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The following commit(s) were added to refs/heads/master by this push:
new 100cdb6 [ZEPPELIN-5481] Support to run R interpreter in yarn mode
with customized conda env
100cdb6 is described below
commit 100cdb6021f3f8132ca9b3ed3beff507125cce78
Author: Jeff Zhang <zjf...@apache.org>
AuthorDate: Mon Aug 9 22:28:25 2021 +0800
[ZEPPELIN-5481] Support to run R interpreter in yarn mode with customized
conda env
### What is this PR for?
Simple PR to make R interpreter run in yarn mode with customized conda env.
### What type of PR is it?
[ Feature ]
### Todos
* [ ] - Task
### What is the Jira issue?
* https://issues.apache.org/jira/browse/ZEPPELIN-5481
### How should this be tested?
* Manually tested
### Screenshots (if appropriate)
### Questions:
* Does the licenses files need update? No
* Is there breaking changes for older versions? No
* Does this needs documentation? No
Author: Jeff Zhang <zjf...@apache.org>
Closes #4199 from zjffdu/ZEPPELIN-5481 and squashes the following commits:
f5f5058794 [Jeff Zhang] update doc
cbf51622a2 [Jeff Zhang] use File.separator
9fbf2626aa [Jeff Zhang] [ZEPPELIN-5481] Support to run R interpreter in
yarn mode with customized conda env
---
docs/interpreter/r.md | 160 +++++++-
.../3. R Conda Env in Yarn Mode_2GB9HRSH9.zpln | 401 +++++++++++++++++++++
.../java/org/apache/zeppelin/r/IRInterpreter.java | 15 +
3 files changed, 557 insertions(+), 19 deletions(-)
diff --git a/docs/interpreter/r.md b/docs/interpreter/r.md
index ef61f4b..2d39126 100644
--- a/docs/interpreter/r.md
+++ b/docs/interpreter/r.md
@@ -27,7 +27,7 @@ limitations under the License.
[R](https://www.r-project.org) is a free software environment for statistical
computing and graphics.
-To run R code and visualize plots in Apache Zeppelin, you will need R on your
master node (or your dev laptop).
+To run R code and visualize plots in Apache Zeppelin, you will need R on your
zeppelin server node (or your dev laptop).
+ For Centos: `yum install R R-devel libcurl-devel openssl-devel`
+ For Ubuntu: `apt-get install r-base`
@@ -87,9 +87,9 @@ Zeppelin supports R language in 3 interpreters
<tr>
<td>%r.r</td>
<td>RInterpreter</td>
- <td>Vanilla r interpreter, with least dependencies, only R environment
installed is required.
- It is always recommended to use the fully qualified interpreter name
<code>%r.r</code>code>, because <code>%r</code> is ambiguous,
- it could mean both <code>%spark.r</code> and <code>%r.r</code></td>
+ <td>Vanilla r interpreter, with least dependencies, only R environment and
knitr are required.
+ It is always recommended to use the fully qualified interpreter name
<code>%r.r</code>, because <code>%r</code> is ambiguous,
+ it could mean <code>%spark.r</code> when current note's default
interpreter is <code>%spark</code> and <code>%r.r</code> when the default
interpreter is <code>%r</code></td>
</tr>
<tr>
<td>%r.ir</td>
@@ -103,7 +103,7 @@ Zeppelin supports R language in 3 interpreters
</tr>
</table>
-If you want to use R with Spark, it is almost the same via `%spark.r`,
`%spark.ir` & `%spark.shiny` . You can refer Spark Interpreter docs for more
details.
+If you want to use R with Spark, it is almost the same via `%spark.r`,
`%spark.ir` & `%spark.shiny` . You can refer Spark interpreter docs for more
details.
## Configuration
@@ -139,38 +139,66 @@ If you want to use R with Spark, it is almost the same
via `%spark.r`, `%spark.i
<td>500px</td>
<td>IFrame height of Shiny App</td>
</tr>
+ <tr>
+ <td>zeppelin.R.shiny.portRange</td>
+ <td>:</td>
+ <td>Shiny app would launch a web app at some port, this property is to
specify the portRange via format 'start':'end', e.g. '5000:5001'. By default it
is ':' which means any port.</td>
+ </tr>
+ <tr>
+ <td>zeppelin.R.maxResult</td>
+ <td>1000</td>
+ <td>Max number of dataframe rows to display when using z.show</td>
+ </tr>
</table>
-## Using the R Interpreter(`%r.r` & `%r.ir`)
+## Interpreter binding mode
+
+The default [interpreter binding
mode](../usage/interpreter/interpreter_binding_mode.html) is `globally shared`.
That means all notes share the same R interpreter.
+So we would recommend you to ues `isolated per note` which means each note has
own R interpreter without affecting each other. But it may run out of your
machine resource if too many R
+interpreters are created. You can [run R in yarn
mode](../interpreter/r.html#run-r-in-yarn-cluster) to avoid this problem.
+
+## How to use R Interpreter
+
+There are two different implementations of R interpreters: `%r.r` and `%r.ir`.
-By default, the R Interpreter appears as two Zeppelin Interpreters, `%r.r` and
`%r.ir`.
+* Vanilla R Interpreter(`%r.r`) behaves like an ordinary REPL and use SparkR
to communicate between R process and JVM process. It requires `knitr` to be
installed.
+* IRKernel R Interpreter(`%r.ir`) behaves like using IRKernel in Jupyter
notebook. It is based on [jupyter interpreter](jupyter.html). Besides jupyter
interpreter's prerequisites, [IRkernel](https://github.com/IRkernel/IRkernel)
needs to be installed as well.
-`%r.r` behaves like an ordinary REPL and use SparkR to communicate between R
process and JVM process.
-`%r.ir` use IRKernel underneath, it behaves like using IRKernel in Jupyter
notebook.
+Take a look at the tutorial note `R Tutorial/1. R Basics` for how to write R
code in Zeppelin.
-R basic expression
+### R basic expressions
+
+R basic expressions are supported in both `%r.r` and `%r.ir`.
<img class="img-responsive"
src="{{BASE_PATH}}/assets/themes/zeppelin/img/docs-img/r_basic.png"
width="800px"/>
-R base plotting is fully supported
+### R base plotting
+
+R base plotting is supported in both `%r.r` and `%r.ir`.
<img class="img-responsive"
src="{{BASE_PATH}}/assets/themes/zeppelin/img/docs-img/r_plotting.png"
width="800px"/>
-Besides R base plotting, you can use other visualization library, e.g.
`ggplot` and `googlevis`
+### Other plotting
+
+Besides R base plotting, you can use other visualization libraries in both
`%r.r` and `%r.ir`, e.g. `ggplot` and `googleVis`
<img class="img-responsive"
src="{{BASE_PATH}}/assets/themes/zeppelin/img/docs-img/r_ggplot.png"
width="800px"/>
<img class="img-responsive"
src="{{BASE_PATH}}/assets/themes/zeppelin/img/docs-img/r_googlevis.png"
width="800px"/>
-You can also use `z.show()` in `%r.ir` to visualize the dataframe, e.g.
+### z.show
+
+`z.show()` is only available in `%r.ir` to visualize R dataframe, e.g.
<img class="img-responsive"
src="{{BASE_PATH}}/assets/themes/zeppelin/img/docs-img/r_zshow.png"
width="800px"/>
-
+By default, `z.show` would only display 1000 rows, you can specify the maxRows
via `z.show(df, maxRows=2000)`
+
## Make Shiny App in Zeppelin
[Shiny](https://shiny.rstudio.com/tutorial/) is an R package that makes it
easy to build interactive web applications (apps) straight from R.
-For developing one Shiny App in Zeppelin, you need to at least 3 paragraphs
(server paragraph, ui paragraph and run type paragraph)
+`%r.shiny` is used for developing R shiny app in Zeppelin notebook. It only
works when IRKernel Interpreter(`%r.ir`) is enabled.
+For developing one Shiny App in Zeppelin, you need to write at least 3
paragraphs (server type paragraph, ui type paragraph and run type paragraph)
* Server type R shiny paragraph
@@ -252,13 +280,14 @@ ui <- fluidPage(
```
-After executing the run type R shiny paragraph, the shiny app will be launched
and embedded as Iframe in paragraph.
+After executing the run type R shiny paragraph, the shiny app will be launched
and embedded as iframe in paragraph.
+Take a look at the tutorial note `R Tutorial/2. Shiny App` for how to develop
R shiny app.
<img class="img-responsive"
src="{{BASE_PATH}}/assets/themes/zeppelin/img/docs-img/r_shiny.png"
width="800px"/>
-### Run multiple shiny app
+### Run multiple shiny apps
-If you want to run multiple shiny app, you can specify `app` in paragraph
local property to differentiate shiny app.
+If you want to run multiple shiny apps, you can specify `app` in paragraph
local property to differentiate different shiny apps.
e.g.
@@ -272,4 +301,97 @@ e.g.
```r
%r.shiny(type=run, app=app_1)
-```
\ No newline at end of file
+```
+
+## Run R in yarn cluster
+
+Zeppelin support to [run interpreter in yarn
cluster](../quickstart/yarn.html). But there's one critical problem to run R in
yarn cluster: how to manage the R environment in yarn container.
+Because yarn cluster is a distributed cluster which is composed of many nodes,
and your R interpreter can start in any node.
+It is not practical to manage R environment in each node.
+
+So in order to run R in yarn cluster, we would suggest you to use conda to
manage your R environment, and Zeppelin can ship your
+R conda environment to yarn container, so that each R interpreter can have its
own R environment without affecting each other.
+
+To be noticed, you can only run IRKernel interpreter(`%r.ir`) in yarn cluster.
So make sure you include at least the following prerequisites in the below
conda env:
+
+* python
+* jupyter
+* grpcio
+* protobuf
+* r-base
+* r-essentials
+* r-irkernel
+
+`python`, `jupyter`, `grpcio` and `protobuf` are required for [jupyter
interpreter](../interpreter/jupyter.html), because IRKernel interpreter is
based on [jupyter interpreter](../interpreter/jupyter.html). Others are for R
runtime.
+
+Following are instructions of how to run R in yarn cluster. You can find all
the code in the tutorial note `R Tutorial/3. R Conda Env in Yarn Mode`.
+
+
+### Step 1
+
+We would suggest you to use conda pack to create archive of conda environment.
+
+Here's one example of yaml file which is used to generate a conda environment
with R and some useful R libraries.
+
+* Create a yaml file for conda environment, write the following content into
file `r_env.yml`
+
+```text
+name: r_env
+channels:
+ - conda-forge
+ - defaults
+dependencies:
+ - python=3.7
+ - jupyter
+ - grpcio
+ - protobuf
+ - r-base=3
+ - r-essentials
+ - r-evaluate
+ - r-base64enc
+ - r-knitr
+ - r-ggplot2
+ - r-irkernel
+ - r-shiny
+ - r-googlevis
+```
+
+* Create conda environment via this yaml file using either `conda` or `mamba`
+
+```bash
+
+conda env create -f r_env.yml
+```
+
+```bash
+
+mamba env create -f r_env.yml
+```
+
+
+* Pack the conda environment using `conda`
+
+```bash
+
+conda pack -n r_env
+```
+
+### Step 2
+
+Specify the following properties to enable yarn mode for R interpreter via
[inline
configuration](../usage/interpreter/overview.html#inline-generic-configuration)
+
+```
+%r.conf
+
+zeppelin.interpreter.launcher yarn
+zeppelin.yarn.dist.archives hdfs:///tmp/r_env.tar.gz#environment
+zeppelin.interpreter.conda.env.name environment
+```
+
+`zeppelin.yarn.dist.archives` is the R conda environment tar file which is
created in step 1. This tar will be shipped to yarn container and untar in the
working directory of yarn container.
+`hdfs:///tmp/r_env.tar.gz` is the R conda archive file you created in step 2.
