Switch to rocker/r2u to speed up dependency installation.

broadinstitute · Mar 13, 2024 · 17a94e5 · 17a94e5
1 parent d656f8c
commit 17a94e5
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Showing 4 changed files with 25 additions and 38 deletions.
diff --git a/.github/workflows/DropSeq.dropulation.r.yml b/.github/workflows/DropSeq.dropulation.r.yml
@@ -18,23 +18,20 @@ on:
 permissions:
   contents: read
 
+# See https://dirk.eddelbuettel.com/blog/code/r4/ for using r2u to speed up dependency loading
 jobs:
   build:
-    runs-on: macos-latest
-    strategy:
-      matrix:
-        r-version: ['4.1.1']
-
+    runs-on: ubuntu-latest
+    container:
+      image: rocker/r2u:latest
     steps:
       - uses: actions/checkout@v3
-      - name: Set up R ${{ matrix.r-version }}
-        uses: r-lib/actions/setup-r@f57f1301a053485946083d7a45022b278929a78a
-        with:
-          r-version: ${{ matrix.r-version }}
+      - name: SessionInfo
+        run: R -q -e 'sessionInfo()'
       - name: Install dependencies
         run: |
           setwd("src/R/packages/DropSeq.dropulation")
-          install.packages(c("remotes", "rcmdcheck"))
+          install.packages(c("rcmdcheck"))
           remotes::install_deps(dependencies = TRUE)
         shell: Rscript {0}
         env:

diff --git a/.github/workflows/DropSeq.utilities.r.yml b/.github/workflows/DropSeq.utilities.r.yml
@@ -20,21 +20,17 @@ permissions:
 
 jobs:
   build:
-    runs-on: macos-latest
-    strategy:
-      matrix:
-        r-version: ['4.1.1']
-
+    runs-on: ubuntu-latest
+    container:
+      image: rocker/r2u:latest
     steps:
       - uses: actions/checkout@v3
-      - name: Set up R ${{ matrix.r-version }}
-        uses: r-lib/actions/setup-r@f57f1301a053485946083d7a45022b278929a78a
-        with:
-          r-version: ${{ matrix.r-version }}
+      - name: SessionInfo
+        run: R -q -e 'sessionInfo()'
       - name: Install dependencies
         run: |
           setwd("src/R/packages/DropSeq.utilities")
-          install.packages(c("remotes", "rcmdcheck"))
+          install.packages(c("rcmdcheck"))
           remotes::install_deps(dependencies = TRUE)
         shell: Rscript {0}
       - name: Check

diff --git a/src/R/packages/DropSeq.dropulation/README.md b/src/R/packages/DropSeq.dropulation/README.md
@@ -8,17 +8,14 @@ Dropulation and Dropulation census functions.
 
 ## Installation
 
-You can install the development version of DropSeq.dropulation from [GitHub](https://github.com/) with:
+The preferred installation method is to go to the latest release in 
+[Releases](https://github.com/broadinstitute/Drop-seq/releases) and follow the
+ instructions there.
 
-``` r
-# install.packages("devtools")
-devtools::install_github("broadinstitute/Drop-seq", subdir="src/R/packages/DropSeq.dropulation")
-```
-
-To install a tagged version v1.2.3:
+It is not recommended to install the latest version of DropSeq.dropulation from 
+[GitHub](https://github.com/), because it is not necessarily stable, but if you choose to do so:
 
 ``` r
 # install.packages("devtools")
-devtools::install_github("broadinstitute/Drop-seq", subdir="src/R/packages/DropSeq.dropulation", ref="v1.2.3")
+devtools::install_github("broadinstitute/Drop-seq", subdir="src/R/packages/DropSeq.dropulation")
 ```
-
diff --git a/src/R/packages/DropSeq.utilities/README.md b/src/R/packages/DropSeq.utilities/README.md
@@ -8,18 +8,15 @@ DropSeq.utilities contains trivial functions to support other DropSeq R packages
 
 ## Installation
 
-You can install the development version of DropSeq.utilities from [GitHub](https://github.com/) with:
+The preferred installation method is to go to the latest release in
+[Releases](https://github.com/broadinstitute/Drop-seq/releases) and follow the
+instructions there.
 
-``` r
-# install.packages("devtools")
-devtools::install_github("broadinstitute/Drop-seq", subdir="src/R/packages/DropSeq.utilities")
-```
-
-To install a tagged version v1.2.3:
+It is not recommended to install the latest version of DropSeq.utilities from
+[GitHub](https://github.com/), because it is not necessarily stable, but if you choose to do so:
 
 ``` r
 # install.packages("devtools")
-devtools::install_github("broadinstitute/Drop-seq", subdir="src/R/packages/DropSeq.utilities", ref="v1.2.3")
+devtools::install_github("broadinstitute/Drop-seq", subdir="src/R/packages/DropSeq.utilities")
 ```
 
-