Merge pull request #4 from saagie/R

(job) add R 3.4.4/3.5.3

.github/workflows/buildOnlyModified.yml

@@ -43,7 +43,7 @@ jobs:
       - name: List all releases
         uses: actions/[email protected]
         with:
-          github-token: ${{secrets.GITHUB_TOKEN}}
+          github-token: ${{secrets.GITHUB_SECRET}}
           script: |
             const result = await github.repos.listReleases(context.repo);
             result.data

certified/job/R/3.4.4/Dockerfile

@@ -0,0 +1,171 @@
+FROM rocker/tidyverse:3.4.4
+
+USER root
+
+
+# Install system libraries required by R packages
+RUN apt-get -y update  && apt-get install -y libcups2 libcups2-dev openjdk-8-jdk systemd \
+  unixodbc-dev libbz2-dev libgsl-dev odbcinst libx11-dev mesa-common-dev libglu1-mesa-dev \
+  gdal-bin proj-bin libgdal-dev libproj-dev libudunits2-dev libtcl8.6 libtk8.6 libgtk2.0-dev && \
+  apt-get clean
+
+# Install Impala ODBC dependency
+RUN cd /tmp && \
+  wget --no-verbose https://downloads.cloudera.com/connectors/impala_odbc_2.5.41.1029/Debian/clouderaimpalaodbc_2.5.41.1029-2_amd64.deb && \
+  dpkg -i clouderaimpalaodbc_2.5.41.1029-2_amd64.deb && \
+  odbcinst -i -d -f /opt/cloudera/impalaodbc/Setup/odbcinst.ini
+
+# Install Saagie's RStudio Addin
+RUN R -e "install.packages('devtools')" && \
+  R -e "devtools::install_github('saagie/rstudio-saagie-addin')"
+
+# Install R packages
+RUN R CMD javareconf && R -e "install.packages('rJava')" && \
+  R -e "install.packages('odbc')" && \
+  R -e "install.packages('RJDBC')" && \
+  R -e "install.packages('implyr')" && \
+  R -e "install.packages('futile.logger')" && \
+  R -e "install.packages('h2o')" && \
+  R -e "install.packages('caret')" && \
+  R -e "install.packages('ROSE')" && \
+  R -e "install.packages('caretEnsemble')" && \
+  R -e "install.packages('randomForest')" && \
+  R -e "install.packages('pROC')" && \
+  R -e "install.packages('rsparkling')" && \
+  R -e "install.packages('xts')" && \
+  R -e "install.packages('dygraphs')" && \
+  R -e "install.packages('forecast')" && \
+  R -e "install.packages('mclust')" && \
+  R -e "install.packages('factoextra')" && \
+  R -e "install.packages('dbscan')" && \
+  R -e "install.packages('dtw')" && \
+  R -e "install.packages('ROCR')" && \
+  R -e "install.packages('Rtsne')" && \
+  R -e "install.packages('corrplot')" && \
+  R -e "install.packages('dummies')" && \
+  R -e "install.packages('xgboost')" && \
+  R -e "install.packages('e1071')" && \
+  R -e "install.packages('DescTools')" && \
+  R -e "install.packages('packrat')" && \
+  R -e "install.packages('tm')" && \
+  R -e "install.packages('RTextTools')" && \
+  R -e "install.packages('networkD3')" && \
+  R -e "install.packages('sqldf')" && \
+  R -e "install.packages('syuzhet')" && \
+  R -e "install.packages('TSclust')" && \
+  R -e "install.packages('arules')" && \
+  R -e "install.packages('arulesSequences')" && \
+  R -e "install.packages('recommenderlab')" && \
+  R -e "install.packages('AUC')" && \
+  R -e "install.packages('kohonen')" && \
+  R -e "install.packages('topicmodels')" && \
+  R -e "install.packages('argparse')" && \
+  R -e "install.packages('lsa')" && \
+  R -e "install.packages('d3heatmap')" && \
+  R -e "install.packages('pvclust')" && \
+  R -e "install.packages('trend')" && \
+  R -e "install.packages('breakpoint')" && \
+  R -e "install.packages('changepoint')" && \
+  R -e "install.packages('mvoutlier')" && \
+  R -e "install.packages('shinydashboard')" && \
+  R -e "install.packages('FNN')" && \
+  R -e "install.packages('plotly')" && \
+  R -e "install.packages('RMySQL')" && \
+  R -e "install.packages('DescTools')" && \
+  R -e "install.packages('doParallel')" && \
+  R -e "install.packages('ff')" && \
