adding test library loads for all installed R libraries

Author: jen-reeve

docker/Dockerfile

@@ -2,36 +2,36 @@ FROM rocker/geospatial:4.5.3
 
 # install system dependencies
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
-        curl \
-        dnsutils \
-        git \
-        jq \
-        ldap-utils \
-        libnss-ldapd \
-        libpam-ldapd \
-        less \
-        nano \
-        nodejs \
-        nscd \
-        nslcd \
-        rsync \
-        unzip \
-        vim \
-        wget \
-        zip \
-        python3 \
-        python3-pip \
-        python3-venv \
-        python3-dev \
-        build-essential \
-        zlib1g-dev \
-        libncurses5-dev \
-        libncursesw5-dev \
-        libbz2-dev \
-        liblzma-dev \
-        libcurl4-openssl-dev \
-        libssl-dev \
-        default-jre \
+    curl \
+    dnsutils \
+    git \
+    jq \
+    ldap-utils \
+    libnss-ldapd \
+    libpam-ldapd \
+    less \
+    nano \
+    nodejs \
+    nscd \
+    nslcd \
+    rsync \
+    unzip \
+    vim \
+    wget \
+    zip \
+    python3 \
+    python3-pip \
+    python3-venv \
+    python3-dev \
+    build-essential \
+    zlib1g-dev \
+    libncurses5-dev \
+    libncursesw5-dev \
+    libbz2-dev \
+    liblzma-dev \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    default-jre \
     && rm -rf /var/lib/apt/lists/*
 
 
@@ -145,11 +145,11 @@ RUN wget https://github.com/alexdobin/STAR/releases/download/2.7.11b/STAR_2.7.11
 # Install QualiMap (resilient)
 RUN set -eux; \
     curl -fSL --retry 5 --retry-connrefused --retry-delay 3 \
-      -o qualimap_v2.3.zip \
-      https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.3.zip \
+    -o qualimap_v2.3.zip \
+    https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.3.zip \
     || curl -fSL --retry 5 --retry-connrefused --retry-delay 3 \
-      -o qualimap_v2.3.zip \
-      http://qualimap.conesalab.org/qualimap_v2.3.zip; \
+    -o qualimap_v2.3.zip \
+    http://qualimap.conesalab.org/qualimap_v2.3.zip; \
     unzip -q qualimap_v2.3.zip; \
     mv qualimap_v2.3 /opt/qualimap; \
     printf '%s\n' '#!/bin/bash' 'exec java -Xms32m -Xmx2g -jar /opt/qualimap/qualimap.jar "$@"' > /usr/local/bin/qualimap; \
@@ -171,7 +171,21 @@ RUN Rscript -e 'install.packages("BiocManager", repos = "https://cloud.r-project
     && Rscript -e 'BiocManager::install("GO.db")' \
     && Rscript -e 'BiocManager::install("org.Sc.sgd.db")' \
     && Rscript -e 'install.packages("ggiraph")' \
-    && Rscript -e 'install.packages("plotly")' \
+    && Rscript -e 'install.packages("plotly")'
+
+# confirm all R packages load
+RUN Rscript -e 'library(BiocManager)' \
+    && Rscript -e 'library(limma)' \
+    && Rscript -e 'library(edgeR)' \
+    && Rscript -e 'library(DESeq2)' \
+    && Rscript -e 'library(beeswarm)' \
+    && Rscript -e 'library(knitr)' \
+    && Rscript -e 'library(gplots)' \
+    && Rscript -e 'library(goseq)' \
+    && Rscript -e 'library(GO.db)' \
+    && Rscript -e 'library(org.Sc.sgd.db)' \
+    && Rscript -e 'library(ggiraph)' \
+    && Rscript -e 'library(plotly)'
 
 # Set up environment variables for the virtual environment
 ENV PATH="/opt/venv/bin:$PATH"