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Restructure R library loading

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Bryan Roessler
2024-08-02 19:22:18 -04:00
parent 815c7615e7
commit 374936c28f
1 changed files with 7 additions and 4 deletions
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11
workflow/qhtcp-workflow
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@@ -439,14 +439,18 @@ install_dependencies() {
# Install system-wide dependencies
echo "Installing system dependencies"
echo "You may be prompted for your sudo password to install packages using your system package manager"
case "$(uname -s)" in
Linux*|CYGWIN*|MINGW*)
ask "Detected Linux platform, continue?" || return 1
echo "You may be prompted for your sudo password to install system packages"
if hash dnf &>/dev/null; then
ask "Detected Linux RPM platform, continue?" || return 1
sudo dnf install "${depends_rpm[@]}"
elif hash apt &>/dev/null; then
ask "Detected Linux DEB platform, continue?" || return 1
sudo apt install "${depends_deb[@]}"
else
echo "Sorry, your Linux platform is not supported for automatic dependency installation"
echo "You will need to resolve dependencies manually"
fi
;;
Darwin*)
@@ -478,10 +482,9 @@ install_dependencies() {
}
depends_r_to_string
# Install R packages
for d in "${depends_r[@]}"; do
debug "$RSCRIPT -e \"if (!require(\"$d\", quietly = TRUE)); install.packages(\"$d\", dep=TRUE, repos=\"https://cloud.r-project.org\")\""
debug "$RSCRIPT -e \"if (!require(\"$d\", quietly = TRUE)); {install.packages(\"$d\", dep=TRUE, repos=\"https://cloud.r-project.org\")}\""
"$RSCRIPT" -e "if (!require(\"$d\", quietly = TRUE)); {install.packages(\"$d\", dep=TRUE, repos=\"https://cloud.r-project.org\")}"
done