sdk/go/stats
sdk/go/crunchrunner
sdk/cwl
+sdk/R
tools/sync-groups
tools/crunchstat-summary
tools/keep-exercise
PYTHONPATH=
GEMHOME=
PERLINSTALLBASE=
+R_LIBS=
short=
only_install=
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() {
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"
export PERLINSTALLBASE
export PERLLIB="$PERLINSTALLBASE/lib/perl5:${PERLLIB:+$PERLLIB}"
+export R_LIBS
export GOPATH
mkdir -p "$GOPATH/src/git.curoverse.com"
}
do_install sdk/ruby ruby_sdk
+install_R_sdk() {
+ cd "$WORKSPACE/sdk/R" \
+ && R --quiet --vanilla <<EOF
+options(repos=structure(c(CRAN="http://cran.wustl.edu/")))
+if (!requireNamespace("devtools")) {
+ install.packages("devtools")
+}
+if (!requireNamespace("roxygen2")) {
+ install.packages("roxygen2")
+}
+if (!requireNamespace("pkgdown")) {
+ devtools::install_github("hadley/pkgdown")
+}
+devtools::install_dev_deps()
+EOF
+}
+do_install sdk/R R_sdk
+
install_perl_sdk() {
cd "$WORKSPACE/sdk/perl" \
&& perl Makefile.PL INSTALL_BASE="$PERLINSTALLBASE" \
}
do_test sdk/ruby ruby_sdk
+test_R_sdk() {
+ cd "$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 \