From 205d298a6ec213e760a587eaa9cc8652df50346d Mon Sep 17 00:00:00 2001 From: Waldir Leoncio Date: Mon, 11 Oct 2021 13:27:29 +0200 Subject: [PATCH 1/4] Opening CI for all branches Particularly useful for temporary branches like this one, that should be squashed and merged once CI is fixed. --- .github/workflows/r.yml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml index 3f112ec..e85adc6 100644 --- a/.github/workflows/r.yml +++ b/.github/workflows/r.yml @@ -10,12 +10,7 @@ # Determines when the action is triggered # # ======================================================== # -on: - push: - branches: [ develop ] - pull_request: - branches: [ develop ] - +on: [push, pull_request] name: R-CMD-check # ======================================================== # From ad2ef0e78938c020542cd4b14a6d374c261e100a Mon Sep 17 00:00:00 2001 From: Waldir Leoncio Date: Mon, 11 Oct 2021 13:57:03 +0200 Subject: [PATCH 2/4] Installing libcurl on Ubuntu VM --- .github/workflows/r.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml index e85adc6..cafd29d 100644 --- a/.github/workflows/r.yml +++ b/.github/workflows/r.yml @@ -65,6 +65,7 @@ jobs: - name: Installing system dependencies if: runner.os == 'Linux' run: | + apt install libcurl4-openssl-dev while read -r cmd do eval sudo $cmd From ee4d35ee857558422856fa9e6d7d9f338ead99d4 Mon Sep 17 00:00:00 2001 From: Waldir Leoncio Date: Mon, 11 Oct 2021 14:00:00 +0200 Subject: [PATCH 3/4] Fixup to apt command on ad2ef0e --- .github/workflows/r.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml index cafd29d..c78b346 100644 --- a/.github/workflows/r.yml +++ b/.github/workflows/r.yml @@ -65,7 +65,7 @@ jobs: - name: Installing system dependencies if: runner.os == 'Linux' run: | - apt install libcurl4-openssl-dev + sudo apt-get install libcurl4-openssl-dev while read -r cmd do eval sudo $cmd From aec2049a334b01e4f9e7352621ef7896e3eba45f Mon Sep 17 00:00:00 2001 From: Waldir Leoncio Date: Wed, 10 Nov 2021 12:24:00 +0100 Subject: [PATCH 4/4] Explicitly installing GenomicRanges --- .github/workflows/r.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml index c78b346..3f3ea2c 100644 --- a/.github/workflows/r.yml +++ b/.github/workflows/r.yml @@ -75,6 +75,7 @@ jobs: - name: Installing package dependencies run: | remotes::install_cran(c("rcmdcheck", "BiocManager")) + BiocManager::install("GenomicRanges") BiocManager::install("Rsamtools") remotes::install_deps(dependencies = TRUE) shell: Rscript {0}