+  R -e "install.packages('ffbase')" && \
+  R -e "install.packages('jsonlite')" && \
+  R -e "install.packages('forecast')" && \
+  R -e "install.packages('tseries')" && \
+  R -e "install.packages('trend')" && \
+  R -e "install.packages('rvest')" && \
+  R -e "install.packages('curl')" && \
+  R -e "install.packages('RSelenium')" && \
+  R -e "install.packages('Rcpp')" && \
+  R -e "install.packages('ggplot2')" && \
+  R -e "install.packages('rpart.plot')" && \
+  R -e "install.packages('labeling')" && \
+  R -e "install.packages('reshape2')" && \
+  R -e "install.packages('shiny')" && \
+  R -e "install.packages('markdown')" && \
+  R -e "install.packages('shinydashboard')" && \
+  R -e "install.packages('knitr')" && \
+  R -e "install.packages('shinyjs')" && \
+  R -e "install.packages('shinythemes')" && \
+  R -e "install.packages('dtplyr')" && \
+  R -e "install.packages('stringr')" && \
+  R -e "install.packages('data.table')" && \
+  R -e "install.packages('xlsx')" && \
+  R -e "install.packages('sas7bdat')" && \
+  R -e "install.packages('readxl')" && \
+  R -e "install.packages('readr')" && \
+  R -e "install.packages('rjson')" && \
+  R -e "install.packages('leaflet')" && \
+  R -e "install.packages('RColorBrewer')" && \
+  R -e "install.packages('classInt')" && \
+  R -e "install.packages('maptools')" && \
+  R -e "install.packages('colorspace')" && \
+  R -e "install.packages('colourpicker')" && \
+  R -e "install.packages('mapproj')" && \
+  R -e "install.packages('maps')" && \
+  R -e "install.packages('scales')" && \
+  R -e "install.packages('sp')" && \
+  R -e "install.packages('FactoMineR')" && \
+  R -e "install.packages('FactoInvestigate')" && \
+  R -e "install.packages('missMDA')" && \
+  R -e "install.packages('RcmdrMisc')" && \
+  R -e "install.packages('ade4')" && \
+  R -e "install.packages('RTextTools')" && \
+  R -e "install.packages('tree')" && \
+  R -e "install.packages('kknn')" && \
+  R -e "install.packages('kernlab')" && \
+  R -e "install.packages('rpart')" && \
+  R -e "install.packages('e1071')" && \
+  R -e "install.packages('randomForest')" && \
+  R -e "install.packages('pls')" && \
+  R -e "install.packages('betareg')" && \
+  R -e "install.packages('glmnet')" && \
+  R -e "install.packages('leaps')" && \
+  R -e "install.packages('mlogit')" && \
+  R -e "install.packages('pROC')" && \
+  R -e "install.packages('caret')" && \
+  R -e "install.packages('wordcloud')" && \
+  R -e "install.packages('stringi')" && \
+  R -e "install.packages('SnowballC')" && \
+  R -e "install.packages('RWeka')" && \
+  R -e "install.packages('hunspell')" && \
+  R -e "install.packages('topicmodels')" && \
+  R -e "install.packages('magrittr')" && \
+  R -e "install.packages('cluster')" && \
+  R -e "install.packages('proxy')" && \
+  R -e "install.packages('skmeans')" && \
+  R -e "install.packages('LDAvis')" && \
+  R -e "install.packages('lsa')" && \
+  R -e "install.packages('doSNOW')" && \
+  R -e "install.packages('cartography')" && \
+  R -e "install.packages('Factoshiny')" && \
+  R -e "install.packages('cairoDevice', INSTALL_opts='--no-test-load')" && \
+  R -e "install.packages('rattle')"
+
+RUN mkdir /root/.R/
+RUN echo CXXFLAGS=-DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION > /root/.R/Makevars
+RUN R -e "install.packages('prophet')"
+
+# Be sure rstudio user has full access to his home directory
+RUN mkdir -p /home/rstudio && \
+  chown -R rstudio:rstudio /home/rstudio && \
+  chmod -R 755 /home/rstudio
+
+ENV HADOOP_CONF_DIR=/etc/hadoop/conf
+
+#UPDATE SECURITY PACKAGE BEGIN
+RUN apt-get update && apt-get upgrade -y
+#UPDATE SECURITY PACKAGE END
+
+COPY entrypoint /entrypoint
+RUN chmod 755 /entrypoint
+
+WORKDIR /sandbox
+
+CMD ["/bin/sh", "-c", "/entrypoint"]

