rocker-org · eitsupi · May 7, 2022 · Apr 29, 2022 · Apr 29, 2022 · May 1, 2022
diff --git a/.github/workflows/scripts-test.yml b/.github/workflows/scripts-test.yml
@@ -39,7 +39,8 @@ jobs:
       - name: Prepare build
         id: prep
         run: |
-          test_name="${{ matrix.base_image }}-${{ matrix.tag }}-${{ matrix.script_name }}-${{ matrix.script_arg }}"
+          lower_script_name=$(echo ${{ matrix.script_name }} | tr '[:upper:]' '[:lower:]')
+          test_name="${{ matrix.base_image }}-${{ matrix.tag }}-${lower_script_name}-${{ matrix.script_arg }}"
           echo ::set-output name=output_tag::"${test_name/"/"/"-"}"
       - name: test build
         run: |

diff --git a/dockerfiles/binder_4.0.0.Dockerfile b/dockerfiles/binder_4.0.0.Dockerfile
@@ -7,12 +7,11 @@ LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
 
 ENV NB_USER=rstudio
 
-RUN /rocker_scripts/install_python.sh
 RUN /rocker_scripts/install_binder.sh
 
 EXPOSE 8888
 
-CMD jupyter notebook --ip 0.0.0.0
+CMD ["/bin/sh", "-c", "jupyter notebook --ip 0.0.0.0"]
 
 USER ${NB_USER}
 

diff --git a/dockerfiles/binder_4.0.1.Dockerfile b/dockerfiles/binder_4.0.1.Dockerfile
@@ -7,12 +7,11 @@ LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
 
 ENV NB_USER=rstudio
 
-RUN /rocker_scripts/install_python.sh
 RUN /rocker_scripts/install_binder.sh
 
 EXPOSE 8888
 
-CMD jupyter notebook --ip 0.0.0.0
+CMD ["/bin/sh", "-c", "jupyter notebook --ip 0.0.0.0"]
 
 USER ${NB_USER}
 

diff --git a/dockerfiles/binder_4.0.2.Dockerfile b/dockerfiles/binder_4.0.2.Dockerfile
@@ -7,12 +7,11 @@ LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
 
 ENV NB_USER=rstudio
 
-RUN /rocker_scripts/install_python.sh
 RUN /rocker_scripts/install_binder.sh
 
 EXPOSE 8888
 
-CMD jupyter notebook --ip 0.0.0.0
+CMD ["/bin/sh", "-c", "jupyter notebook --ip 0.0.0.0"]
 
 USER ${NB_USER}
 

diff --git a/dockerfiles/binder_4.0.3.Dockerfile b/dockerfiles/binder_4.0.3.Dockerfile
@@ -7,12 +7,11 @@ LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
 
 ENV NB_USER=rstudio
 
-RUN /rocker_scripts/install_python.sh
 RUN /rocker_scripts/install_binder.sh
 
 EXPOSE 8888
 
-CMD jupyter notebook --ip 0.0.0.0
+CMD ["/bin/sh", "-c", "jupyter notebook --ip 0.0.0.0"]
 
 USER ${NB_USER}
 

diff --git a/dockerfiles/binder_4.0.4.Dockerfile b/dockerfiles/binder_4.0.4.Dockerfile
@@ -7,12 +7,11 @@ LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
 
 ENV NB_USER=rstudio
 
-RUN /rocker_scripts/install_python.sh
 RUN /rocker_scripts/install_binder.sh
 
 EXPOSE 8888
 
-CMD jupyter notebook --ip 0.0.0.0
+CMD ["/bin/sh", "-c", "jupyter notebook --ip 0.0.0.0"]
 
 USER ${NB_USER}
 

diff --git a/dockerfiles/binder_4.0.5.Dockerfile b/dockerfiles/binder_4.0.5.Dockerfile
@@ -7,12 +7,11 @@ LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
 
 ENV NB_USER=rstudio
 
-RUN /rocker_scripts/install_python.sh
 RUN /rocker_scripts/install_binder.sh
 
 EXPOSE 8888
 
-CMD jupyter notebook --ip 0.0.0.0
+CMD ["/bin/sh", "-c", "jupyter notebook --ip 0.0.0.0"]
 
 USER ${NB_USER}
 

diff --git a/dockerfiles/binder_4.1.0.Dockerfile b/dockerfiles/binder_4.1.0.Dockerfile
@@ -7,12 +7,11 @@ LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
 
 ENV NB_USER=rstudio
 
-RUN /rocker_scripts/install_python.sh
 RUN /rocker_scripts/install_binder.sh
 
 EXPOSE 8888
 
-CMD jupyter notebook --ip 0.0.0.0
+CMD ["/bin/sh", "-c", "jupyter notebook --ip 0.0.0.0"]
 
 USER ${NB_USER}
 

diff --git a/dockerfiles/binder_4.1.1.Dockerfile b/dockerfiles/binder_4.1.1.Dockerfile
@@ -7,12 +7,11 @@ LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
 
