From 17a94e5ed9dd2927bad6f8b43dee415b6d302458 Mon Sep 17 00:00:00 2001 From: Alec Wysoker Date: Wed, 13 Mar 2024 10:13:14 -0400 Subject: [PATCH] Switch to rocker/r2u to speed up dependency installation. --- .github/workflows/DropSeq.dropulation.r.yml | 17 +++++++---------- .github/workflows/DropSeq.utilities.r.yml | 16 ++++++---------- src/R/packages/DropSeq.dropulation/README.md | 15 ++++++--------- src/R/packages/DropSeq.utilities/README.md | 15 ++++++--------- 4 files changed, 25 insertions(+), 38 deletions(-) diff --git a/.github/workflows/DropSeq.dropulation.r.yml b/.github/workflows/DropSeq.dropulation.r.yml index 6fdf7288..e4616cbf 100644 --- 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 index 5588c889..49b7b2d4 100644 --- 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 index 28847300..4486f9f5 100644 --- 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 index 72c61506..a24a6af2 100644 --- 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") ``` -