`environment` in `hdfs:///tmp/r_env.tar.gz#environment` is the folder name
after untar.
+This folder name should be the same as `zeppelin.interpreter.conda.env.name`.
+
+### Step 3
+
+Now you can use run R interpreter in yarn container and also use any R
libraries you specify in step 1.
diff --git a/notebook/R Tutorial/3. R Conda Env in Yarn Mode_2GB9HRSH9.zpln
b/notebook/R Tutorial/3. R Conda Env in Yarn Mode_2GB9HRSH9.zpln
new file mode 100644
index 0000000..288dc22
--- /dev/null
+++ b/notebook/R Tutorial/3. R Conda Env in Yarn Mode_2GB9HRSH9.zpln
@@ -0,0 +1,401 @@
+{
+ "paragraphs": [
+ {
+ "text": "%md\n\nThis tutorial is for how to use customize R runtime
environment via conda in yarn mode.\nIn this approach, the R interpreter runs
in yarn container instead of in the zeppelin server host. And remmeber this
only works for IRKernel(`%r.ir`) but not for vanilla R(`%r.r`), so make sure
you include the following python packages in your conda env.\n* python\n*
jupyter\n* grpcio\n* protobuf\n* r-base\n* r-essentials\n* r-irkernel\n\n\n\n",
+ "user": "anonymous",
+ "dateUpdated": "2021-08-09 10:55:29.815",
+ "progress": 0,
+ "config": {
+ "tableHide": false,
+ "editorSetting": {
+ "language": "markdown",
+ "editOnDblClick": true,
+ "completionKey": "TAB",
+ "completionSupport": false
+ },
+ "colWidth": 12.0,
+ "editorMode": "ace/mode/markdown",
+ "fontSize": 9.0,
+ "editorHide": false,
+ "title": false,
+ "results": {},
+ "enabled": true
+ },
+ "settings": {
+ "params": {},
+ "forms": {}
+ },
+ "results": {
+ "code": "SUCCESS",
+ "msg": [
+ {
+ "type": "HTML",
+ "data": "<div class=\"markdown-body\">\n<p>This tutorial is for how to
use customize R runtime environment via conda in yarn mode.<br />\nIn this
approach, the R interpreter runs in yarn container instead of in the zeppelin
server host. And remmeber this only works for IRKernel(<code>%r.ir</code>) but
not for vanilla R(<code>%r.r</code>), so make sure you include the following
python packages in your conda
env.</p>\n<ul>\n<li>python</li>\n<li>jupyter</li>\n<li>grpcio</li>\n<li>prot
[...]
+ }
+ ]
+ },
+ "apps": [],
+ "runtimeInfos": {},
+ "progressUpdateIntervalMs": 500,
+ "jobName": "paragraph_1624111096909_1969681448",
+ "id": "paragraph_1616510705826_532544979",
+ "dateCreated": "2021-06-19 21:58:16.909",
+ "dateStarted": "2021-08-09 10:55:29.817",
+ "dateFinished": "2021-08-09 10:55:29.825",
+ "status": "FINISHED"
+ },
+ {
+ "title": "Create R conda env",
+ "text": "%sh\n\n# make sure you have miniconda, conda-pack and mamba
installed.\n# install miniconda:
https://docs.conda.io/en/latest/miniconda.html\n# install conda-pack:
https://conda.github.io/conda-pack/\n# install mamba:
https://github.com/mamba-org/mamba\n\necho \"name: r_env\nchannels:\n -
conda-forge\n - defaults\ndependencies:\n - python=3.7 \n - jupyter\n -
grpcio\n - protobuf\n - r-base=3\n - r-essentials\n - r-evaluate\n -
r-base64enc\n - r-knitr\n - r-ggplot2\ [...]
