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Understanding DNF Package Manager in AlmaLinux
AlmaLinux DNF Package Management

Understanding DNF Package Manager in AlmaLinux

Published Jul 19, 2025

Master the DNF package manager in AlmaLinux with this comprehensive guide. Learn essential commands, repository management, module streams, troubleshooting techniques, and enterprise package management best practices

18 min read
0 views
Table of Contents

Introduction

DNF (Dandified YUM) serves as the default package manager for AlmaLinux, providing a powerful and efficient system for software installation, updates, and dependency management. As the next-generation replacement for YUM, DNF offers improved performance, better dependency resolution, and enhanced features that make package management more reliable and user-friendly. This comprehensive guide explores every aspect of DNF, from basic operations to advanced repository management and troubleshooting techniques.

Understanding DNF Architecture

Evolution from YUM

DNF represents a complete rewrite of YUM using modern technologies:

  • libsolv: Advanced dependency resolver
  • hawkey: High-level package management library
  • librepo: Repository metadata downloading
  • libcomps: Package group metadata handling

Key Improvements Over YUM

  1. Performance: 3-5x faster dependency resolution
  2. Memory Usage: Reduced memory footprint
  3. API: Clean, well-documented Python API
  4. Dependency Resolution: More predictable behavior
  5. Python 3: Native Python 3 support

DNF Configuration

Main Configuration File

The primary configuration file /etc/dnf/dnf.conf controls DNF behavior:

[main]
# Basic settings
gpgcheck=1
installonly_limit=3
clean_requirements_on_remove=True
best=True
skip_if_unavailable=False

# Performance settings
fastestmirror=True
max_parallel_downloads=10
minrate=1000
timeout=30
retries=10

# Cache settings
keepcache=0
metadata_expire=6h
metadata_timer_sync=10800

# Security settings
repo_gpgcheck=1
localpkg_gpgcheck=1

# Output settings
color=auto
color_update_installed=normal
color_update_local=bold
color_update_remote=normal
color_list_installed_newer=red
color_list_installed_older=yellow
color_list_installed_reinstall=cyan
color_list_installed_extra=magenta
color_list_available_upgrade=bold_blue
color_list_available_downgrade=yellow
color_list_available_install=bold_cyan
color_list_available_reinstall=cyan
color_search_match=bold_magenta

# Debug settings
debuglevel=2
errorlevel=6
obsoletes=1

Repository Configuration

Repository files are stored in /etc/yum.repos.d/:

# List repository files
ls -la /etc/yum.repos.d/

# Example repository configuration
cat > /etc/yum.repos.d/custom.repo << 'EOF'
[custom-repo]
name=Custom Repository
baseurl=https://repo.example.com/el9/$basearch/
enabled=1
gpgcheck=1
gpgkey=https://repo.example.com/RPM-GPG-KEY-custom
priority=90
module_hotfixes=1
countme=1
EOF

Essential DNF Commands

Package Installation

Basic Installation

# Install single package
sudo dnf install package_name

# Install multiple packages
sudo dnf install package1 package2 package3

# Install with automatic yes
sudo dnf install -y httpd mariadb-server php

# Install specific version
sudo dnf install package_name-1.2.3

# Install from local RPM file
sudo dnf install ./local-package.rpm

# Install only from specific repository
sudo dnf install --repo=epel package_name

Advanced Installation Options

# Install without dependencies (dangerous!)
sudo dnf install --nodeps package_name

# Install with weak dependencies
sudo dnf install --setopt=install_weak_deps=True package_name

# Install and assume yes for GPG key import
sudo dnf install --assumeyes --nogpgcheck package_name

# Download only without installing
sudo dnf download package_name

# Install all packages from a group
sudo dnf group install "Development Tools"

Package Updates

System Updates

# Update all packages
sudo dnf update

# Update specific package
sudo dnf update package_name

# Update all except specific packages
sudo dnf update --exclude=kernel* --exclude=php*

# Check for updates without installing
sudo dnf check-update

# Update to specific version
sudo dnf update-to package_name-1.2.3

# Minimal update (security only)
sudo dnf update-minimal

# Update with bug fixes and security
sudo dnf update --bugfix --security

Automatic Updates

# Install automatic updates
sudo dnf install dnf-automatic

# Configure automatic updates
sudo vim /etc/dnf/automatic.conf

# Enable automatic updates timer
sudo systemctl enable --now dnf-automatic.timer

# Check timer status
sudo systemctl status dnf-automatic.timer

Package Removal

# Remove package
sudo dnf remove package_name

# Remove with dependencies
sudo dnf autoremove package_name

# Remove leaving dependencies
sudo dnf remove --nodeps package_name

# Remove obsolete packages
sudo dnf remove $(dnf repoquery --extras)

# Clean up unused dependencies
sudo dnf autoremove

Package Queries

Search Operations

# Search for packages
dnf search keyword

# Search in package names only
dnf search --name keyword

# Search in summary and description
dnf search --all keyword

# Search by file
dnf provides /usr/bin/htop

# Search with wildcards
dnf search 'python3-*'

# Advanced search with grep
dnf list available | grep -i pattern

Information Queries

# Show package information
dnf info package_name

# List installed packages
dnf list installed

# List available packages
dnf list available

# List all packages
dnf list all

# List recent packages
dnf list recent

# List extras (packages not in any repo)
dnf list extras

# List obsoletes
dnf list obsoletes

# Show package dependencies
dnf deplist package_name

# Show which package provides a file
dnf provides /path/to/file

# Show package changelog
dnf changelog package_name

Repository Management

Repository Operations

# List enabled repositories
dnf repolist

# List all repositories
dnf repolist all

# Enable repository
sudo dnf config-manager --set-enabled repository_name

# Disable repository
sudo dnf config-manager --set-disabled repository_name

# Add repository
sudo dnf config-manager --add-repo https://example.com/repo.repo

# Show repository configuration
dnf repoinfo repository_name

# Clean repository metadata
sudo dnf clean metadata

# Clean all cached data
sudo dnf clean all

# Rebuild cache
sudo dnf makecache

# Synchronize packages with repository
sudo dnf distro-sync

Working with Third-Party Repositories

EPEL Repository

# Install EPEL repository
sudo dnf install epel-release

# Verify EPEL installation
dnf repolist | grep epel

# Install package from EPEL
sudo dnf install --enablerepo=epel package_name

ELRepo Repository

# Import GPG key
sudo rpm --import https://www.elrepo.org/RPM-GPG-KEY-elrepo.org

# Install ELRepo
sudo dnf install https://www.elrepo.org/elrepo-release-9.el9.elrepo.noarch.rpm

# List available kernels
dnf list available --enablerepo=elrepo-kernel kernel*

Creating Local Repository

# Install createrepo
sudo dnf install createrepo_c

# Create repository directory
sudo mkdir -p /var/www/html/local-repo

# Copy RPMs to repository
sudo cp *.rpm /var/www/html/local-repo/

# Create repository metadata
sudo createrepo /var/www/html/local-repo/

# Create repository configuration
cat > /etc/yum.repos.d/local.repo << 'EOF'
[local-repo]
name=Local Repository
baseurl=file:///var/www/html/local-repo/
enabled=1
gpgcheck=0
priority=1
EOF

# Update repository metadata
sudo createrepo --update /var/www/html/local-repo/

DNF Modules and Streams

Understanding Modules

DNF modules allow multiple versions of software to be available:

# List all modules
dnf module list

# List specific module
dnf module list nodejs

# Show module information
dnf module info nodejs

# List enabled modules
dnf module list --enabled

# List installed modules
dnf module list --installed

Working with Module Streams

# Enable module stream
sudo dnf module enable nodejs:18

# Install module stream
sudo dnf module install nodejs:18

# Switch module streams
sudo dnf module reset nodejs
sudo dnf module enable nodejs:20
sudo dnf module install nodejs:20

# Install specific profile
sudo dnf module install nodejs:18/development

# Remove module
sudo dnf module remove nodejs:18

# Disable module
sudo dnf module disable nodejs:18

Module Profiles

# List available profiles
dnf module info --profile nodejs

# Install minimal profile
sudo dnf module install nodejs:18/minimal

# Install multiple profiles
sudo dnf module install nodejs:18/development nodejs:18/s2i

Package Groups

Group Management

# List available groups
dnf group list

# List hidden groups
dnf group list --hidden

# Show group information
dnf group info "Development Tools"

# Install group
sudo dnf group install "Development Tools"

# Install with optional packages
sudo dnf group install --with-optional "Development Tools"

# Update group
sudo dnf group update "Development Tools"

# Remove group
sudo dnf group remove "Development Tools"

# Mark group as installed
sudo dnf group mark install "Development Tools"

# Mark group as removed
sudo dnf group mark remove "Development Tools"

Creating Custom Groups

Create a custom group definition:

