diff --git a/.buildkite/wilson-env.yml b/.buildkite/environment.yml similarity index 77% rename from .buildkite/wilson-env.yml rename to .buildkite/environment.yml index edf27f7..84ff75b 100644 --- a/.buildkite/wilson-env.yml +++ b/.buildkite/environment.yml @@ -1,8 +1,7 @@ -name: wilson channels: - - defaults - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - r-base - r-shiny @@ -17,12 +16,9 @@ dependencies: - r-shinyjs - r-viridis - r-rje -# - r-grdevices # base package -# - r-grid # base package - r-plyr - r-circlize - bioconductor-complexheatmap -# - r-stats # base package - r-gplots - r-reshape - r-rintrojs @@ -38,11 +34,11 @@ dependencies: - r-shinycssloaders - r-log4r - r-openssl -# - r-methods # base package - r-r6 + - r-stringi >=1.2.3 - r-devtools - - "readline==6.3" - r-roxygen2 - r-rmarkdown - r-testthat -# - r-vdiffr # not yet in conda-forge + - r-vdiffr + - qpdf diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index 1fbcec0..2032985 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -1,14 +1,11 @@ steps: - - label: "Build Conda-environment" + - label: ":stopwatch: Running checks for Wilson" command: -# - "conda env create -f .buildkite/wilson-env.yml --force" - - ". /etc/profile.d/conda.sh" - - "conda activate wilson" -# - "Rscript -e 'install.packages(\"rje\")'" - "R CMD build ." - "R CMD check *tar.gz --as-cran" - -# - wait - -# - label: "Package check" -# command: + plugins: + https://github.com/loosolab/conda-buildkite-plugin.git#v0.1.0: + environment: .buildkite/environment.yml + update: true + artifact_paths: + - "wilson.Rcheck/*" diff --git a/README.md b/README.md index d55d544..49ba437 100644 --- a/README.md +++ b/README.md @@ -42,7 +42,7 @@ CLARION is a data format especially developed to be used with WIlsON, which reli Please check the following link for details considering the [CLARION format](https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format/). ## How to cite -*Schultheis H, Kuenne C, Preussner J, Wiegandt R, Fust A, Bentsen M, Looso M*. WIlsON: Webbased Interactive Omics VisualizatioN. (2018), doi: https://XY +*Schultheis H, Kuenne C, Preussner J, Wiegandt R, Fust A, Bentsen M, Looso M*. WIlsON: Webbased Interactive Omics VisualizatioN. (2018), doi: https://doi.org/10.1093/bioinformatics/bty711 ## License This project is licensed under the MIT license.