From b48e609afe629bf5edfcd537f6aeff2b7655d570 Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Sat, 5 Jan 2019 09:50:22 +0100
Subject: [PATCH] gitlab pkg cache

---
 .Rbuildignore  |  4 ++--
 .gitlab-ci.R   | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++
 .gitlab-ci.yml | 25 ++++++++++++++--------
 3 files changed, 74 insertions(+), 11 deletions(-)
 create mode 100644 .gitlab-ci.R

diff --git a/.Rbuildignore b/.Rbuildignore
index ac953bdc..98066496 100755
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,5 +1,7 @@
 ^.*\.Rproj$
 ^\.gitlab-ci\.yml$
+^\.gitlab-ci\.R$
+^\.Renviron$
 ^\.Rprofile$
 ^\.Rproj\.user$
 ^\.travis\.yml$
@@ -7,7 +9,6 @@
 ^_noinclude$
 ^_pkgdown\.yml$
 ^appveyor\.yml$
-^ci.R$
 ^cran-comments\.md$
 ^CRAN-RELEASE$
 ^doc$
@@ -17,6 +18,5 @@
 ^index\.md$
 ^installed_deps$
 ^Meta$
-^packrat/
 ^pkgdown$
 ^public$
diff --git a/.gitlab-ci.R b/.gitlab-ci.R
new file mode 100644
index 00000000..6993de43
--- /dev/null
+++ b/.gitlab-ci.R
@@ -0,0 +1,56 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# AUTHORS                                                              #
+# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)           #
+#                                                                      #
+# LICENCE                                                              #
+# This package is free software; you can redistribute it and/or modify #
+# it under the terms of the GNU General Public License version 2.0,    #
+# as published by the Free Software Foundation.                        #
+#                                                                      #
+# This R package is distributed in the hope that it will be useful,    #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of       #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the        #
+# GNU General Public License version 2.0 for more details.             #
+# ==================================================================== #
+
+install_if_needed <- function(pkg, repos, quiet) {
+  package_path <- find.package(pkg, quiet = quiet)
+  if (length(package_path) == 0) {
+    message("NOTE: pkg ", pkg, " missing, installing...")
+    install.packages(pkg, repos = repos, quiet = quiet)
+  }
+}
+
+gl_update_pkg_all <- function(repos = "https://cran.rstudio.com",
+                              quiet = TRUE,
+                              install_pkgdown = FALSE) {
+  # update existing
+  update.packages(ask = FALSE, repos = repos, quiet = quiet)
+
+  install_if_needed(pkg = "devtools", repos = repos, quiet = quiet)
+  if (install_pkgdown = TRUE) {
+    install_if_needed(pkg = "pkgdown", repos = repos, quiet = quiet)
+  }
+
+  devtools::install_dev_deps(repos = repos, quiet = quiet, upgrade = TRUE)
+
+  cat("\nINSTALLED:\n\n")
+  instld <- as.data.frame(installed.packages())
+  rownames(instld) <- NULL
+  print(instld[, c("Package", "Version")])
+
+  return(invisible(TRUE))
+
+  # which ones are needed now?
+  # pkg_needed <-
+
+  # if (length(pkg_needed) > 0) {
+  #  # install them
+  #  for (i %in% 1:length(pkg_needed)) {
+  #    install_if_needed(pkg = pkg_needed[i], repos = repos, quiet = quiet)
+  #  }
+  # }
+}
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ee6b3f62..12e62691 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -29,16 +29,23 @@ stages:
   - test
   - deploy
 
-image: debian:buster-slim
+image: debian:stretch-slim
 
 before_script:
   - apt-get update
-  # install dependencies for package
+  # install dependencies for packages
   - apt-get -y install libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev pandoc r-base
-  - mkdir installed_deps
-  - Rscript -e '.libPaths("installed_deps")'
-  - Rscript -e 'install.packages(c("devtools", "rlang"), repos = "https://cran.rstudio.com")'
-  - Rscript -e 'devtools::install_dev_deps(repos = "https://cran.rstudio.com")'
+  # cache R packages
+  - mkdir -p installed_deps
+  - echo 'R_LIBS="installed_deps"' > .Renviron
+  - echo 'R_LIBS_USER="installed_deps"' >> .Renviron
+  - echo 'R_LIBS_SITE="installed_deps"' >> .Renviron
+  - Rscript -e '.libPaths()'
+  # install missing and outdated packages
+  - Rscript -e 'source(".gitlab-ci.R")'
+  - Rscript -e 'gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
+  #- Rscript -e 'install.packages(c("devtools", "rlang"), repos = "https://cran.rstudio.com", quiet = TRUE)'
+  #- Rscript -e 'devtools::install_dev_deps(repos = "https://cran.rstudio.com", quiet = TRUE)'
 
 cache:
   key: "$CI_COMMIT_REF_SLUG"
@@ -50,8 +57,8 @@ R 3:
   allow_failure: true
   script:
     # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
-    - rm -rf vignettes
-    - Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
+    #- rm -rf vignettes
+    #- Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
     # build package
     - R CMD build . --no-build-vignettes --no-manual
     - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
@@ -79,7 +86,7 @@ pages:
   only:
     - master
   script:
-    - Rscript -e "install.packages('pkgdown', repos = 'https://cran.rstudio.com')"
+    #- Rscript -e "install.packages('pkgdown', repos = 'https://cran.rstudio.com')"
     - Rscript -e "devtools::install(build = TRUE, upgrade = FALSE)"
     - R -e "pkgdown::build_site(examples = FALSE, override = list(destination = 'public'))"
   artifacts: