Fedora Fix

Makefile

@@ -7,7 +7,8 @@ all: stow
 
 # Full Setup
 setup:
-	@rm -f $(REBOOT_MARKER); \
+	@set -e; \
+	rm -f $(REBOOT_MARKER); \
 	bash ./scripts/base.sh; \
 	if [ -f $(REBOOT_MARKER) ]; then \
 		rm -f $(REBOOT_MARKER); \
@@ -50,7 +51,7 @@ clean:
 # Pull Git Updates
 update:
 	git pull origin main
-	make setup
+	$(MAKE) setup
 
 # Language Setups
 node:

scripts/base.sh

@@ -33,7 +33,7 @@ PACKAGES=(
     python bison mercurial
     ripgrep fd bat fzf jq
     btop httpie gnupg
-    zoxide stow
+    zoxide stow direnv
     bind nmap socat tcpdump net-tools
     strace gdb hexyl
     ninja-build libcurl4-openssl-dev
@@ -134,6 +134,7 @@ fi
 
 if is_fedora_family; then
     FINAL_PACKAGES+=(ca-certificates pkgconf-pkg-config cmake)
+    FINAL_PACKAGES+=(R-core gcc-gfortran bzip2 bzip2-devel readline-devel sqlite sqlite-devel tk-devel libffi-devel xz xz-devel ncurses-devel zlib-devel findutils llvm)
 fi
 
 echo -e "${BLUE}    LOG:${YELLOW} Installing: ${NC}${FINAL_PACKAGES[*]}"
@@ -159,8 +160,24 @@ cp -f "$REPO_ROOT/bin/"* "$HOME/.local/bin/"
 chmod +x "$HOME/.local/bin/"*
 
 if ! command -v rclone &> /dev/null; then
-    echo -e "${BLUE}    LOG:${YELLOW} Installing Rclone (Latest)...${NC}"
+    echo -e "${BLUE}    LOG:${YELLOW} Installing Rclone CLI...${NC}"
-    curl https://rclone.org/install.sh | sudo bash
+
+    case "$ARCH" in
+        x86_64)
+            RCLONE_ARCH="amd64"
+            ;;
+        aarch64)
+            RCLONE_ARCH="arm64"
+            ;;
+    esac
+
+    TEMP_DIR="$(mktemp -d)"
+    RCLONE_ZIP="$TEMP_DIR/rclone.zip"
+
+    curl -fLsS "https://downloads.rclone.org/rclone-current-linux-${RCLONE_ARCH}.zip" -o "$RCLONE_ZIP"
+    unzip -q "$RCLONE_ZIP" -d "$TEMP_DIR"
+    install -m 755 "$TEMP_DIR"/rclone-*-linux-"${RCLONE_ARCH}"/rclone "$HOME/.local/bin/rclone"
+    rm -rf "$TEMP_DIR"
 fi
 
 if ! command -v earthly &> /dev/null; then
@@ -236,8 +253,17 @@ rm -f "$HOME/.zshrc" "$HOME/.zsh_aliases"
 touch "$HOME/.zsh_secrets"
 
 # 7. Set Shell
-if [ "$SHELL" != "$(which zsh)" ]; then
+TARGET_SHELL="$(command -v zsh)"
-    sudo chsh -s "$(which zsh)" $(whoami)
+CURRENT_LOGIN_SHELL="$(getent passwd "$(whoami)" | cut -d: -f7)"
+
+if [ "$CURRENT_LOGIN_SHELL" != "$TARGET_SHELL" ]; then
+    if command -v chsh >/dev/null 2>&1; then
+        sudo chsh -s "$TARGET_SHELL" "$(whoami)"
+    elif command -v usermod >/dev/null 2>&1; then
+        sudo usermod -s "$TARGET_SHELL" "$(whoami)"
+    else
+        echo -e "${YELLOW}    NOTE:${NC} Could not find chsh/usermod. Please change your login shell to $TARGET_SHELL manually."
+    fi
 fi
 
 echo -e "${GREEN}    LOG: Base System Setup Complete.${NC}"

scripts/lib/distro.sh

@@ -39,6 +39,39 @@ mark_reboot_required() {
     echo ""
 }
 
+get_atomic_requested_packages() {
+    local python_bin=""
+    local candidate
+
+    for candidate in python3 python /usr/libexec/platform-python; do
+        if command -v "$candidate" >/dev/null 2>&1; then
+            python_bin="$candidate"
+            break
+        fi
+    done
+
+    if [ -z "$python_bin" ]; then
+        return 0
+    fi
+
+    rpm-ostree status --json 2>/dev/null | "$python_bin" -c '
+import json, sys
+
+try:
+    data = json.load(sys.stdin)
+except Exception:
+    raise SystemExit(0)
+
+for deployment in data.get("deployments", []):
+    if deployment.get("booted"):
+        for key in ("requested-packages", "requested-local-packages"):
+            for package in deployment.get(key, []):
+                if package:
+                    print(package)
+        break
+'
+}
+
 install_packages() {
     local packages=("$@")
 
@@ -59,11 +92,25 @@ install_packages() {
 
     if is_fedora_family; then
         if is_atomic_fedora; then
+            local requested_pkg
             local missing_packages=()
+            declare -A requested_packages=()
             local pkg
 
+            while IFS= read -r requested_pkg; do
+                [ -n "$requested_pkg" ] && requested_packages["$requested_pkg"]=1
+            done < <(get_atomic_requested_packages)
+
             for pkg in "${packages[@]}"; do
-                rpm -q "$pkg" >/dev/null 2>&1 || missing_packages+=("$pkg")
+                if rpm -q "$pkg" >/dev/null 2>&1; then
+                    continue
+                fi
+
+                if [ -n "${requested_packages[$pkg]:-}" ]; then
+                    continue
+                fi
+
+                missing_packages+=("$pkg")
             done
 
             if [ ${#missing_packages[@]} -eq 0 ]; then

scripts/r.sh

@@ -82,7 +82,7 @@ elif is_fedora_family; then
 
     echo -e "${BLUE}    LOG:${YELLOW} Fedora detected. Using system R...${NC}"
     install_status=0
-    install_packages R gcc-gfortran curl tar || install_status=$?
+    install_packages R-core gcc-gfortran curl tar || install_status=$?
     if [ "$install_status" -eq 42 ]; then
         exit 0
     elif [ "$install_status" -ne 0 ]; then
@@ -96,8 +96,8 @@ else
     exit 1
 fi
 
-echo -e "${BLUE}    LOG:${YELLOW} Installing 'renv' package globally...${NC}"
+echo -e "${BLUE}    LOG:${YELLOW} Installing 'renv' package in the user R library...${NC}"
 
-$R_BIN -e 'if (!require("renv", quietly=TRUE)) install.packages("renv", repos="https://cloud.r-project.org")'
+$R_BIN -e 'user_lib <- path.expand(Sys.getenv("R_LIBS_USER", unset = "~/R/library")); dir.create(user_lib, recursive = TRUE, showWarnings = FALSE); .libPaths(c(user_lib, .libPaths())); if (!require("renv", quietly=TRUE)) install.packages("renv", lib = user_lib, repos = "https://cloud.r-project.org")'
 
 echo -e "${GREEN}    SUCCESS:${NC} R setup completed."