[ARVADOS] updated: 1.1.2-270-g2173fac
Git user
git at public.curoverse.com
Fri Feb 9 09:20:44 EST 2018
Summary of changes:
.gitignore | 1 +
build/run-tests.sh | 5 +++++
doc/Rakefile | 14 +++++++++++++-
doc/_config.yml | 2 ++
.../R.html.textile.liquid} | 4 ++--
doc/sdk/index.html.textile.liquid | 1 +
sdk/R/.Rbuildignore | 1 +
sdk/R/DESCRIPTION | 2 +-
tools/arvbox/bin/arvbox | 5 ++++-
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 2 +-
tools/arvbox/lib/arvbox/docker/common.sh | 1 +
tools/arvbox/lib/arvbox/docker/service/doc/run-service | 16 ++++++++++++++++
12 files changed, 48 insertions(+), 6 deletions(-)
copy doc/sdk/{python/python.html.textile.liquid => R/R.html.textile.liquid} (86%)
via 2173fac2d9acd783b9306696ce6857b2c511e0cf (commit)
via 4fca56d2393f754a0f8ff21225fd975ca4b1f782 (commit)
from 47cb4506cc97c701639038a12f08374e8f06c41b (commit)
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commit 2173fac2d9acd783b9306696ce6857b2c511e0cf
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Fri Feb 9 09:11:18 2018 -0500
11876: Arvbox support for building R docs
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/tools/arvbox/bin/arvbox b/tools/arvbox/bin/arvbox
index 234d15a..3429a1b 100755
--- a/tools/arvbox/bin/arvbox
+++ b/tools/arvbox/bin/arvbox
@@ -57,6 +57,7 @@ GEMS="$ARVBOX_DATA/gems"
PIPCACHE="$ARVBOX_DATA/pip"
NPMCACHE="$ARVBOX_DATA/npm"
GOSTUFF="$ARVBOX_DATA/gopath"
+RLIBS="$ARVBOX_DATA/Rlibs"
getip() {
docker inspect $ARVBOX_CONTAINER | grep \"IPAddress\" | head -n1 | tr -d ' ":,\n' | cut -c10-
@@ -188,7 +189,7 @@ run() {
updateconf
wait_for_arvbox
else
- mkdir -p "$PG_DATA" "$VAR_DATA" "$PASSENGER" "$GEMS" "$PIPCACHE" "$NPMCACHE" "$GOSTUFF"
+ mkdir -p "$PG_DATA" "$VAR_DATA" "$PASSENGER" "$GEMS" "$PIPCACHE" "$NPMCACHE" "$GOSTUFF" "$RLIBS"
if ! test -d "$ARVADOS_ROOT" ; then
@@ -220,6 +221,7 @@ run() {
"--volume=$PIPCACHE:/var/lib/pip:rw" \
"--volume=$NPMCACHE:/var/lib/npm:rw" \
"--volume=$GOSTUFF:/var/lib/gopath:rw" \
+ "--volume=$RLIBS:/var/lib/Rlibs:rw" \
"--env=SVDIR=/etc/test-service" \
arvados/arvbox-dev$TAG
@@ -262,6 +264,7 @@ run() {
"--volume=$PIPCACHE:/var/lib/pip:rw" \
"--volume=$NPMCACHE:/var/lib/npm:rw" \
"--volume=$GOSTUFF:/var/lib/gopath:rw" \
+ "--volume=$RLIBS:/var/lib/Rlibs:rw" \
$PUBLIC \
arvados/arvbox-dev$TAG
updateconf
diff --git a/tools/arvbox/lib/arvbox/docker/Dockerfile.base b/tools/arvbox/lib/arvbox/docker/Dockerfile.base
index c95bc48..0cc36eb 100644
--- a/tools/arvbox/lib/arvbox/docker/Dockerfile.base
+++ b/tools/arvbox/lib/arvbox/docker/Dockerfile.base
@@ -19,7 +19,7 @@ RUN apt-get update && \
apt-transport-https ca-certificates slurm-wlm \
linkchecker python3-virtualenv python-virtualenv xvfb iceweasel \
libgnutls28-dev python3-dev vim cadaver cython gnupg dirmngr \
- libsecret-1-dev r-base r-cran-testthat libxml2-dev && \
+ libsecret-1-dev r-base r-cran-testthat libxml2-dev pandoc && \
apt-get clean
ENV RUBYVERSION_MINOR 2.3
diff --git a/tools/arvbox/lib/arvbox/docker/common.sh b/tools/arvbox/lib/arvbox/docker/common.sh
index 2cb8473..319889b 100644
--- a/tools/arvbox/lib/arvbox/docker/common.sh
+++ b/tools/arvbox/lib/arvbox/docker/common.sh
@@ -8,6 +8,7 @@ export GEM_HOME=/var/lib/gems
export GEM_PATH=/var/lib/gems
export npm_config_cache=/var/lib/npm
export npm_config_cache_min=Infinity
+export R_LIBS=/var/lib/Rlibs
if test -s /var/run/localip_override ; then
localip=$(cat /var/run/localip_override)
diff --git a/tools/arvbox/lib/arvbox/docker/service/doc/run-service b/tools/arvbox/lib/arvbox/docker/service/doc/run-service
index b8bf740..97cc79d 100755
--- a/tools/arvbox/lib/arvbox/docker/service/doc/run-service
+++ b/tools/arvbox/lib/arvbox/docker/service/doc/run-service
@@ -11,6 +11,21 @@ set -ex -o pipefail
cd /usr/src/arvados/doc
run_bundler --without=development
+cd /usr/src/arvados/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
+
if test "$1" = "--only-deps" ; then
exit
fi
@@ -42,6 +57,7 @@ http {
}
EOF
+cd /usr/src/arvados/doc
bundle exec rake generate baseurl=http://$localip:${services[doc]} arvados_api_host=$localip:${services[api]} arvados_workbench_host=http://$localip
