel
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allow_failure: true
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script:
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@ -107,7 +125,7 @@ R-devel:
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lintr:
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stage: lint
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allow_failure: true
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when: on_success
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when: always
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cache:
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key: release_4_0
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paths:
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@ -122,6 +140,7 @@ lintr:
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pages:
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stage: website
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allow_failure: true
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when: always
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only:
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- master
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@ -134,7 +153,7 @@ pages:
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codecovr:
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stage: coverage
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allow_failure: true
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when: on_success
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when: always
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cache:
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key: release_4_0
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paths:
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.1.0.9000
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Version: 1.1.0.9002
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Date: 2020-04-30
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.1.0.9000
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# AMR 1.1.0.9002
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## <small>Last updated: 30-Apr-2020</small>
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### Changed
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@ -51,7 +51,7 @@ matrix:
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- R_VERSION: "devel"
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build_script:
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- travis_tool.sh clean_library # turn off for caching, turn on for release of new R versions
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# - travis_tool.sh clean_library # turn off for caching, turn on for release of new R versions
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- travis_tool.sh install_deps
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test_script:
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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">1.1.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</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">1.1.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</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">1.1.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</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">1.1.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</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">1.1.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</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">1.1.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
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</span>
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</div>
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@ -229,9 +229,9 @@
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<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1-1-0-9000" class="section level1">
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<h1 class="page-header" data-toc-text="1.1.0.9000">
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<a href="#amr-1-1-0-9000" class="anchor"></a>AMR 1.1.0.9000<small> Unreleased </small>
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<div id="amr-1-1-0-9002" class="section level1">
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<h1 class="page-header" data-toc-text="1.1.0.9002">
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<a href="#amr-1-1-0-9002" class="anchor"></a>AMR 1.1.0.9002<small> Unreleased </small>
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</h1>
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<div id="last-updated-30-apr-2020" class="section level2">
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<h2 class="hasAnchor">
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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: 2020-04-30T07:04Z
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last_built: 2020-04-30T16:46Z
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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">1.1.0.9000</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
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</span>
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</div>
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@ -63,21 +63,20 @@ if [ -z "$3" ]; then
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# no version number set, so get latest tags to create it
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git pull --tags --quiet
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current_tag=`git describe --tags --abbrev=0 | sed 's/v//'`
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# current_commit=`git describe --tags | sed 's/.*-\(.*\)-.*/\1/'`
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if [ -z "current_tag" ]; then
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echo "FATAL - could not determine current tag"
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exit 1
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fi
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current_tag_dots=`echo $current_tag | grep -o "[.]" | wc -l`
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if (( "$current_tag_dots" < 3 )); then
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# contains two dots, so version number is like "1.0.0", commit nr is 0
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current_tag_full=`git describe --tags | sed 's/v//'`
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current_tag_dashes=`echo $current_tag_full | grep -o "[-]" | wc -l`
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if (( "$current_tag_dashes" < 1 )); then
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# so version number is like "1.0.0", commit nr is 0
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current_commit=0
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echo "---------------"
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echo "Mind NEWS.md! Assuming sequence number 9000."
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echo "---------------"
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else
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current_commit=`git describe --tags | sed 's/.*[.]//'`
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current_commit=`git describe --tags | sed 's/.*-\(.*\)-.*/\1/'`
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fi
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if [ -z "current_commit" ]; then
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echo "FATAL - could not determine last commit index number"
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