+ "user": "anonymous",
+ "dateUpdated": "2021-08-09 10:55:29.917",
+ "progress": 0,
+ "config": {
+ "editorSetting": {
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+ "editOnDblClick": false,
+ "completionKey": "TAB",
+ "completionSupport": false
+ },
+ "colWidth": 12.0,
+ "editorMode": "ace/mode/sh",
+ "fontSize": 9.0,
+ "title": true,
+ "results": {},
+ "enabled": true
+ },
+ "settings": {
+ "params": {},
+ "forms": {}
+ },
+ "results": {
+ "code": "SUCCESS",
+ "msg": [
+ {
+ "type": "TEXT",
+ "data": "\nRemove all packages in environment
/mnt/disk1/jzhang/miniconda3/envs/r_env:\n\npkgs/main/noarch
\npkgs/main/linux-64 \npkgs/r/linux-64 \nconda-forge/noarch
\npkgs/r/noarch \nconda-forge/linux-64 \nTransaction\n\n
Prefix: /mnt/disk1/jzhang/miniconda3/envs/r_env\n\n Updating specs:\n\n -
python=3.7\n - jupyter\n - grpcio\n - protobuf\n - r-base=3\n -
r-essentials\n - r-evaluate\n - r-base64enc\n - r-knit [...]
+ }
+ ]
+ },
+ "apps": [],
+ "runtimeInfos": {},
+ "progressUpdateIntervalMs": 500,
+ "jobName": "paragraph_1624111096910_1941489893",
+ "id": "paragraph_1617163651950_276096757",
+ "dateCreated": "2021-06-19 21:58:16.910",
+ "dateStarted": "2021-08-09 10:55:29.920",
+ "dateFinished": "2021-08-09 10:55:59.548",
+ "status": "FINISHED"
+ },
+ {
+ "title": "Create R conda tar",
+ "text": "%sh\n\nrm -rf r_env.tar.gz\nconda pack -n r_env\n",
+ "user": "anonymous",
+ "dateUpdated": "2021-08-09 10:55:59.555",
+ "progress": 0,
+ "config": {
+ "editorSetting": {
+ "language": "sh",
+ "editOnDblClick": false,
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+ "colWidth": 12.0,
+ "editorMode": "ace/mode/sh",
+ "fontSize": 9.0,
+ "title": true,
+ "results": {},
+ "enabled": true
+ },
+ "settings": {
+ "params": {},
+ "forms": {}
+ },
+ "results": {
+ "code": "SUCCESS",
+ "msg": [
+ {
+ "type": "TEXT",
+ "data": "Collecting packages...\nPacking environment at
'/mnt/disk1/jzhang/miniconda3/envs/r_env' to 'r_env.tar.gz'\n\r[
] | 0% Completed | 0.0s\r[
] | 0% Completed | 0.1s\r[ ]
| 0% Completed | 0.2s\r[ ] | 0%
Completed | 0.3s\r[ ] | 0% Completed |
0.4s\r[ [...]
+ }
+ ]
+ },
+ "apps": [],
+ "runtimeInfos": {},
+ "progressUpdateIntervalMs": 500,
+ "jobName": "paragraph_1624111096910_883123029",
+ "id": "paragraph_1617170106834_1523620028",
+ "dateCreated": "2021-06-19 21:58:16.910",
+ "dateStarted": "2021-08-09 10:55:59.557",
+ "dateFinished": "2021-08-09 10:57:09.103",
+ "status": "FINISHED"
+ },
+ {
+ "title": "Upload R conda tar to hdfs (Optional)",
+ "text": "%sh\n\nhadoop fs -rmr /tmp/r_env.tar.gz\nhadoop fs -put
r_env.tar.gz /tmp\n# The python conda tar should be publicly accessible by
others, so need to change permission here.\nhadoop fs -chmod 644
/tmp/r_env.tar.gz\n",
+ "user": "anonymous",
+ "dateUpdated": "2021-08-09 10:57:09.143",
+ "progress": 0,
+ "config": {
+ "editorSetting": {
+ "language": "sh",
+ "editOnDblClick": false,
+ "completionKey": "TAB",
+ "completionSupport": false
+ },
+ "colWidth": 12.0,
+ "editorMode": "ace/mode/sh",
+ "fontSize": 9.0,
+ "title": true,
+ "results": {},