 ENV NB_USER=rstudio
 
-RUN /rocker_scripts/install_python.sh
 RUN /rocker_scripts/install_binder.sh
 
 EXPOSE 8888
 
-CMD jupyter notebook --ip 0.0.0.0
+CMD ["/bin/sh", "-c", "jupyter notebook --ip 0.0.0.0"]
 
 USER ${NB_USER}
 

diff --git a/dockerfiles/binder_4.1.2.Dockerfile b/dockerfiles/binder_4.1.2.Dockerfile
@@ -7,12 +7,11 @@ LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
 
 ENV NB_USER=rstudio
 
-RUN /rocker_scripts/install_python.sh
 RUN /rocker_scripts/install_binder.sh
 
 EXPOSE 8888
 
-CMD jupyter notebook --ip 0.0.0.0
+CMD ["/bin/sh", "-c", "jupyter notebook --ip 0.0.0.0"]
 
 USER ${NB_USER}
 

diff --git a/dockerfiles/binder_4.1.3.Dockerfile b/dockerfiles/binder_4.1.3.Dockerfile
@@ -7,12 +7,11 @@ LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
 
 ENV NB_USER=rstudio
 
-RUN /rocker_scripts/install_python.sh
 RUN /rocker_scripts/install_binder.sh
 
 EXPOSE 8888
 
-CMD jupyter notebook --ip 0.0.0.0
+CMD ["/bin/sh", "-c", "jupyter notebook --ip 0.0.0.0"]
 
 USER ${NB_USER}
 

diff --git a/dockerfiles/binder_4.2.0.Dockerfile b/dockerfiles/binder_4.2.0.Dockerfile
@@ -7,12 +7,11 @@ LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
 
 ENV NB_USER=rstudio
 
-RUN /rocker_scripts/install_python.sh
 RUN /rocker_scripts/install_binder.sh
 
 EXPOSE 8888
 
-CMD jupyter notebook --ip 0.0.0.0
+CMD ["/bin/sh", "-c", "jupyter notebook --ip 0.0.0.0"]
 
 USER ${NB_USER}
 

diff --git a/dockerfiles/binder_devel.Dockerfile b/dockerfiles/binder_devel.Dockerfile
@@ -7,12 +7,11 @@ LABEL org.opencontainers.image.licenses="GPL-2.0-or-later" \
 
 ENV NB_USER=rstudio
 
-RUN /rocker_scripts/install_python.sh
 RUN /rocker_scripts/install_binder.sh
 
 EXPOSE 8888
 
-CMD jupyter notebook --ip 0.0.0.0
+CMD ["/bin/sh", "-c", "jupyter notebook --ip 0.0.0.0"]
 
 USER ${NB_USER}
 

diff --git a/scripts/default_user.sh b/scripts/default_user.sh
@@ -27,5 +27,7 @@ if [ -x "$(command -v shiny-server)" ]; then
 fi
 
 ## configure git not to request password each time
-git config --system credential.helper 'cache --timeout=3600'
-git config --system push.default simple
+if [ -x "$(command -v git)" ]; then
+    git config --system credential.helper 'cache --timeout=3600'
+    git config --system push.default simple
+fi
diff --git a/scripts/install_binder.sh b/scripts/install_binder.sh
@@ -1,31 +1,56 @@
 #!/bin/bash
 set -e
 
-## force install of last working version of rstudio, if necessary
-# RSTUDIO_VERSION=1.3.959 /rocker_scripts/install_rstudio.sh
+## build ARGs
+NCPUS=${NCPUS:-"-1"}
+
+NB_USER=${NB_USER:-${DEFAULT_USER:-"rstudio"}}
+
+# a function to install apt packages only if they are not installed
+function apt_install() {
+    if ! dpkg -s "$@" >/dev/null 2>&1; then
+        if [ "$(find /var/lib/apt/lists/* | wc -l)" = "0" ]; then
+            apt-get update
+        fi
+        apt-get install -y --no-install-recommends "$@"
+    fi
+}
+
+apt_install \
+    sudo \
+    libzmq3-dev
+
+# set up the default user if it does not exist
+if ! id -u "${NB_USER}" >/dev/null 2>&1; then
+    /rocker_scripts/default_user.sh "${NB_USER}"
+fi
+
+# install python
+/rocker_scripts/install_python.sh
 
-## NOTE: this runs as user NB_USER!
 PYTHON_VENV_PATH=${PYTHON_VENV_PATH:-/opt/venv/reticulate}
-DEFAULT_USER=${DEFAULT_USER:-rstudio}
-NB_USER=${NB_USER:-${DEFAULT_USER}}
-NB_UID=${NB_UID:-1000}
 WORKDIR=${WORKDIR:-/home/${NB_USER}}
-usermod -l "${NB_USER}" "${DEFAULT_USER}"
 # Create a venv dir owned by unprivileged user & set up notebook in it
 # This allows non-root to install python libraries if required
 mkdir -p "${PYTHON_VENV_PATH}"
 chown -R "${NB_USER}" "${PYTHON_VENV_PATH}"
 
