13076: Get rid of pkgdown, just call knitr

Converts README.Rmd to README.html for documentation.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

diff --git a/build/run-tests.sh b/build/run-tests.sh
index b89c8d9e5bc51c6f0acd1b1938ad1cd540192f15..f567cf41d586bb24993b9543bb8ec814396ea169 100755 (executable)
--- a/build/run-tests.sh
+++ b/build/run-tests.sh
@@ -246,9 +246,9 @@ sanity_checks() {
     if [[ "$NEED_SDK_R" = true ]]; then
       # R SDK stuff
       echo -n 'R: '
-      which R || fatal "No R. Try: apt-get install r-base"
+      which Rscript || fatal "No Rscript. Try: apt-get install r-base"
       echo -n 'testthat: '
-      R -q -e "library('testthat')" || fatal "No testthat. Try: apt-get install r-cran-testthat"
+      Rscript -e "library('testthat')" || fatal "No testthat. Try: apt-get install r-cran-testthat"
       # needed for roxygen2, needed for devtools, needed for R sdk
       pkg-config --exists libxml-2.0 || fatal "No libxml2. Try: apt-get install libxml2-dev"
       # needed for pkgdown, builds R SDK doc pages
@@ -802,7 +802,7 @@ do_install sdk/ruby ruby_sdk
 install_R_sdk() {
   if [[ "$NEED_SDK_R" = true ]]; then
     cd "$WORKSPACE/sdk/R" \
-       && R --quiet --vanilla --file=install_deps.R
+       && Rscript --vanilla install_deps.R
   fi
 }
 do_install sdk/R R_sdk
@@ -981,7 +981,7 @@ do_test sdk/ruby ruby_sdk
 test_R_sdk() {
   if [[ "$NEED_SDK_R" = true ]]; then
     cd "$WORKSPACE/sdk/R" \
-        && R --quiet --file=run_test.R
+        && Rscript --vanilla run_test.R
   fi
 }
 

diff --git a/doc/Rakefile b/doc/Rakefile
index eaa5410100992dfc8bc4482e2b6974d54b0ff8a0..4870eb19e246621c76589213c22ed2f9f31bef85 100644 (file)
--- a/doc/Rakefile
+++ b/doc/Rakefile
@@ -29,10 +29,10 @@ file "sdk/R/arvados/index.html" do |t|
   `which R`
   if $? == 0
     Dir.chdir("../sdk/R/") do
-      STDERR.puts `R --quiet --vanilla -e 'pkgdown::build_site()' 2>&1`
+      STDERR.puts `Rscript createDoc.R README.Rmd index.html 2>&1`
     end
     raise if $? != 0
-    cp_r("../sdk/R/docs", "sdk/R/arvados")
+    cp_r("../sdk/R/README.html", "sdk/R/")
   else
     puts "Warning: R not found, R documentation will not be generated".colorize(:light_red)
   end

diff --git a/doc/sdk/R/index.html.textile.liquid b/doc/sdk/R/index.html.textile.liquid
index 7b788a16a5e6f04d231b162a32456432a0dbee63..1d7803a48a1aa613880fc88a575fa3cd1615c6a6 100644 (file)
--- a/doc/sdk/R/index.html.textile.liquid
+++ b/doc/sdk/R/index.html.textile.liquid
@@ -12,4 +12,4 @@ Copyright (C) The Arvados Authors. All rights reserved.
 SPDX-License-Identifier: CC-BY-SA-3.0
 {% endcomment %}
 
-notextile. <iframe src="arvados/" style="width:100%; height:100%; border:none" />
+notextile. <iframe src="README.html" style="width:100%; height:100%; border:none" />

diff --git a/sdk/R/install_deps.R b/sdk/R/install_deps.R
index a54a9a23facdda1769520e7d653b976c293ce4bd..5314c86e28b0d3d7352733943019a3602dbf019b 100644 (file)
--- a/sdk/R/install_deps.R
+++ b/sdk/R/install_deps.R
@@ -5,14 +5,11 @@ if (!requireNamespace("devtools")) {
 if (!requireNamespace("roxygen2")) {
   install.packages("roxygen2")
 }
-
-# These install from github so install known-good versions instead of
-# letting any push to master break our build.
-if (!requireNamespace("pkgload")) {
-  devtools::install_github("r-lib/pkgload", ref="7a97de62adf1793c03e73095937e4655baad79c9")
+if (!requireNamespace("knitr")) {
+  install.packages("knitr")
 }
-if (!requireNamespace("pkgdown")) {
-  devtools::install_github("r-lib/pkgdown", ref="897ffbc016549c11c4263cb5d1f6e9f5c99efb45")
+if (!requireNamespace("markdown")) {
+  install.packages("markdown")
 }
 
 devtools::install_dev_deps()