certified/job/R/3.4.4/build.gradle.kts

@@ -0,0 +1,22 @@
+/*
+ * SPDX-License-Identifier: Apache-2.0
+ *
+ * Copyright 2019 Pierre Leresteux.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import com.bmuschko.gradle.docker.DockerRemoteApiPlugin
+import com.saagie.technologies.SaagieTechnologiesGradlePlugin
+
+apply<DockerRemoteApiPlugin>()
+apply<SaagieTechnologiesGradlePlugin>()

certified/job/R/3.4.4/entrypoint

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+set -euo pipefail
+
+if test -f main_script;
+then sh ./main_script;
+else exec "$@"
+fi;

certified/job/R/3.4.4/image_test.yml

@@ -0,0 +1,137 @@
+schemaVersion: "2.0.0"
+
+metadataTest:
+  env:
+    - key: LANG
+      value: "en_US.UTF-8"
+    - key: LC_ALL
+      value: "en_US.UTF-8"
+    - key: RSTUDIO_VERSION
+      value: "1.1.447"
+    - key: R_VERSION
+      value: "3.4.4"
+    - key: "HADOOP_CONF_DIR"
+      value: "/etc/hadoop/conf"
+
+fileExistenceTests:
+  - name: "/home/rstudio"
+    path: "/home/rstudio"
+    shouldExist: true
+    permissions: "drwxr-xr-x"
+  - name: "entrypoint"
+    path: "/entrypoint"
+    shouldExist: true
+    permissions: "-rwxr-xr-x"
+
+commandTests:
+  - name: "R version"
+    command: "Rscript"
+    expectedOutput: ["R version 3.4.4*"]
+    args: ["-e", "R.version.string; getOption('repos')"]
+  - name: "Workdir"
+    command: "pwd"
+    expectedOutput: ["/sandbox"]
+  - name: check All libs
+    command: "bash"
+    args: [
+      "-c",
+      "
+        Rscript -e 'library(sqldf)' &&
+        Rscript -e 'library(syuzhet)' &&
+        Rscript -e 'library(TSclust)' &&
+        Rscript -e 'library(arules)' &&
+        Rscript -e 'library(arulesSequences)' &&
+        Rscript -e 'library(recommenderlab)' &&
+        Rscript -e 'library(AUC)' &&
+        Rscript -e 'library(kohonen)' &&
+        Rscript -e 'library(topicmodels)' &&
+        Rscript -e 'library(argparse)' &&
+        Rscript -e 'library(lsa)' &&
+        Rscript -e 'library(d3heatmap)' &&
+        Rscript -e 'library(pvclust)' &&
+        Rscript -e 'library(trend)' &&
+        Rscript -e 'library(breakpoint)' &&
+        Rscript -e 'library(changepoint)' &&
+        Rscript -e 'library(mvoutlier)' &&
+        Rscript -e 'library(shinydashboard)' &&
+        Rscript -e 'library(FNN)' &&
+        Rscript -e 'library(plotly)' &&
+        Rscript -e 'library(RMySQL)' &&
+        Rscript -e 'library(DescTools)' &&
+        Rscript -e 'library(doParallel)' &&
+        Rscript -e 'library(ff)' &&
+        Rscript -e 'library(ffbase)' &&
+        Rscript -e 'library(jsonlite)' &&
+        Rscript -e 'library(forecast)' &&
+        Rscript -e 'library(tseries)' &&
+        Rscript -e 'library(trend)' &&
+        Rscript -e 'library(rvest)' &&
+        Rscript -e 'library(curl)' &&
+        Rscript -e 'library(RSelenium)' &&
+        Rscript -e 'library(Rcpp)' &&
+        Rscript -e 'library(ggplot2)' &&
+        Rscript -e 'library(rpart)' &&
+        Rscript -e 'library(labeling)' &&
+        Rscript -e 'library(reshape2)' &&
+        Rscript -e 'library(shiny)' &&
+        Rscript -e 'library(markdown)' &&
+        Rscript -e 'library(shinydashboard)' &&
