Add dependency for 'fs' R package

.github/workflows/hadolint.yml

@@ -0,0 +1,22 @@
+---
+name: hadolint
+
+"on":
+  pull_request:
+    branches:
+      - develop
+
+jobs:
+  hadolint:
+    name: hadolint
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6
+      - name: Run hadolint (R images)
+        uses: hadolint/hadolint-action@v3.3.0
+        with:
+          dockerfile: images/labkey/*/Dockerfile
+          recursive: true
+          failure-threshold: 'warning'
+          ignore: 'DL3008'  # Don't worry about pinning versions

.github/workflows/shellcheck.yml

@@ -0,0 +1,16 @@
+---
+name: 'Run Shellcheck'
+
+"on":
+  - pull_request
+
+jobs:
+  shellcheck:
+    name: Shellcheck
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+
+      - name: Run ShellCheck
+        uses: ludeeus/action-shellcheck@2.0.0

.github/workflows/validate_pr.yml

@@ -0,0 +1,26 @@
+---
+# Workflow to validate Pull Request branches
+name: PR Validation
+
+# Trigger on PR creation
+"on":
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - ready_for_review
+
+jobs:
+  validate_pr:
+    if: github.event.pull_request.head.repo.owner.login == 'LabKey'
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Validate PR Branches
+        uses: LabKey/gitHubActions/validate-pr@develop
+        with:
+          pr_base: ${{ github.event.pull_request.base.ref }}
+          pr_head: ${{ github.event.pull_request.head.ref }}
+          pr_number: ${{ github.event.pull_request.number }}
+          pr_title: ${{ github.event.pull_request.title }}
+          github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/yamllint.yml

@@ -0,0 +1,16 @@
+---
+name: 'Yamllint GitHub Actions'
+
+"on":
+  - pull_request
+
+jobs:
+  yamllint:
+    name: 'Yamllint'
+    runs-on: ubuntu-latest
+    steps:
+      - name: 'Checkout'
+        uses: actions/checkout@v6
+
+      - name: yaml-lint
+        uses: ibiqlik/action-yamllint@v3

.gitignore

@@ -0,0 +1 @@
+.claude/

images/labkey/r/Dockerfile

@@ -2,12 +2,9 @@ ARG VERSION=18.04
 FROM ubuntu:${VERSION}
 
 RUN apt-get update && \
-    apt-get install -y --no-install-recommends apt-transport-https apt-utils software-properties-common
-
-RUN apt-get install -y --no-install-recommends build-essential dos2unix libopenblas-dev libssl-dev libxml2-dev nano pandoc procps xvfb x11-common
-
-# NOTE much faster to use apt to install prebuilt packages than using "install.packages()"
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y \ 
+    apt-get install -y --no-install-recommends apt-transport-https apt-utils software-properties-common && \
+    apt-get install -y --no-install-recommends build-essential dos2unix libopenblas-dev libssl-dev libxml2-dev nano pandoc procps xvfb x11-common && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
     r-base \
     r-cran-bitops \
     r-cran-cairo \
@@ -28,12 +25,14 @@ RUN DEBIAN_FRONTEND=noninteractive apt-get install -y \
     r-cran-markdown \
     r-cran-scales \
     r-cran-stringr \
-    r-cran-tidyr 
+    r-cran-tidyr && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
 
 COPY install.R /tmp/
-RUN R --vanilla -f /tmp/install.R 
+RUN R --vanilla -f /tmp/install.R
 
-RUN ln -fs /usr/share/zoneinfo/America/Los_Angeles/etc/localtime && \
+RUN ln -fs /usr/share/zoneinfo/America/Los_Angeles /etc/localtime && \
     dpkg-reconfigure --frontend noninteractive tzdata
 
 RUN R --version

images/labkey/rsandbox/Dockerfile

@@ -3,7 +3,7 @@ FROM rocker/r-ver:${VERSION}
 
 RUN apt-get update && \
 	apt-get install -y --no-install-recommends apt-transport-https apt-utils software-properties-common && \
-	apt-get install -y --no-install-recommends build-essential dos2unix libopenblas-dev libxml2-dev nano pandoc procps xvfb x11-common && \
+	apt-get install -y --no-install-recommends build-essential dos2unix libopenblas-dev libxml2-dev nano pandoc procps xvfb x11-common libuv1-dev && \
 	apt-get install -y --no-install-recommends sudo && \
 	apt-get install -y --no-install-recommends  \
 		curl libcurl4-openssl-dev \

images/labkey/rstudio-base/Dockerfile

@@ -1,9 +1,11 @@
 ARG VERSION=4.0.5
 FROM rocker/rstudio:${VERSION}
 
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
 RUN apt-get update && \
     apt-get install -y --no-install-recommends apt-utils && \
-    apt-get install -y --no-install-recommends dos2unix nano procps libxml2-dev xvfb zlib1g-dev && \
+    apt-get install -y --no-install-recommends dos2unix nano procps libxml2-dev xvfb zlib1g-dev libuv1-dev && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
@@ -23,4 +25,4 @@
 
 COPY cleanupSessionFiles.sh /
 RUN dos2unix /cleanupSessionFiles.sh
 RUN chmod 755 /cleanupSessionFiles.sh