From fd567ad29fb11fb3e9a7c10bc800e7751f9d52bf Mon Sep 17 00:00:00 2001
From: phauchamps <philippehauchamps@hotmail.com>
Date: Tue, 9 Jan 2024 16:07:36 +0100
Subject: [PATCH] testing again with GHA workflow (wip)

---
 .github/workflows/check-bioc.yml | 65 ++++++++++++++------------------
 1 file changed, 28 insertions(+), 37 deletions(-)

diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
index b199649..0a6462c 100644
--- a/.github/workflows/check-bioc.yml
+++ b/.github/workflows/check-bioc.yml
@@ -173,47 +173,38 @@ jobs:
         run: |
           BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
         shell: Rscript {0}
-        
-      - name: pre-install rlang with specific c-compiler flags
+
+      - name: Install dependencies
         run: |
           withr::with_makevars(
             c(CFLAGS = "-w",
               CXXFLAGS = "-w"),
-            BiocManager::install("rlang"),
-            assignment = "+=")
-        shell: Rscript {0}  
+            {
+                ## Try installing the package dependencies in steps. First the local
+                ## dependencies, then any remaining dependencies to avoid the
+                ## issues described at
+                ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
+                ## https://github.com/r-lib/remotes/issues/296
+                ## Ideally, all dependencies should get installed in the first pass.
+    
+                ## Pass #1 at installing dependencies
+                message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
+                local_deps <- remotes::local_package_deps(dependencies = TRUE)
+                deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
+                BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]])
         
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}  
-
-      - name: Install dependencies
-        run: |
-          ## Try installing the package dependencies in steps. First the local
-          ## dependencies, then any remaining dependencies to avoid the
-          ## issues described at
-          ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
-          ## https://github.com/r-lib/remotes/issues/296
-          ## Ideally, all dependencies should get installed in the first pass.
-
-          ## Pass #1 at installing dependencies
-          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
-          local_deps <- remotes::local_package_deps(dependencies = TRUE)
-          deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
-          BiocManager::install(local_deps[local_deps %in% deps$package[deps$diff != 0]])
-
-          ## Pass #2 at installing dependencies
-          message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
-          deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
-          BiocManager::install(deps$package[deps$diff != 0])
-
-          ## For running the checks
-          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
-          remotes::install_cran("rcmdcheck")
-          BiocManager::install("BiocCheck")
+                ## Pass #2 at installing dependencies
+                message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
+                deps <- remotes::dev_package_deps(dependencies = TRUE, repos = BiocManager::repositories())
+                BiocManager::install(deps$package[deps$diff != 0])
+    
+                ## For running the checks
+                message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
+                remotes::install_cran("rcmdcheck")
+                BiocManager::install("BiocCheck") 
+            },
+            assignment = "+=")
+          
         shell: Rscript {0}
         
       - name: Session info
@@ -267,7 +258,7 @@ jobs:
         ##if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         if: env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
-          remotes::install_github("r-lib/pkgdown"),
+          remotes::install_github("r-lib/pkgdown")
         shell: Rscript {0}
 
       - name: Session info