+        Rscript -e 'library(knitr)' &&
+        Rscript -e 'library(shinyjs)' &&
+        Rscript -e 'library(shinythemes)' &&
+        Rscript -e 'library(dtplyr)' &&
+        Rscript -e 'library(stringr)' &&
+        Rscript -e 'library(data.table)' &&
+        Rscript -e 'library(xlsx)' &&
+        Rscript -e 'library(sas7bdat)' &&
+        Rscript -e 'library(readxl)' &&
+        Rscript -e 'library(readr)' &&
+        Rscript -e 'library(rjson)' &&
+        Rscript -e 'library(leaflet)' &&
+        Rscript -e 'library(RColorBrewer)' &&
+        Rscript -e 'library(classInt)' &&
+        Rscript -e 'library(maptools)' &&
+        Rscript -e 'library(colorspace)' &&
+        Rscript -e 'library(colourpicker)' &&
+        Rscript -e 'library(mapproj)' &&
+        Rscript -e 'library(maps)' &&
+        Rscript -e 'library(scales)' &&
+        Rscript -e 'library(sp)' &&
+        Rscript -e 'library(FactoMineR)' &&
+        Rscript -e 'library(FactoInvestigate)' &&
+        Rscript -e 'library(missMDA)' &&
+        Rscript -e 'library(RcmdrMisc)' &&
+        Rscript -e 'library(ade4)' &&
+        Rscript -e 'library(RTextTools)' &&
+        Rscript -e 'library(tree)' &&
+        Rscript -e 'library(kknn)' &&
+        Rscript -e 'library(kernlab)' &&
+        Rscript -e 'library(rpart)' &&
+        Rscript -e 'library(e1071)' &&
+        Rscript -e 'library(randomForest)' &&
+        Rscript -e 'library(pls)' &&
+        Rscript -e 'library(betareg)' &&
+        Rscript -e 'library(glmnet)' &&
+        Rscript -e 'library(leaps)' &&
+        Rscript -e 'library(mlogit)' &&
+        Rscript -e 'library(pROC)' &&
+        Rscript -e 'library(caret)' &&
+        Rscript -e 'library(wordcloud)' &&
+        Rscript -e 'library(stringi)' &&
+        Rscript -e 'library(SnowballC)' &&
+        Rscript -e 'library(RWeka)' &&
+        Rscript -e 'library(hunspell)' &&
+        Rscript -e 'library(topicmodels)' &&
+        Rscript -e 'library(magrittr)' &&
+        Rscript -e 'library(cluster)' &&
+        Rscript -e 'library(proxy)' &&
+        Rscript -e 'library(skmeans)' &&
+        Rscript -e 'library(LDAvis)' &&
+        Rscript -e 'library(lsa)' &&
+        Rscript -e 'library(doSNOW)' &&
+        Rscript -e 'library(cartography)' &&
+        Rscript -e 'library(Factoshiny)' &&
+        Rscript -e 'library(rattle)' &&
+        Rscript -e 'library(prophet);'",
+    ]
+    exitCode: 0

certified/job/R/3.4.4/metadata.yml

@@ -0,0 +1,30 @@
+version:
+  label: 3.4.4
+  isAvailable: true
+  defaultResources:
+    cpu: 0.3
+    memory: 512
+    disk: 512
+  features:
+    - field: COMMAND_LINE
+      label: Command line
+      isMandatory: true
+      comment: Linux shell command to launch the job.
+      defaultValue: Rscript {file} arg1 arg2
+    - field: ARTIFACT
+      label: Package
+      isMandatory: false
+      comment: "Compatible upload file : .r"
+    - field: SCHEDULER
+      label: Scheduled
+      isMandatory: true
+
+techno:
+  id: df7226be-f11a-4c6f-8e7d-ee5d7964f340
+  label: R
+  available: false
+  icon: r
+  recommendedVersion: 3.4.4
+  docker:
+    image: saagie/r-image
+    version: 3.4.4-0.5.0_R