single R script to install remotes

r/Dockerfile

@@ -75,21 +75,24 @@ ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
 # Install BigelowLab dev R libs
 # RUN installGithub.R BigelowLab/rasf BigelowLab/ohwobpg  # not working on GH but works locally :-/
-RUN Rscript -e "remotes::install_cran('assertthat', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_cran('ggspatial', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_cran('plot.matrix', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_cran('isdparser', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_cran('geonames', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_cran('rnoaa', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_github('hadley/emo', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_github('BigelowLab/ohwobpg', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_github('BigelowLab/rasf', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_github('BigelowLab/xyzt', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_github('BigelowLab/ghrsst', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_github('BigelowLab/bsw', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_github('BigelowLab/ersst', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_github('BigelowLab/hycom', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
-    Rscript -e "remotes::install_github('kwstat/pals', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)"
+#RUN Rscript -e "remotes::install_cran('assertthat', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
+#    Rscript -e "remotes::install_cran('ggspatial', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
+#    Rscript -e "remotes::install_cran('plot.matrix', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
+#    Rscript -e "remotes::install_cran('isdparser', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
+#    Rscript -e "remotes::install_cran('geonames', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
+#    Rscript -e "remotes::install_cran('rnoaa', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
+#    Rscript -e "remotes::install_github('hadley/emo', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
+#    Rscript -e "remotes::install_github('BigelowLab/ohwobpg', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
+#    Rscript -e "remotes::install_github('BigelowLab/rasf', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
+#    Rscript -e "remotes::install_github('BigelowLab/xyzt', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
+#    Rscript -e "remotes::install_github('BigelowLab/ghrsst', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
+#    Rscript -e "remotes::install_github('BigelowLab/bsw', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
+#    Rscript -e "remotes::install_github('BigelowLab/ersst', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
+#    Rscript -e "remotes::install_github('BigelowLab/hycom', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)" && \
+#    Rscript -e "remotes::install_github('kwstat/pals', dependencies=FALSE, upgrade_dependencies=FALSE, upgrade=FALSE)"
+COPY ./install.R ./remotes.yml ./
+
+RUN Rscript install.R remotes.yml
 
 COPY CONDARC ./.condarc
 

r/install.R

@@ -0,0 +1,45 @@
+# Install one or more R packages using remotes package
+#
+# Input/Output:
+# @param single argument with fully qualified name to (yaml) configuration file
+# @return 0 for success, non-zero if an issue arises.  Fails soon.
+#
+# Usage:
+# Rscript /path/to/install.R /path/to/remotes.yml
+#
+library(yaml)
+library(remotes)
+
+x <- yaml::read_yaml(commandArgs(trailingOnly = TRUE)[1])
+
+args <- x$extra
+
+if ('install_cran' %in% names(x)){
+  for (p in x[['install_cran']]){
+    ok <- try(remotes::install_cran(p,
+                                    dependencies=args$dependencies, 
+                                    upgrade_dependencies=args$upgrade_dependencies, 
+                                    upgrade=args$upgrade))
+    if (inherits(ok, 'try-error')){
+      print("unable to install package:", p)
+      print(ok)
+      quit(save = "no", status = 1)
+    }
+  }
+}
+
+if ('install_github' %in% names(x)){
+  for (p in x[['install_github']]){
+    ok <- try(remotes::install_github(p,
+                                    dependencies=args$dependencies, 
+                                    upgrade_dependencies=args$upgrade_dependencies, 
+                                    upgrade=args$upgrade))
+    if (inherits(ok, 'try-error')){
+
+      print(ok)
+      quit(save = "no", status = 1)
+    }
+  }
+}
+
+quit(save = "no", status = 0)

r/remotes.yml

@@ -0,0 +1,22 @@
+extra:
+  dependencies: no
+  upgrade_dependencies: no
+  upgrade: no
+install_cran:
+- assertthat
+- ggspatial
+- plot.matrix
+- isdparser
+- geonames
+- rnoaa
+install_github:
+- hadley/emo
+- BigelowLab/ohwobpg
+- BigelowLab/rasf
+- BigelowLab/xyzt
+- BigelowLab/ghrsst
+- BigelowLab/bsw
+- BigelowLab/ersst
+- BigelowLab/ersst
+- BigelowLab/hycom
+- kwstat/pals