update CICD pipeline

.gitlab-ci.yml

-# .gitlab-ci.yml for inldata
-
-image: rocker/geospatial
-
-stages:
-  - check
+image: artifactory.wma.chs.usgs.gov/docker-official-mirror/rocker/geospatial:latest
 
 variables:
   _R_CHECK_CRAN_INCOMING_: "false"
-  _R_CHECK_SUGGESTS_ONLY: "false"
   _R_CHECK_FORCE_SUGGESTS_: "true"
-  APT_CACHE: "$CI_PROJECT_DIR/ci/lib/apt-cache"
-  CRAN_MIRROR: "https://cloud.r-project.org"
+  _R_CHECK_DONTTEST_EXAMPLES_: "false"
+  NOT_CRAN: "true"
+  R_REMOTES_NO_ERRORS_FROM_WARNINGS: "false"
+  R_PROFILE: "$R_HOME/etc/Rprofile.site"
   R_LIBS_USER: "$CI_PROJECT_DIR/ci/lib"
   R_LIBS: "$CI_PROJECT_DIR/ci/lib"
-  BUILD_LOGS_DIR: "$CI_PROJECT_DIR/ci/logs"
-  NOT_CRAN: "true"
+  APT_CACHE: "$CI_PROJECT_DIR/ci/lib/apt-cache"
+  CRAN: "https://cloud.r-project.org"
 
-getready:
-  stage: .pre
-  script:
-    - mkdir -p $R_LIBS_USER
-    - mkdir -p $APT_CACHE
-    - R -e 'install.packages(c("knitr", "dataRetrieval", "inlmisc"), repos=Sys.getenv("CRAN_MIRROR"), lib=Sys.getenv("R_LIBS_USER"))'
-  cache:
-    paths:
-      - $R_LIBS_USER
-  artifacts:
-    paths:
-      - $R_LIBS_USER
+cache:
+  paths:
+    - $R_LIBS_USER
+
+before_script:
+  - mkdir -p $APT_CACHE
+  - echo "options(Ncpus=$(nproc --all), repos=c(CRAN='$CRAN'))" >> $R_PROFILE
+  - apt-get update && apt-get -o dir::cache::archives=$APT_CACHE install --yes --no-install-recommends qpdf pandoc pandoc-citeproc r-cran-devtools
+  - Rscript -e "utils::install.packages('remotes')"
+  - Rscript -e "remotes::install_deps(dependencies=TRUE)"
 
-buildcheck:
-  stage: check
+test:
+  stage: test
   script:
-    - mkdir -p $BUILD_LOGS_DIR
-    - apt-get update
-    - apt-get -o dir::cache::archives=${APT_CACHE} install -y --no-install-recommends qpdf pandoc pandoc-citeproc
     - R CMD build . --no-build-vignettes --no-manual
-    - R -e 'devtools::check(document=FALSE, args="--no-tests", error_on="warning", check_dir=Sys.getenv("BUILD_LOGS_DIR"))'
+    - R -e "devtools::check(document=FALSE, args='--no-tests', error_on='warning', check_dir='.', vignettes=FALSE)"
   artifacts:
     paths:
-      - $BUILD_LOGS_DIR
+      - "*.Rcheck"