<!-- /etc/dnf/comps.d/custom-group.xml -->
<comps>
  <group>
    <id>custom-web-stack</id>
    <name>Custom Web Stack</name>
    <description>Custom LAMP stack components</description>
    <default>true</default>
    <uservisible>true</uservisible>
    <packagelist>
      <packagereq type="mandatory">httpd</packagereq>
      <packagereq type="mandatory">mariadb-server</packagereq>
      <packagereq type="mandatory">php</packagereq>
      <packagereq type="default">php-mysqlnd</packagereq>
      <packagereq type="optional">phpmyadmin</packagereq>
    </packagelist>
  </group>
</comps>

DNF Plugins

Essential Plugins

# Install DNF plugins core
sudo dnf install dnf-plugins-core

# List installed plugins
dnf list installed 'dnf-plugin*'

# Available plugins
dnf search dnf-plugin

Useful Plugins

1. versionlock Plugin

# Install versionlock
sudo dnf install python3-dnf-plugin-versionlock

# Lock package version
sudo dnf versionlock add kernel-5.14.0-362.8.1.el9_3

# List locked packages
dnf versionlock list

# Remove version lock
sudo dnf versionlock delete kernel-5.14.0-362.8.1.el9_3

# Clear all locks
sudo dnf versionlock clear

2. needs-restarting Plugin

# Check which services need restart
sudo dnf needs-restarting

# Check which processes need restart
sudo dnf needs-restarting --reboothint

# List affected services
sudo dnf needs-restarting --services

3. config-manager Plugin

# Add repository
sudo dnf config-manager --add-repo https://example.com/repo

# Enable/disable repository
sudo dnf config-manager --set-enabled powertools
sudo dnf config-manager --set-disabled testing

# Save repository configuration
sudo dnf config-manager --save --setopt=epel.priority=10

DNF History and Rollback

History Management

# View transaction history
dnf history

# View detailed history
dnf history list

# Show specific transaction
dnf history info 12

# Show packages affected by transaction
dnf history info 12 --verbose

# Search history
dnf history list kernel

# Show history statistics
dnf history stats

# Show user who ran transaction
dnf history userinstalled

Transaction Rollback

# Undo last transaction
sudo dnf history undo last

# Undo specific transaction
sudo dnf history undo 12

# Redo transaction
sudo dnf history redo 12

# Rollback to transaction
sudo dnf history rollback 12

# Repeat transaction
sudo dnf history repeat 12

# Store rollback data
sudo dnf history store

Performance Optimization

DNF Speed Improvements

# Enable fastest mirror
echo 'fastestmirror=True' | sudo tee -a /etc/dnf/dnf.conf

# Increase parallel downloads
echo 'max_parallel_downloads=10' | sudo tee -a /etc/dnf/dnf.conf

# Set minimum download speed
echo 'minrate=100k' | sudo tee -a /etc/dnf/dnf.conf

# Reduce timeout for slow mirrors
echo 'timeout=10' | sudo tee -a /etc/dnf/dnf.conf

# Enable deltarpm
sudo dnf install deltarpm
echo 'deltarpm=True' | sudo tee -a /etc/dnf/dnf.conf

Cache Management

# Keep cache after installation
echo 'keepcache=1' | sudo tee -a /etc/dnf/dnf.conf

# Set metadata expiration
echo 'metadata_expire=6h' | sudo tee -a /etc/dnf/dnf.conf

# Clean specific cache types
sudo dnf clean packages
sudo dnf clean metadata
sudo dnf clean expire-cache
sudo dnf clean all

# Build cache
sudo dnf makecache

# Timer-based makecache
sudo systemctl enable --now dnf-makecache.timer

Security Best Practices

GPG Key Management

# Import GPG key
sudo rpm --import https://repo.almalinux.org/almalinux/RPM-GPG-KEY-AlmaLinux-9

# List imported keys
rpm -qa gpg-pubkey*

# Show key information
rpm -qi gpg-pubkey-34d8786d-6229e051

# Remove GPG key
sudo rpm -e gpg-pubkey-34d8786d-6229e051

# Verify package signature
rpm -K package.rpm

Security Configuration

# Enable GPG checking globally
echo 'gpgcheck=1' | sudo tee -a /etc/dnf/dnf.conf
echo 'repo_gpgcheck=1' | sudo tee -a /etc/dnf/dnf.conf
echo 'localpkg_gpgcheck=1' | sudo tee -a /etc/dnf/dnf.conf

# Disable GPG check for specific repository
sudo dnf install --disablerepo=* --enablerepo=trusted-repo --nogpgcheck package

