Adding additional packages (R and Bioconductor) for testing

images/labkey/rstudio-base/Dockerfile

@@ -1,4 +1,4 @@
-ARG VERSION=4.0.5
+ARG VERSION=4.3.1
 FROM rocker/rstudio:${VERSION}
 
 RUN apt-get update && \

images/labkey/rstudio-singleuser/Dockerfile

@@ -1,4 +1,4 @@
-ARG VERSION=4.0.5
+ARG VERSION=4.3.1
 FROM rocker/rstudio:${VERSION}
 
 COPY rstudio-singleuser /

images/labkey/rstudio/Dockerfile

@@ -3,13 +3,24 @@ FROM labkey/rstudio-base:${VERSION}
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends  \
-	curl libcurl4-openssl-dev \
+    curl libcurl4-openssl-dev \
         libgd-dev libcairo2 libcairo2-dev libxt-dev pandoc \
-        libssl-dev openssl && \
+        libssl-dev openssl cmake libnlopt-dev libgit2-dev libfontconfig1-dev \
+        libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
 COPY install.R /
 RUN dos2unix install.R && \
     R --no-site-file -f install.R &&  \
     chmod -R 755 /usr/local/lib/R/site-library
+
+COPY extra.R /
+RUN dos2unix extra.R && \
+    R --no-site-file -f extra.R &&  \
+    chmod -R 755 /usr/local/lib/R/site-library
+
+COPY bioConductor.R /
+RUN dos2unix bioConductor.R && \
+    R --no-site-file -f bioConductor.R &&  \
+    chmod -R 755 /usr/local/lib/R/site-library

images/labkey/rstudio/bioConductor.R

@@ -0,0 +1,7 @@
+#!/usr/bin/env Rscript
+BiocManager::install("flowCore")
+BiocManager::install("flowViz")
+BiocManager::install("cytolib")
+BiocManager::install("ncdfFlow")
+BiocManager::install("flowWorkspace")
+BiocManager::install("CytoML")

images/labkey/rstudio/extra.R

@@ -0,0 +1,44 @@
+##
+#  Copyright (c) 2017 LabKey Corporation
+# 
+#  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
+# 
+#      http://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.
+##
+install.packages("BiocManager", repos = "https://cloud.r-project.org")
+install.packages("devtools", repos = "https://cloud.r-project.org/")
+install.packages(c(
+  "locfit",
+  "ks",
+  "hdrcde",
+  "rainbow",
+  "fds",
+  "fda"
+  ),
+  repos='https://cran.rstudio.com/')
+install.packages(c(
+  "latticeExtra",
+  "lme4",
+  "lmtest",
+  "openssl",
+  "plotly",
+  "plyr",
+  "png",
+  "readxl",
+  "reshape2",
+  "RSQLite",
+  "stringr",
+  "stringi",
+  "tidyverse",
+  "tibble",
+  "tidyr"
+  ),
+  repos='https://cran.rstudio.com/')

images/labkey/rstudio/make

@@ -2,7 +2,7 @@
 
 echo requires docker 17.05.0 or greater
 
-export VERSION=${1-4.0.5}
+export VERSION=${1-4.3.1}
 shift
 
 echo build VERSION=${VERSION}