Update Install_packages.R file

Author: atheo89

rstudio/c9s-python-3.12/Dockerfile.cpu

@@ -94,7 +94,7 @@ RUN wget --progress=dot:giga https://download2.rstudio.org/server/rhel9/x86_64/$
     mkdir -p /usr/share/doc/R && \
     # package installation
     # install necessary texlive-framed package to make Knit R markup to PDF rendering possible
-    dnf install -y libsodium-devel.x86_64 libgit2-devel.x86_64 libcurl-devel harfbuzz-devel.x86_64 fribidi-devel.x86_64 cmake "flexiblas-*" texlive-framed && \
+    dnf install -y libgit2-devel.x86_64 libcurl-devel harfbuzz-devel.x86_64 fribidi-devel.x86_64 cmake "flexiblas-*" texlive-framed && \
     dnf clean all && \
     rm -rf /var/cache/yum && \
     (cd /tmp/utils && ./cve_remediation.sh)

rstudio/c9s-python-3.12/Dockerfile.cuda

@@ -94,7 +94,7 @@ RUN wget --progress=dot:giga https://download2.rstudio.org/server/rhel9/x86_64/$
     mkdir -p /usr/share/doc/R && \
     # package installation
     # install necessary texlive-framed package to make Knit R markup to PDF rendering possible
-    dnf install -y libsodium-devel.x86_64 libgit2-devel.x86_64 libcurl-devel harfbuzz-devel.x86_64 fribidi-devel.x86_64 cmake "flexiblas-*" texlive-framed && \
+    dnf install -y libgit2-devel.x86_64 libcurl-devel harfbuzz-devel.x86_64 fribidi-devel.x86_64 cmake "flexiblas-*" texlive-framed && \
     dnf clean all && \
     rm -rf /var/cache/yum && \
     (cd /tmp/utils && ./cve_remediation.sh)

rstudio/c9s-python-3.12/install_packages.R

@@ -1,13 +1,21 @@
 # install_packages.R
 
+# Configure CRAN mirror and user library (aligns with rsession.conf 4.5)
+options(repos = c(CRAN = Sys.getenv("R_CRAN_MIRROR", "https://cloud.r-project.org")))
+lib <- Sys.getenv("R_LIBS_USER", "/opt/app-root/src/Rpackages/4.5")
+dir.create(lib, recursive = TRUE, showWarnings = FALSE)
+.libPaths(c(lib, .libPaths()))
+options(Ncpus = as.integer(Sys.getenv("R_COMPILE_NCPUS", 2L)))
+
 # Load or install 'remotes' package
 if (!requireNamespace("remotes", quietly = TRUE)) {
     install.packages("remotes")
 }
 
 # Install specific versions of packages
-remotes::install_version('Rcpp', '1.0.14')
-remotes::install_version('tidyverse', '2.0.0')
-remotes::install_version('tidymodels', '1.4.1')
-remotes::install_version('vetiver', '0.2.5')
-remotes::install_version('devtools', '2.4.5')
+# Install specific versions of packages
+remotes::install_version('Rcpp',       '1.0.14', lib = lib, dependencies = TRUE, upgrade = "never")
+remotes::install_version('tidyverse',  '2.0.0',  lib = lib, dependencies = TRUE, upgrade = "never")
+remotes::install_version('tidymodels', '1.4.1',  lib = lib, dependencies = TRUE, upgrade = "never")
+remotes::install_version('vetiver',    '0.2.5',  lib = lib, dependencies = TRUE, upgrade = "never")
+remotes::install_version('devtools',   '2.4.5',  lib = lib, dependencies = TRUE, upgrade = "never")

rstudio/rhel9-python-3.12/install_packages.R

@@ -1,13 +1,20 @@
 # install_packages.R
 
+# Configure CRAN mirror and user library (aligns with rsession.conf 4.5)
+options(repos = c(CRAN = Sys.getenv("R_CRAN_MIRROR", "https://cloud.r-project.org")))
+lib <- Sys.getenv("R_LIBS_USER", "/opt/app-root/src/Rpackages/4.5")
+dir.create(lib, recursive = TRUE, showWarnings = FALSE)
+.libPaths(c(lib, .libPaths()))
+options(Ncpus = as.integer(Sys.getenv("R_COMPILE_NCPUS", 2L)))
+
 # Load or install 'remotes' package
 if (!requireNamespace("remotes", quietly = TRUE)) {
     install.packages("remotes")
 }
 
 # Install specific versions of packages
-remotes::install_version('Rcpp', '1.0.14')
-remotes::install_version('tidyverse', '2.0.0')
-remotes::install_version('tidymodels', '1.4.1')
-remotes::install_version('vetiver', '0.2.5')
-remotes::install_version('devtools', '2.4.5')
+remotes::install_version('Rcpp',       '1.0.14', lib = lib, dependencies = TRUE, upgrade = "never")
+remotes::install_version('tidyverse',  '2.0.0',  lib = lib, dependencies = TRUE, upgrade = "never")
+remotes::install_version('tidymodels', '1.4.1',  lib = lib, dependencies = TRUE, upgrade = "never")
+remotes::install_version('vetiver',    '0.2.5',  lib = lib, dependencies = TRUE, upgrade = "never")
+remotes::install_version('devtools',   '2.4.5',  lib = lib, dependencies = TRUE, upgrade = "never")