Merge branch 'bundle_update_2023' of github.com:sigven/cpsr into bund…

…le_update_2023

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.1.9006
+current_version = 1.0.1.9007
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<dev>\d+))?

.github/workflows/build_conda.yaml

@@ -9,7 +9,7 @@ env:
   atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }}
   recipe_path: conda/recipe
   env_yml_path: conda/env/yml
-  VERSION: '1.0.1.9006' # versioned by bump2version
+  VERSION: '1.0.1.9007' # versioned by bump2version
 jobs:
   build_conda_pkgs:
     # When merging to one of the branches above and the commit message matches

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: cpsr
 Type: Package
 Title: Cancer Predisposition Sequencing Reporter (CPSR)
-Version: 1.0.1.9006
+Version: 1.0.1.9007
 Date: 2024-05-27
 Authors@R:
     c(person(given = "Sigve",
@@ -45,8 +45,6 @@ Imports:
 Depends:
     R (>= 4.0)
 Suggests:
-    testthat,
-    devtools,
     BSgenome.Hsapiens.UCSC.hg19,
     BSgenome.Hsapiens.UCSC.hg38,
     knitr,

conda/env/yml/pkgdown.yml

@@ -5,6 +5,6 @@ channels:
   - bioconda
 dependencies:
   - r-pcgrr
-  - r-cpsr ==1.0.1.9006 # versioned by bump2version
+  - r-cpsr ==1.0.1.9007 # versioned by bump2version
   - r-pkgdown
   - pandoc

conda/recipe/cpsr/build.sh

@@ -1,5 +1,4 @@
 #!/bin/bash
 
 export DISABLE_AUTOBREW=1
-${R} -e "install.packages('openxlsx2', repos = 'https://cloud.r-project.org/', lib = '${PREFIX}/lib/R/library')"
 ${R} CMD INSTALL --build . ${R_ARGS}

conda/recipe/cpsr/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: r-cpsr
-  version: 1.0.1.9006 # versioned by bump2version
+  version: 1.0.1.9007 # versioned by bump2version
 
 source:
   path: ../../../
@@ -17,10 +17,12 @@ requirements:
     - git
   host:
     - r-base ==4.3.3
+    - r-assertable
     - r-assertthat
     - r-dplyr
     - r-ggplot2
     - r-glue
+    - r-openxlsx2
     - r-pcgrr
     - r-quarto
     - quarto
@@ -31,10 +33,12 @@ requirements:
     - r-tidyr
   run:
     - r-base
+    - r-assertable
     - r-assertthat
     - r-dplyr
     - r-ggplot2
     - r-glue
+    - r-openxlsx2
     - r-pcgrr
     - r-quarto
     - quarto