Patch cuda dev tools (#736) (#743)

Author: cboettig

dockerfiles/cuda_4.3.1.Dockerfile

@@ -11,7 +11,9 @@ ENV TZ=Etc/UTC
 ENV NVBLAS_CONFIG_FILE=/etc/nvblas.conf
 ENV PYTHON_CONFIGURE_OPTS=--enable-shared
 ENV RETICULATE_AUTOCONFIGURE=0
-ENV PATH=${PATH}:${CUDA_HOME}/bin
+ENV PURGE_BUILDDEPS=false
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH=${PATH}:${VIRTUAL_ENV}/bin:${CUDA_HOME}/bin
 
 COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 

dockerfiles/cuda_4.3.2.Dockerfile

@@ -11,7 +11,9 @@ ENV TZ=Etc/UTC
 ENV NVBLAS_CONFIG_FILE=/etc/nvblas.conf
 ENV PYTHON_CONFIGURE_OPTS=--enable-shared
 ENV RETICULATE_AUTOCONFIGURE=0
-ENV PATH=${PATH}:${CUDA_HOME}/bin
+ENV PURGE_BUILDDEPS=false
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH=${PATH}:${VIRTUAL_ENV}/bin:${CUDA_HOME}/bin
 
 COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 

dockerfiles/cuda_devel.Dockerfile

@@ -11,7 +11,9 @@ ENV TZ=Etc/UTC
 ENV NVBLAS_CONFIG_FILE=/etc/nvblas.conf
 ENV PYTHON_CONFIGURE_OPTS=--enable-shared
 ENV RETICULATE_AUTOCONFIGURE=0
-ENV PATH=${PATH}:${CUDA_HOME}/bin
+ENV PURGE_BUILDDEPS=false
+ENV VIRTUAL_ENV=/opt/venv
+ENV PATH=${PATH}:${VIRTUAL_ENV}/bin:${CUDA_HOME}/bin
 
 COPY scripts/install_R_source.sh /rocker_scripts/install_R_source.sh
 

scripts/install_R_source.sh

@@ -11,6 +11,7 @@
 set -e
 
 R_VERSION=${1:-${R_VERSION:-"latest"}}
+PURGE_BUILDDEPS=${PURGE_BUILDDEPS=-"true"}
 
 # shellcheck source=/dev/null
 source /etc/os-release
@@ -158,7 +159,9 @@ rm -rf "R.tar.gz"
 cp /usr/bin/checkbashisms /usr/local/bin/checkbashisms
 
 # shellcheck disable=SC2086
-apt-get remove --purge -y ${BUILDDEPS}
+if [ "${PURGE_BUILDDEPS}" == "true" ]; then
+    apt-get remove --purge -y ${BUILDDEPS}
+fi
 apt-get autoremove -y
 apt-get autoclean -y
 rm -rf /var/lib/apt/lists/*

scripts/install_python.sh

@@ -41,7 +41,7 @@ python3 -m pip --no-cache-dir install --upgrade \
 # Make the venv owned by the staff group, so users can install packages
 # without having to be root
 chown -R root:staff "${VIRTUAL_ENV}"
-chmod g+ws "${VIRTUAL_ENV}"
+chmod -R g+ws "${VIRTUAL_ENV}"
 
 install2.r --error --skipmissing --skipinstalled -n "$NCPUS" reticulate
 

scripts/setup_R.sh

@@ -10,6 +10,7 @@
 set -e
 
 CRAN=${1:-${CRAN:-"https://cran.r-project.org"}}
+PURGE_BUILDDEPS=${PURGE_BUILDDEPS=-"true"}
 
 ARCH=$(uname -m)
 
@@ -68,7 +69,9 @@ if [ ! -x "$(command -v r)" ]; then
 
     # Clean up
     # shellcheck disable=SC2086
-    apt-get remove --purge -y ${BUILDDEPS}
+    if [ "${PURGE_BUILDDEPS}" == "true" ]; then
+        apt-get remove --purge -y ${BUILDDEPS}
+    fi
     apt-get autoremove -y
     apt-get autoclean -y
 fi

stacks/4.3.1.json

@@ -203,7 +203,9 @@
         "NVBLAS_CONFIG_FILE": "/etc/nvblas.conf",
         "PYTHON_CONFIGURE_OPTS": "--enable-shared",
         "RETICULATE_AUTOCONFIGURE": "0",
-        "PATH": "${PATH}:${CUDA_HOME}/bin"
+        "PURGE_BUILDDEPS": "false",
+        "VIRTUAL_ENV": "/opt/venv",
+        "PATH": "${PATH}:${VIRTUAL_ENV}/bin:${CUDA_HOME}/bin"
       },
       "COPY_a_script": "scripts/install_R_source.sh /rocker_scripts/install_R_source.sh",
       "RUN_a_script": "/rocker_scripts/install_R_source.sh",

stacks/4.3.2.json

@@ -257,7 +257,9 @@
         "NVBLAS_CONFIG_FILE": "/etc/nvblas.conf",
         "PYTHON_CONFIGURE_OPTS": "--enable-shared",
         "RETICULATE_AUTOCONFIGURE": "0",
-        "PATH": "${PATH}:${CUDA_HOME}/bin"
+        "PURGE_BUILDDEPS": "false",
+        "VIRTUAL_ENV": "/opt/venv",
+        "PATH": "${PATH}:${VIRTUAL_ENV}/bin:${CUDA_HOME}/bin"
       },
       "COPY_a_script": "scripts/install_R_source.sh /rocker_scripts/install_R_source.sh",
       "RUN_a_script": "/rocker_scripts/install_R_source.sh",

stacks/devel.json

@@ -156,7 +156,9 @@
         "NVBLAS_CONFIG_FILE": "/etc/nvblas.conf",
         "PYTHON_CONFIGURE_OPTS": "--enable-shared",
         "RETICULATE_AUTOCONFIGURE": "0",
-        "PATH": "${PATH}:${CUDA_HOME}/bin"
+        "PURGE_BUILDDEPS": "false",
+        "VIRTUAL_ENV": "/opt/venv",
+        "PATH": "${PATH}:${VIRTUAL_ENV}/bin:${CUDA_HOME}/bin"
       },
       "COPY_a_script": "scripts/install_R_source.sh /rocker_scripts/install_R_source.sh",
       "RUN_a_script": "/rocker_scripts/install_R_source.sh",