+# to use pyenv in a RStudio session, we need to include the PATH in the .profile file
+# https://github.com/rocker-org/rocker-versioned2/issues/428
 PATH=/opt/pyenv/bin:${PATH}
-
-# And set ENV for R! It doesn't read from the environment...
-echo "PATH=${PATH}" >>"${R_HOME}/etc/Renviron.site"
 echo "export PATH=${PATH}" >>"${WORKDIR}/.profile"
 
 cd "${WORKDIR}"
 ## This gets run as user
 sudo -u "${NB_USER}" python3 -m venv "${PYTHON_VENV_PATH}"
-pip3 install --no-cache-dir jupyter-rsession-proxy notebook jupyterlab >=2.0
 
-R --quiet -e "devtools::install_github('IRkernel/IRkernel')"
+python3 -m pip install --no-cache-dir jupyter-rsession-proxy notebook jupyterlab
+
+install2.r --error --skipinstalled -n "$NCPUS" remotes
+
+R --quiet -e "remotes::install_github('IRkernel/IRkernel')"
 R --quiet -e "IRkernel::installspec(prefix='${PYTHON_VENV_PATH}')"
+
+# Clean up
+rm -rf /var/lib/apt/lists/*
+rm -rf /tmp/downloaded_packages
diff --git a/scripts/install_cuda-10.1.sh b/scripts/install_cuda-10.1.sh
@@ -1,25 +1,36 @@
 #!/bin/bash
 set -e
 
-apt-get update
-apt-get install -y --no-install-recommends \
-    gnupg2 curl ca-certificates
-curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub | apt-key add -
+# a function to install apt packages only if they are not installed
+function apt_install() {
+    if ! dpkg -s "$@" >/dev/null 2>&1; then
+        if [ "$(find /var/lib/apt/lists/* | wc -l)" = "0" ]; then
+            apt-get update
+        fi
+        apt-get install -y --no-install-recommends "$@"
+    fi
+}
+
+apt_install \
+    gnupg2 \
+    curl \
+    ca-certificates
+
+apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub
+apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
 echo "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64 /" >/etc/apt/sources.list.d/cuda.list
 echo "deb https://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1804/x86_64 /" >/etc/apt/sources.list.d/nvidia-ml.list
-apt-get purge --autoremove -y curl
-rm -rf /var/lib/apt/lists/*
+apt-get update
 
 CUDA_VERSION=${CUDA_VERSION:-10.1.243}
 CUDA_PKG_VERSION=${CUDA_PKG_VERSION:-10-1=$CUDA_VERSION-1}
 
 # For libraries in the cuda-compat-* package: https://docs.nvidia.com/cuda/eula/index.html#attachment-a
-apt-get update
-apt-get install -y --no-install-recommends \
+apt_install \
     "cuda-cudart-${CUDA_PKG_VERSION}" \
-    cuda-compat-10-1 &&
-    ln -s cuda-10.1 /usr/local/cuda &&
-    rm -rf /var/lib/apt/lists/*
+    cuda-compat-10-1
+
+ln -s cuda-10.1 /usr/local/cuda
 
 # Required for nvidia-docker v1
 echo "/usr/local/nvidia/lib" >>/etc/ld.so.conf.d/nvidia.conf &&
@@ -47,8 +58,7 @@ LIBNVINFER_MAJOR_VERSION=6
 # There appears to be a regression in libcublas10=10.2.2.89-1 which
 # prevents cublas from initializing in TF. See
 # https://github.com/tensorflow/tensorflow/issues/9489#issuecomment-562394257
-apt-get update
-apt-get install -y --no-install-recommends --allow-downgrades \
+apt_install \
     build-essential \
     cuda-command-line-tools-10-1 \
     libcublas10=10.2.1.243-1 \
@@ -67,11 +77,10 @@ apt-get install -y --no-install-recommends --allow-downgrades \
     unzip
 
 # Install TensorRT if not building for PowerPC
-apt-get update
-apt-get install -y --no-install-recommends libnvinfer${LIBNVINFER_MAJOR_VERSION}=${LIBNVINFER}+cuda${CUDA} \
+apt_install \
+    libnvinfer${LIBNVINFER_MAJOR_VERSION}=${LIBNVINFER}+cuda${CUDA} \
     libnvinfer-plugin${LIBNVINFER_MAJOR_VERSION}=${LIBNVINFER}+cuda${CUDA}
 apt-get clean
-rm -rf /var/lib/apt/lists/*
 
 # For CUDA profiling, TensorFlow requires CUPTI.
 LD_LIBRARY_PATH=${LD_LIBRARY_PATH:-/usr/local/cuda/extras/CUPTI/lib64:/usr/local/cuda/lib64:$LD_LIBRARY_PATH}
@@ -87,3 +96,6 @@ ldconfig
 
 ## Add tensorflow-gpu==1.15 dependencies on the CUDA 10.0 libraries:
 /rocker_scripts/install_tf1_cuda_10_0.sh
+
+# Clean up
+rm -rf /var/lib/apt/lists/*