+ "enabled": true
+ },
+ "settings": {
+ "params": {},
+ "forms": {}
+ },
+ "results": {
+ "code": "SUCCESS",
+ "msg": [
+ {
+ "type": "TEXT",
+ "data": "rmr: DEPRECATED: Please use '-rm -r' instead.\n21/08/09
10:57:10 INFO fs.TrashPolicyDefault: Moved:
'hdfs://emr-header-1.cluster-46718:9000/tmp/r_env.tar.gz' to trash at:
hdfs://emr-header-1.cluster-46718:9000/user/hadoop/.Trash/Current/tmp/r_env.tar.gz1628477830555\n"
+ }
+ ]
+ },
+ "apps": [],
+ "runtimeInfos": {},
+ "progressUpdateIntervalMs": 500,
+ "jobName": "paragraph_1624111096911_217029483",
+ "id": "paragraph_1617163700271_1335210825",
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+ "dateStarted": "2021-08-09 10:57:09.148",
+ "dateFinished": "2021-08-09 10:57:16.029",
+ "status": "FINISHED"
+ },
+ {
+ "title": "Configure R Interpreter",
+ "text": "%r.conf\n\n# set zeppelin.interpreter.launcher to be yarn, so that
R interpreter run in yarn container, \n# otherwise R interpreter run as local
process in the zeppelin server host.\nzeppelin.interpreter.launcher yarn\n\n#
zeppelin.yarn.dist.archives can be either local file or hdfs
file\nzeppelin.yarn.dist.archives
hdfs:///tmp/r_env.tar.gz#environment\n\nzeppelin.interpreter.conda.env.name
environment\n\n",
+ "user": "anonymous",
+ "dateUpdated": "2021-08-09 10:57:16.052",
+ "progress": 0,
+ "config": {
+ "editorSetting": {
+ "language": "text",
+ "editOnDblClick": false,
+ "completionKey": "TAB",
+ "completionSupport": false
+ },
+ "colWidth": 12.0,
+ "editorMode": "ace/mode/text",
+ "fontSize": 9.0,
+ "title": true,
+ "results": {},
+ "enabled": true
+ },
+ "settings": {
+ "params": {},
+ "forms": {}
+ },
+ "results": {
+ "code": "SUCCESS",
+ "msg": []
+ },
+ "apps": [],
+ "runtimeInfos": {},
+ "progressUpdateIntervalMs": 500,
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+ "id": "paragraph_1616750271530_2029224504",
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+ "dateFinished": "2021-08-09 10:57:16.058",
+ "status": "FINISHED"
+ },
+ {
+ "title": "Base plotting",
+ "text": "%r.ir\n\npairs(iris)\n",
+ "user": "anonymous",
+ "dateUpdated": "2021-08-09 10:57:16.155",
+ "progress": 0,
+ "config": {
+ "editorSetting": {
+ "language": "r",
+ "editOnDblClick": false,
+ "completionSupport": true
+ },
+ "colWidth": 12.0,
+ "editorMode": "ace/mode/r",
+ "fontSize": 9.0,
+ "results": {},
+ "enabled": true,
+ "title": true
+ },
+ "settings": {
+ "params": {},
+ "forms": {}
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+ "results": {
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+ "dateCreated": "2021-06-19 23:00:03.899",
+ "dateStarted": "2021-08-09 10:57:16.158",
+ "dateFinished": "2021-08-09 10:57:47.946",
+ "status": "FINISHED"
+ },
+ {
+ "title": "Use ggplot2",
+ "text": "%r.ir\n\nlibrary(ggplot2)\npres_rating <- data.frame(\n rating =
as.numeric(presidents),\n year = as.numeric(floor(time(presidents))),\n
quarter = as.numeric(cycle(presidents))\n)\np <- ggplot(pres_rating,
aes(x=year, y=quarter, fill=rating))\np + geom_raster()\n",
+ "user": "anonymous",
+ "dateUpdated": "2021-08-09 10:57:47.983",
