Merge remote-tracking branch 'official/master'

.buildkite/wilson-env.yml → .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

.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/*"

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.