Merge pull request #227 from umccr/conda_deps2

Bump r-base to 4.3.3

.github/workflows/build_conda_recipes.yaml

@@ -5,7 +5,7 @@ on:
     branches:
       - master
       - bundle_update_2023
-      - conda_deps
+      - conda_deps2
 env:
   atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }}
   recipe_path: conda/recipe
@@ -30,7 +30,7 @@ jobs:
           environment-file: ${{ env.env_yml_path }}/condabuild.yml
       - name: 🐍 Conda pkg build and upload
         run: |
-          conda mambabuild ${recipe_path}/pcgrr -c umccr -c conda-forge -c bioconda --token ${atoken}
+          conda mambabuild ${recipe_path}/pcgrr -c conda-forge -c bioconda --token ${atoken}
   build_pcgr_conda_pkg:
     # When merging to one of the branches above and the commit message matches
     if: "startsWith(github.event.head_commit.message, 'Bump version:')"

conda/recipe/pcgrr/build.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 export DISABLE_AUTOBREW=1
-${R} -e "install.packages('devtools', repos = 'https://cloud.r-project.org/', lib = '${PREFIX}/lib/R/library')"
+${R} -e "install.packages('remotes', repos = 'https://cloud.r-project.org/', lib = '${PREFIX}/lib/R/library')"
 ${R} -e "install.packages('openxlsx2', repos = 'https://cloud.r-project.org/', lib = '${PREFIX}/lib/R/library')"
-${R} -e "devtools::install_github(repo = 'caravagnalab/CNAqc', ref = '274cde9', lib = '${PREFIX}/lib/R/library')"
+${R} -e "remotes::install_github(repo = 'caravagnalab/CNAqc', ref = '274cde9', lib = '${PREFIX}/lib/R/library')"
 ${R} CMD INSTALL --build . ${R_ARGS}

conda/recipe/pcgrr/meta.yaml

@@ -16,7 +16,7 @@ requirements:
   build:
     - git
   host:
-    - r-base ==4.2.3
+    - r-base ==4.3.3
     - r-assertable
     - r-assertthat
     - bioconductor-biostrings
@@ -48,7 +48,7 @@ requirements:
     - r-yaml
 
   run:
-    - r-base ==4.2.3
+    - r-base ==4.3.3
     - r-assertable
     - r-assertthat
     - bioconductor-biostrings