11876: Pin R deps that are installed from gitub.

[arvados.git] / build / run-tests.sh

diff --git a/build/run-tests.sh b/build/run-tests.sh
index a02f732cb374e05f8dccfb3dadc9867c42e9456b..48b3eab38ac864ab0c66d4a40d17502f60d4cdb3 100755 (executable)
--- a/build/run-tests.sh
+++ b/build/run-tests.sh
@@ -74,6 +74,7 @@ doc
 lib/cli
 lib/cmd
 lib/crunchstat
+lib/dispatchcloud
 services/api
 services/arv-git-httpd
 services/crunchstat
@@ -108,6 +109,7 @@ sdk/go/asyncbuf
 sdk/go/stats
 sdk/go/crunchrunner
 sdk/cwl
+sdk/R
 tools/sync-groups
 tools/crunchstat-summary
 tools/keep-exercise
@@ -132,6 +134,7 @@ VENV3DIR=
 PYTHONPATH=
 GEMHOME=
 PERLINSTALLBASE=
+R_LIBS=
 
 short=
 only_install=
@@ -239,6 +242,16 @@ sanity_checks() {
     which Xvfb || fatal "No xvfb. Try: apt-get install xvfb"
     echo -n 'graphviz: '
     dot -V || fatal "No graphviz. Try: apt-get install graphviz"
+
+    # R SDK stuff
+    echo -n 'R: '
+    which R || fatal "No R. Try: apt-get install r-base"
+    echo -n 'testthat: '
+    R -q -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
+    which pandoc || fatal "No pandoc. Try: apt-get install pandoc"
 }
 
 rotate_logfile() {
@@ -367,7 +380,7 @@ if [[ -z "$temp" ]]; then
 fi
 
 # Set up temporary install dirs (unless existing dirs were supplied)
-for tmpdir in VENVDIR VENV3DIR GOPATH GEMHOME PERLINSTALLBASE
+for tmpdir in VENVDIR VENV3DIR GOPATH GEMHOME PERLINSTALLBASE R_LIBS
 do
     if [[ -z "${!tmpdir}" ]]; then
         eval "$tmpdir"="$temp/$tmpdir"
@@ -476,6 +489,7 @@ setup_virtualenv() {
 export PERLINSTALLBASE
 export PERLLIB="$PERLINSTALLBASE/lib/perl5:${PERLLIB:+$PERLLIB}"
 
+export R_LIBS
 
 export GOPATH
 mkdir -p "$GOPATH/src/git.curoverse.com"
@@ -765,6 +779,12 @@ install_ruby_sdk() {
 }
 do_install sdk/ruby ruby_sdk
 
+install_R_sdk() {
+    cd "$WORKSPACE/sdk/R" \
+       && R --quiet --vanilla --file=install_deps.R
+}
+do_install sdk/R R_sdk
+
 install_perl_sdk() {
     cd "$WORKSPACE/sdk/perl" \
         && perl Makefile.PL INSTALL_BASE="$PERLINSTALLBASE" \
@@ -857,6 +877,7 @@ gostuff=(
     lib/cli
     lib/cmd
     lib/crunchstat
+    lib/dispatchcloud
     sdk/go/arvados
     sdk/go/arvadosclient
     sdk/go/blockdigest
@@ -935,6 +956,12 @@ test_ruby_sdk() {
 }
 do_test sdk/ruby ruby_sdk
 
+test_R_sdk() {
+    cd "$WORKSPACE/sdk/R" \
+        && R --quiet --file=run_test.R
+}
+do_test sdk/R R_sdk
+
 test_cli() {
     cd "$WORKSPACE/sdk/cli" \
         && mkdir -p /tmp/keep \