Fix URIs matching error in sdrfToNfConf.R #8
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| name: R script check | |
| on: | |
| push: | |
| branches: | |
| - develop | |
| pull_request: | |
| branches: | |
| - develop | |
| jobs: | |
| run_script: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout code | |
| uses: actions/checkout@v3 | |
| - name: set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 3.6.3 | |
| - name: install devtools related dependencies | |
| run: sudo apt install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libcurl4-openssl-dev libbz2-dev liblzma-dev | |
| - name: install dependencies | |
| run: | | |
| Rscript -e 'install.packages(c("data.table", "optparse", "devtools"))' | |
| Rscript -e 'devtools::install_github("ebi-gene-expression-group/workflow-scripts-common")' | |
| - name: run test | |
| run: | | |
| set -e | |
| out_test1=$(pwd)/test1 | |
| Rscript bin/sdrfToNfConf.R --sdrf=tests/E-MTAB-4850.homo_sapiens.sdrf.txt --idf=tests/E-MTAB-4850.homo_sapiens.idf.txt --name=E-MTAB-4850 --verbose --out_conf $out_test1 | |
| - name: check for errors | |
| run: Rscript -e 'stopifnot(identical(geterrmessage(), ""))' |