Merge pull request #625 from Sage-Bionetworks/FDS-2542-software-updates

Fds 2542 software updates

.Rbuildignore

@@ -4,3 +4,5 @@
 ^.venv
 ^schematic$
 ^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$

.Rprofile

@@ -2,8 +2,8 @@ source("renv/activate.R")
 .First <- function() {
   options(
     repos = c(
-      CRAN = "https://cran.rstudio.com/",
-      Sage = "http://ran.synapse.org"
+      binaries = "https://packagemanager.posit.co/cran/__linux__/noble/latest",
+      CRAN = "https://cran.rstudio.com/"
     ),
     sass.cache = FALSE, # turn of styling caching
     stringsAsFactors = FALSE # no needed if R >= 4.0.0

Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/afwillia/shiny-base:release-1.12
+FROM ghcr.io/afwillia/shiny-base:release-1.13
 
 # add version tag as a build argument
 ARG DCA_VERSION
@@ -7,7 +7,7 @@ ENV DCA_VERSION=$DCA_VERSION
 
 USER root
 RUN apt-get update
-RUN apt-get install -y libxml2 libglpk-dev libicu-dev libicu70 curl
+RUN apt-get install -y libxml2 libglpk-dev libicu-dev curl
 
 # overwrite the default config with our modified copy
 COPY shiny-server.conf /etc/shiny-server/shiny-server.conf
@@ -20,6 +20,6 @@ COPY --chown=shiny ./ ./
 
 # set up r packages via renv. Use binary lib matching the shiny-base ubuntu version
 # to speed up installatioon.
-RUN Rscript -e 'renv::restore(repos="https://packagemanager.rstudio.com/all/__linux__/jammy/latest"); renv::install("./")'
+RUN Rscript -e 'renv::restore(repos="https://packagemanager.posit.co/cran/__linux__/noble/latest"); renv::install("./")'
 
 CMD ["./dca_startup.sh"]

Shiny_App.Rproj

@@ -11,3 +11,7 @@ Encoding: UTF-8
 
 RnwWeave: Sweave
 LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source