[ci] pipeline rules for benchmark tests

[ci] check if package can be loaded in second stage

[ci] check for singularity

[ci] singularity & go installation

[ci] singularity setup in separate bash script

[ci] test custom container

[ci] 2 stage test custom container

[ci] remove installation of vtk and miniconda as already available in container

.CI-setup.sh

+#!/bin/bash
+
+### Setup singularity ###
+# adapted from: https://sylabs.io/guides/3.0/user-guide/installation.html
+# install dependencies
+apt-get update
+apt-get install -y \
+    build-essential \
+    libssl-dev \
+    uuid-dev \
+    libgpgme11-dev \
+    squashfs-tools \
+    libseccomp-dev \
+    pkg-config \
+    wget
+# yum update -y && \
+#     yum groupinstall -y 'Development Tools' && \
+#     yum install -y \
+#     openssl-devel \
+#     libuuid-devel \
+#     libseccomp-devel \
+#     wget \
+#     squashfs-tools
+
+
+
+# install go
+export GOVERSION=1.15.6 OS=linux ARCH=amd64
+wget https://dl.google.com/go/go$GOVERSION.$OS-$ARCH.tar.gz
+tar -C /usr/local -xzvf go$GOVERSION.$OS-$ARCH.tar.gz
+rm go$GOVERSION.$OS-$ARCH.tar.gz
+
+# install singularity
+export VERSION=3.9.1
+mkdir -p $GOPATH/src/github.com/sylabs
+cd $GOPATH/src/github.com/sylabs
+wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz
+tar -xzf singularity-ce-${VERSION}.tar.gz
+cd ./singularity
+./mconfig
+make -C ./builddir
+make -C ./builddir install
\ No newline at end of file

.Rbuildignore

@@ -10,3 +10,4 @@
 ^doc$
 ^Meta$
 ^data-raw$
+^.CI-setup.sh

.gitlab-ci.yml

-image: rocker/tidyverse
+
+stages:
+  - test
+  - benchmark-test
 
 test:
+  image: $CI_REGISTRY_IMAGE
   stage: test
   tags:
     - envinf2
@@ -15,11 +19,10 @@ test:
     # checks if the packages from the Imports, Suggests, LinkinTo field
     # are already installed in the cache
     - R -e '.libPaths(new = Sys.getenv("R_LIBS_USER"))'
-    # python dependencies
-    - if [ ! -d "$RETICULATE_MINICONDA_PATH" ]; then R -e 'reticulate::install_miniconda()'; fi
-    - R -e 'if(tryCatch(reticulate::import("vtk"), error = function(e) return(TRUE))) reticulate::py_install("vtk")'
+    # Build and Check r2ogs6
     - R CMD build . --no-build-vignettes --no-manual
     - R CMD check $(ls -1t *.tar.gz | head -n 1) --no-build-vignettes --no-manual
+    #echo First Stage!
   cache:
     key: "$CI_COMMIT_REF_SLUG"
     untracked: true
@@ -27,7 +30,16 @@ test:
       - "$R_LIBS_USER"
       - "$RETICULATE_MINICONDA_PATH"
       - "$RETICULATE_PYTHON_ENV"
-  # script will only run then attempting to merge/push to master
-  only:
-    - merge_requests
-    - master
+  rules:
+    - if: '$CI_PIPELINE_SOURCE == "merge_request_event" || $CI_PIPELINE_SOURCE == "web"'
+
+benchmark-test:
+  image: $CI_REGISTRY_IMAGE
+  stage: benchmark-test
+  rules:
+    - if: '$CI_PIPELINE_SOURCE == "web" || $CI_PIPELINE_SOURCE == "merge_request_event"'
+      when: on_success
+  script:
+    - R -e 'print("HELLO R")'
+    - singularity --version
+