From 7b8f938148d9a5e4c125582b3e4848ad2007e471 Mon Sep 17 00:00:00 2001
From: jasenfinch <jsf9@aber.ac.uk>
Date: Wed, 29 Mar 2023 18:10:39 +0100
Subject: [PATCH 1/4] Bump version to 0.6.2

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6b9bf7d..2068517 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: projecttemplates
 Title: Project Templates for Reproducible Research and Analyses
-Version: 0.6.1
+Version: 0.6.2
 Authors@R: 
     person(given = "Jasen",
            family = "Finch",

From 92adb3b1af2d0058743bf878215bdba508356f3f Mon Sep 17 00:00:00 2001
From: jasenfinch <jsf9@aber.ac.uk>
Date: Wed, 29 Mar 2023 18:14:41 +0100
Subject: [PATCH 2/4] Fix for renv initialisation when Bioconductor
 dependencies are included in argument `dependencies`

---
 R/renv.R | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/R/renv.R b/R/renv.R
index bd68f7c..a05a38b 100644
--- a/R/renv.R
+++ b/R/renv.R
@@ -29,8 +29,20 @@ renvInitialise <- function(project_directory,
                bare = TRUE)
     
     if (length(dependencies) > 0) {
-      renv::install(dependencies,project = project_directory)  
-    }
+      
+      if (!isFALSE(bioconductor)){
+        dependencies <- c(
+          'BiocManager',
+          dependencies
+        ) 
+      }
+      
+      dependencies %>%
+        lapply(
+          function(x,project_directory){renv::install(x,project = project_directory)},
+          project_directory = project_directory
+        )
+      }
     
     renv::hydrate(project = project_directory)
     

From 42ea0d6673c339d81918dc3b6c372911a0811ded Mon Sep 17 00:00:00 2001
From: jasenfinch <jsf9@aber.ac.uk>
Date: Wed, 29 Mar 2023 18:15:52 +0100
Subject: [PATCH 3/4] Update package NEWS

---
 NEWS.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 34ba075..3c5f348 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# projecttemplates 0.6.2
+
+* Fix for [`renv`](https://rstudio.github.io/renv/index.html) when Bioconductor dependencies are included in argument `dependencies`.
+
 # projecttemplates 0.6.1
 
 * Added the `sandbox` argument to `renvInitialise()` to allow the selection of whether sandboxing is used during [`renv`](https://rstudio.github.io/renv/index.html) initialisation.

From 5bb982b6ffac86374d559e06fd5fded6a435de35 Mon Sep 17 00:00:00 2001
From: jasenfinch <jsf9@aber.ac.uk>
Date: Wed, 29 Mar 2023 18:44:50 +0100
Subject: [PATCH 4/4] renv initialisation fix

---
 R/renv.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/renv.R b/R/renv.R
index a05a38b..42f583d 100644
--- a/R/renv.R
+++ b/R/renv.R
@@ -37,8 +37,8 @@ renvInitialise <- function(project_directory,
         ) 
       }
       
-      dependencies %>%
         lapply(
+          dependencies,
           function(x,project_directory){renv::install(x,project = project_directory)},
           project_directory = project_directory
         )