From 4dbf9aa328c34d23e2b548fa7678efd3f2c8488c Mon Sep 17 00:00:00 2001
From: jgw17 <jweberpals@bwh.harvard.edu>
Date: Tue, 18 Jul 2023 13:15:34 -0400
Subject: [PATCH] using r-ver docker image for PRPM access
---
.gitlab-ci.yml | 76 +++++++++++++++++++++++++++++++-------------------
1 file changed, 48 insertions(+), 28 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 69503dc..a1f8046 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,4 +1,4 @@
-image: rocker/tidyverse:4.2.1
+image: rocker/r-ver:latest
default:
tags:
@@ -11,66 +11,86 @@ stages:
- build
- deploy
+variables:
+ RENV_CONFIG_REPOS_OVERRIDE: "http://cran.r-project.org"
+ RENV_PATHS_CACHE: ${CI_PROJECT_DIR}/cache
+ RENV_PATHS_LIBRARY: ${CI_PROJECT_DIR}/renv/library
+
+cache:
+ key: ${CI_JOB_NAME}
+ paths:
+ - ${RENV_PATHS_CACHE}
+ - ${RENV_PATHS_LIBRARY}
+
before_script:
- - apt-get update
+ - Rscript -e "if (!requireNamespace('renv', quietly = TRUE)) install.packages('renv')"
+ - Rscript -e "renv::restore()"
check:
stage: check
script:
- - r -e 'devtools::check(vignettes = FALSE)'
+ - r -e 'devtools::check()'
artifacts:
- expire_in: 1 day
+ expire_in: 1 min
checkerrors:
stage: check
script:
- r -e 'if (!identical(devtools::check(vignettes = FALSE, document = FALSE, args = "--no-tests")[["errors"]], character(0))) stop("Check with Errors")'
artifacts:
- expire_in: 1 day
+ expire_in: 1 min
checkwarnings:
stage: check
script:
- r -e 'if (!identical(devtools::check(vignettes = FALSE, document = FALSE, args = "--no-tests")[["warnings"]], character(0))) stop("Check with Warnings")'
artifacts:
- expire_in: 1 day
+ expire_in: 1 min
checknotes:
stage: check
script:
- r -e 'if (!identical(devtools::check(vignettes = FALSE, document = FALSE, args = "--no-tests")[["notes"]], character(0))) stop("Check with Notes")'
artifacts:
- expire_in: 1 day
+ expire_in: 1 min
-# unittests:
-# stage: test
-# script:
-# - r -e 'if (any(as.data.frame(devtools::test())[["failed"]] > 0)) stop("Some tests failed.")'
+CRANcheck:
+ stage: check
+ script:
+ - r -e 'devtools::check(remote = TRUE, manual = TRUE)'
+ artifacts:
+ expire_in: 1 min
-# testcov:
-# stage: test
-# script:
-# - r -e "install.packages(c('covr', 'DT'))"
-# - r -e 'devtools::test_coverage()'
+unittests:
+ stage: test
+ script:
+ - r -e 'if (any(as.data.frame(devtools::test())[["failed"]] > 0)) stop("Some tests failed.")'
+ artifacts:
+ expire_in: 1 min
install:
stage: install
script:
- r -e 'devtools::install()'
artifacts:
- expire_in: 1 day
+ expire_in: 1 min
-# buildbinary:
-# stage: build
-# script:
-# - r -e 'devtools::build(binary = TRUE)'
+buildbinary:
+ stage: build
+ script:
+ - r -e 'devtools::build()'
+ artifacts:
+ expire_in: 1 min
-# buildsite:
-# stage: deploy
-# script:
-# - Rscript -e 'install.packages(c("covr", "DT"))'
-# - r -e 'covr::gitlab(file = "coverage.html")'
-# - r -e 'build_site()'
+buildsite:
+ stage: deploy
+ script:
+ - r -e 'covr::gitlab()'
+ - r -e 'pkgdown::build_site()'
+ artifacts:
+ paths:
+ - public
+ expire_in: 1 min
pages:
stage: deploy
@@ -79,6 +99,6 @@ pages:
artifacts:
paths:
- public
- expire_in: 1 day
+ expire_in: 1 min
rules:
- if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
--
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