+ "progress": 0,
+ "config": {
+ "editorSetting": {
+ "language": "r",
+ "editOnDblClick": false,
+ "completionKey": "TAB",
+ "completionSupport": true
+ },
+ "colWidth": 6.0,
+ "editorMode": "ace/mode/r",
+ "fontSize": 9.0,
+ "title": true,
+ "results": {},
+ "enabled": true
+ },
+ "settings": {
+ "params": {},
+ "forms": {}
+ },
+ "results": {
+ "code": "SUCCESS",
+ "msg": [
+ {
+ "type": "TEXT",
+ "data": "\nAttaching package: ‘ggplot2’\n\n\nThe following object is
masked from ‘package:SparkR’:\n\n expr\n\n\n\n"
+ },
+ {
+ "type": "IMG",
+ "data":
"iVBORw0KGgoAAAANSUhEUgAAA0gAAANICAIAAAByhViMAAAACXBIWXMAABJ0AAASdAHeZh94\nAAAgAElEQVR4nO3deXxU5aH4/zMhqyFssuMGFSwouNSrFNGXerEuxaK+kBYXFK+CVmu9gq2A\n3wIutL1cEau2Ki5U0VIVitQFb6l1o1irgtBbLQjWiqCoSGQL2eb3x9xfGsGGmMnJJM+836/8\nkZk5zznPhDH5eM6cOYlkMhkBANDy5WR6AgAANA5hBwAQCGEHABAIYQcAEAhhBwAQCGEHABAI\nYQcAEAhhBwAQiNxMT+BztmzZUllZmZFN5+fnJxKJnTt3ZmTrLVdBQUFhYeH27dsrKioyPZcW\npqioqKKiIlMv+JarqKgoPz9/y5Yt1dXVmZ5LC1NcXLxjxw4/ty+rdevWrVq1Ki0tzfREWp6S\nkpItW7Y0eHj79u0bcTLZo3mFXXV1dVVVV
[...]
+ }
+ ]
+ },
+ "apps": [],
+ "runtimeInfos": {},
+ "progressUpdateIntervalMs": 500,
+ "jobName": "paragraph_1624111096911_1421779245",
+ "id": "paragraph_1623916874799_812799753",
+ "dateCreated": "2021-06-19 21:58:16.911",
+ "dateStarted": "2021-08-09 10:57:47.986",
+ "dateFinished": "2021-08-09 10:57:48.701",
+ "status": "FINISHED"
+ },
+ {
+ "title": "Use googleVis",
+ "text": "%r.ir\n\nlibrary(googleVis)\ndf=data.frame(country=c(\"US\",
\"GB\", \"BR\"), \n val1=c(10,13,14), \n
val2=c(23,12,32))\nBar <- gvisBarChart(df)\nprint(Bar, tag = 'chart')\n",
+ "user": "anonymous",
+ "dateUpdated": "2021-08-09 10:57:48.786",
+ "progress": 0,
+ "config": {
+ "editorSetting": {
+ "language": "r",
+ "editOnDblClick": false,
+ "completionKey": "TAB",
+ "completionSupport": true
+ },
+ "colWidth": 6.0,
+ "editorMode": "ace/mode/r",
+ "fontSize": 9.0,
+ "title": true,
+ "results": {},
+ "enabled": true
+ },
+ "settings": {
+ "params": {},
+ "forms": {}
+ },
+ "results": {
+ "code": "SUCCESS",
+ "msg": [
+ {
+ "type": "TEXT",
+ "data": "\nWelcome to googleVis version 0.6.10\n\nPlease read Google's
Terms of Use\nbefore you start using the
package:\nhttps://developers.google.com/terms/\n\nNote, the plot method of
googleVis will by default use\nthe standard browser to display its
output.\n\nSee the googleVis package vignettes for more details,\nor visit
https://github.com/mages/googleVis.\n\nTo suppress this message
use:\nsuppressPackageStartupMessages(library(googleVis))\n\n\n\n"
+ },
+ {
+ "type": "HTML",
+ "data": "<!-- BarChart generated in R 3.6.3 by googleVis 0.6.10 package
-->\n<!-- Mon Aug 9 10:57:48 2021 -->\n\n\n<!-- jsHeader -->\n<script
type=\"text/javascript\">\n \n// jsData \nfunction
gvisDataBarChartID32796be86efc () {\nvar data = new
google.visualization.DataTable();\nvar datajson =\n[\n
[\n\"US\",\n10,\n23\n],\n[\n\"GB\",\n13,\n12\n],\n[\n\"BR\",\n14,\n32\n]
\n];\ndata.addColumn('string','country');\ndata.addColumn('number','val1');\ndata.addColumn('number','val2');\nd
[...]
