From 2e9ec368c81a68b5737a3a8a3a968079077ae56e Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Fri, 31 May 2024 22:52:41 +1000
Subject: [PATCH 1/2] openxlsx2: install from conda

---
 DESCRIPTION                 | 2 --
 conda/recipe/cpsr/build.sh  | 1 -
 conda/recipe/cpsr/meta.yaml | 4 ++++
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a34424b..17a4c4d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -45,8 +45,6 @@ Imports:
 Depends:
     R (>= 4.0)
 Suggests:
-    testthat,
-    devtools,
     BSgenome.Hsapiens.UCSC.hg19,
     BSgenome.Hsapiens.UCSC.hg38,
     knitr,
diff --git a/conda/recipe/cpsr/build.sh b/conda/recipe/cpsr/build.sh
index f9f5ea7..a42a6a2 100644
--- a/conda/recipe/cpsr/build.sh
+++ b/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}
diff --git a/conda/recipe/cpsr/meta.yaml b/conda/recipe/cpsr/meta.yaml
index 92d7d31..6239b99 100644
--- a/conda/recipe/cpsr/meta.yaml
+++ b/conda/recipe/cpsr/meta.yaml
@@ -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

From 17b5de311614fd56a6d4e9e9124a4e7728dcc5a5 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Sat, 1 Jun 2024 01:15:20 +1000
Subject: [PATCH 2/2] =?UTF-8?q?Bump=20version:=201.0.1.9006=20=E2=86=92=20?=
 =?UTF-8?q?1.0.1.9007?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .bumpversion.cfg                   | 2 +-
 .github/workflows/build_conda.yaml | 2 +-
 DESCRIPTION                        | 2 +-
 conda/env/yml/pkgdown.yml          | 2 +-
 conda/recipe/cpsr/meta.yaml        | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index 64c07e6..1c1aece 100644
--- a/.bumpversion.cfg
+++ b/.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+))?
diff --git a/.github/workflows/build_conda.yaml b/.github/workflows/build_conda.yaml
index e0cd857..10ea19a 100644
--- a/.github/workflows/build_conda.yaml
+++ b/.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
diff --git a/DESCRIPTION b/DESCRIPTION
index 17a4c4d..b60be44 100644
--- a/DESCRIPTION
+++ b/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",
diff --git a/conda/env/yml/pkgdown.yml b/conda/env/yml/pkgdown.yml
index 80b11e0..ee1fa66 100644
--- a/conda/env/yml/pkgdown.yml
+++ b/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
diff --git a/conda/recipe/cpsr/meta.yaml b/conda/recipe/cpsr/meta.yaml
index 6239b99..4c61097 100644
--- a/conda/recipe/cpsr/meta.yaml
+++ b/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: ../../../