exec nginx -c /var/lib/arvados/doc-nginx.conf
commit 4fca56d2393f754a0f8ff21225fd975ca4b1f782
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Fri Feb 9 09:14:51 2018 -0500
11876: Build R SDK reference pages for doc site
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/.gitignore b/.gitignore
index d41eaee..cc4f17e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -12,6 +12,7 @@ docker/*/generated
docker/config.yml
doc/.site
doc/sdk/python/arvados
+doc/sdk/R/arvados
sdk/perl/MYMETA.*
sdk/perl/Makefile
sdk/perl/blib
diff --git a/build/run-tests.sh b/build/run-tests.sh
index 4ebaf07..ec3c463 100755
--- a/build/run-tests.sh
+++ b/build/run-tests.sh
@@ -249,6 +249,8 @@ sanity_checks() {
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() {
@@ -786,6 +788,9 @@ if (!requireNamespace("devtools")) {
if (!requireNamespace("roxygen2")) {
install.packages("roxygen2")
}
+if (!requireNamespace("pkgdown")) {
+ devtools::install_github("hadley/pkgdown")
+}
devtools::install_dev_deps()
EOF
}
diff --git a/doc/Rakefile b/doc/Rakefile
index f68a964..10bb8b9 100644
--- a/doc/Rakefile
+++ b/doc/Rakefile
@@ -6,7 +6,7 @@
require "rubygems"
require "colorize"
-task :generate => [ :realclean, 'sdk/python/arvados/index.html' ] do
+task :generate => [ :realclean, 'sdk/python/arvados/index.html', 'sdk/R/arvados/index.html' ] do
vars = ['baseurl', 'arvados_api_host', 'arvados_workbench_host']
vars.each do |v|
if ENV[v]
@@ -25,6 +25,17 @@ file "sdk/python/arvados/index.html" do |t|
end
end
+file "sdk/R/arvados/index.html" do |t|
+ `which R`
+ if $? == 0
+ STDERR.puts `R --quiet --vanilla -e 'pkgdown::build_site(pkg="../sdk/R/")' 2>&1`
+ raise if $? != 0
+ cp_r("../sdk/R/docs", "sdk/R/arvados")
+ else
+ puts "Warning: R not found, R documentation will not be generated".colorize(:light_red)
+ end
+end
+
task :linkchecker => [ :generate ] do
Dir.chdir(".site") do
`which linkchecker`
@@ -38,6 +49,7 @@ end
task :clean do
rm_rf "sdk/python/arvados"
+ rm_rf "sdk/R/arvados"
end
require "zenweb/tasks"
diff --git a/doc/_config.yml b/doc/_config.yml
index 08b581c..680f940 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -103,6 +103,8 @@ navbar:
- Go:
- sdk/go/index.html.textile.liquid
- sdk/go/example.html.textile.liquid
+ - R:
+ - sdk/R/R.html.textile.liquid
- Perl:
- sdk/perl/index.html.textile.liquid
- sdk/perl/example.html.textile.liquid
diff --git a/doc/sdk/R/R.html.textile.liquid b/doc/sdk/R/R.html.textile.liquid
new file mode 100644
index 0000000..7b788a1
--- /dev/null
+++ b/doc/sdk/R/R.html.textile.liquid
@@ -0,0 +1,15 @@
+---
+layout: default
+navsection: sdk
+navmenu: R
+title: "R Reference"
+
+no_nav_left: true
+...
+{% comment %}
+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" />
diff --git a/doc/sdk/index.html.textile.liquid b/doc/sdk/index.html.textile.liquid
index e2b6eba..fbc5ca1 100644
--- a/doc/sdk/index.html.textile.liquid
+++ b/doc/sdk/index.html.textile.liquid
@@ -14,6 +14,7 @@ This section documents language bindings for the "Arvados API":{{site.baseurl}}/
* "Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html
* "Command line SDK":{{site.baseurl}}/sdk/cli/install.html ("arv")
* "Go SDK":{{site.baseurl}}/sdk/go/index.html
+* "R SDK":{{site.baseurl}}/sdk/go/index.html
* "Perl SDK":{{site.baseurl}}/sdk/perl/index.html
* "Ruby SDK":{{site.baseurl}}/sdk/ruby/index.html
* "Java SDK":{{site.baseurl}}/sdk/java/index.html
diff --git a/sdk/R/.Rbuildignore b/sdk/R/.Rbuildignore
index 91114bf..4952b99 100644
--- a/sdk/R/.Rbuildignore
+++ b/sdk/R/.Rbuildignore
@@ -1,2 +1,3 @@
^.*\.Rproj$
^\.Rproj\.user$
+^docs$
diff --git a/sdk/R/DESCRIPTION b/sdk/R/DESCRIPTION
index 73738e1..19cf8fb 100644
--- a/sdk/R/DESCRIPTION
+++ b/sdk/R/DESCRIPTION
@@ -2,7 +2,7 @@ Package: ArvadosR
Type: Package
Title: Arvados R SDK
Version: 0.0.2
-Author: Fuad Muhic
+Authors at R: person("Fuad", "Muhic", role = c("aut", "cre"), email = "fmuhic at capeannenterprises.com")
Maintainer: Ward Vandewege <wvandewege at veritasgenetics.com>
Description: This is the Arvados R SDK
URL: http://doc.arvados.org
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