+ }
+ ]
+ },
+ "apps": [],
+ "runtimeInfos": {},
+ "progressUpdateIntervalMs": 500,
+ "jobName": "paragraph_1624111096911_1956298431",
+ "id": "paragraph_1616751026390_1945717741",
+ "dateCreated": "2021-06-19 21:58:16.911",
+ "dateStarted": "2021-08-09 10:57:48.789",
+ "dateFinished": "2021-08-09 10:57:48.851",
+ "status": "FINISHED"
+ },
+ {
+ "text": "%r.ir\n",
+ "user": "anonymous",
+ "dateUpdated": "2021-08-09 10:57:48.889",
+ "progress": 0,
+ "config": {
+ "colWidth": 12.0,
+ "fontSize": 9.0,
+ "enabled": true,
+ "results": {},
+ "editorSetting": {
+ "language": "r",
+ "editOnDblClick": false,
+ "completionSupport": true
+ },
+ "editorMode": "ace/mode/r"
+ },
+ "settings": {
+ "params": {},
+ "forms": {}
+ },
+ "results": {
+ "code": "SUCCESS",
+ "msg": []
+ },
+ "apps": [],
+ "runtimeInfos": {},
+ "progressUpdateIntervalMs": 500,
+ "jobName": "paragraph_1624114845053_735333148",
+ "id": "paragraph_1624114845053_735333148",
+ "dateCreated": "2021-06-19 23:00:45.054",
+ "dateStarted": "2021-08-09 10:57:48.891",
+ "dateFinished": "2021-08-09 10:57:48.946",
+ "status": "FINISHED"
+ }
+ ],
+ "name": "3. R Conda Env in Yarn Mode",
+ "id": "2GB9HRSH9",
+ "defaultInterpreterGroup": "r",
+ "version": "0.10.0-SNAPSHOT",
+ "noteParams": {},
+ "noteForms": {},
+ "angularObjects": {},
+ "config": {
+ "personalizedMode": "false",
+ "looknfeel": "default",
+ "isZeppelinNotebookCronEnable": false
+ },
+ "info": {
+ "isRunning": true
+ }
+}
\ No newline at end of file
diff --git a/rlang/src/main/java/org/apache/zeppelin/r/IRInterpreter.java
b/rlang/src/main/java/org/apache/zeppelin/r/IRInterpreter.java
index ef79fd5..56d0673 100644
--- a/rlang/src/main/java/org/apache/zeppelin/r/IRInterpreter.java
+++ b/rlang/src/main/java/org/apache/zeppelin/r/IRInterpreter.java
@@ -38,6 +38,7 @@ import java.io.InputStream;
import java.io.StringReader;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
+import java.util.Map;
import java.util.Properties;
/**
@@ -153,6 +154,20 @@ public class IRInterpreter extends
JupyterKernelInterpreter {
}
@Override
+ protected Map<String, String> setupKernelEnv() throws IOException {
+ Map<String, String> envs = super.setupKernelEnv();
+ String pathEnv = envs.getOrDefault("PATH", "");
+ if (condaEnv != null) {
+ // add ${PWD}/${condaEnv}/bin to PATH, otherwise
JupyterKernelInterpreter will fail to
+ // find R to launch IRKernel
+ pathEnv = new File(".").getAbsolutePath() + File.separator + condaEnv +
+ File.separator + "bin" + File.pathSeparator + pathEnv;
+ envs.put("PATH", pathEnv);
+ }
+ return envs;
+ }
+
+ @Override
public String getKernelName() {
return "ir";
}