# Security-only updates
sudo dnf update --security

# List security updates
dnf updateinfo list security

# Show security advisories
dnf updateinfo info security

Troubleshooting DNF Issues

Common Problems and Solutions

1. Corrupted Cache

# Clean all cache
sudo dnf clean all
sudo rm -rf /var/cache/dnf/*

# Rebuild cache
sudo dnf makecache

2. Broken Dependencies

# Check for problems
sudo dnf check

# List duplicate packages
dnf list --duplicates

# Remove duplicates
sudo dnf remove --duplicates

# Skip broken packages
sudo dnf update --skip-broken

# Force architecture
sudo dnf install package.x86_64

3. Repository Issues

# Disable problematic repository temporarily
sudo dnf --disablerepo=problematic-repo update

# Skip unavailable repositories
sudo dnf update --skip-if-unavailable

# Test repository configuration
sudo dnf repolist -v

# Check repository metadata
sudo dnf repository-packages repo-name list

4. Transaction Conflicts

# Check running transactions
ps aux | grep dnf

# Remove stale lock
sudo rm -f /var/run/dnf.pid

# Clean up incomplete transactions
sudo dnf clean packages
sudo dnf-3 clean packages  # If using dnf-3

# Reset module state
sudo dnf module reset module-name

Debug Mode

# Increase debug level
sudo dnf -d 10 install package

# Enable debug output
sudo dnf --debuglevel=10 update

# Save debug information
sudo dnf --debugsolver --debuglevel=10 install package 2>&1 | tee dnf-debug.log

# Check DNF database
sudo dnf check --dependencies

DNF Database Recovery

# Rebuild RPM database
sudo rpm --rebuilddb

# Verify database integrity
sudo rpm -vv --verify --all

# Clean DNF database
sudo rm -rf /var/lib/dnf/*
sudo dnf clean all
sudo dnf makecache

Advanced DNF Usage

Scripting with DNF

Python API Example

#!/usr/bin/env python3
import dnf

# Create DNF base object
base = dnf.Base()
base.read_all_repos()
base.fill_sack()

# Query installed packages
query = base.sack.query()
installed = query.installed()

# Find specific package
pkg_query = query.filter(name='httpd')
for pkg in pkg_query:
    print(f"{pkg.name}-{pkg.version}-{pkg.release}")

# Check available updates
updates = query.upgrades()
for pkg in updates:
    print(f"Update available: {pkg.name}")

Shell Scripting

#!/bin/bash
# DNF automation script

# Function to check if package is installed
is_installed() {
    dnf list installed "$1" &>/dev/null
    return $?
}

# Function to install if not present
install_if_missing() {
    local package=$1
    if ! is_installed "$package"; then
        echo "Installing $package..."
        sudo dnf install -y "$package"
    else
        echo "$package is already installed"
    fi
}

# Install required packages
packages=("httpd" "mariadb-server" "php" "php-mysqlnd")
for pkg in "${packages[@]}"; do
    install_if_missing "$pkg"
done

# Update system
echo "Updating system..."
sudo dnf update -y

# Clean up
echo "Cleaning up..."
sudo dnf autoremove -y
sudo dnf clean all

Creating DNF Aliases

Add to ~/.bashrc:

# DNF aliases
alias dnfi='sudo dnf install'
alias dnfu='sudo dnf update'
alias dnfr='sudo dnf remove'
alias dnfs='dnf search'
alias dnfp='dnf provides'
alias dnfc='sudo dnf clean all'
alias dnfl='dnf list installed'
alias dnfh='dnf history'
alias dnfg='dnf group'

# Advanced aliases
alias dnf-security='sudo dnf update --security'
alias dnf-cleanup='sudo dnf autoremove && sudo dnf clean all'
alias dnf-rollback='sudo dnf history undo last'
alias dnf-whatprovides='dnf provides'
alias dnf-leaves='dnf leaves'
alias dnf-broken='sudo dnf check'

DNF Configuration Templates

Minimal Server Configuration

# /etc/dnf/dnf.conf
[main]
gpgcheck=1
installonly_limit=2
clean_requirements_on_remove=True
best=True
skip_if_unavailable=True
fastestmirror=True
max_parallel_downloads=3
keepcache=0
metadata_expire=12h

Development Workstation Configuration

# /etc/dnf/dnf.conf
[main]
gpgcheck=1
installonly_limit=5
clean_requirements_on_remove=True
best=True
skip_if_unavailable=False
fastestmirror=True
max_parallel_downloads=10
keepcache=1
metadata_expire=6h
deltarpm=True

Enterprise Package Management

Package Standardization

# Create package baseline
dnf list installed > /etc/package-baseline.txt

# Compare against baseline
dnf list installed > current-packages.txt
diff /etc/package-baseline.txt current-packages.txt

# Generate package manifest
cat > package-manifest.sh << 'EOF'
#!/bin/bash
# Package manifest for AlmaLinux 9

PACKAGES=(
    # System tools
    "vim-enhanced"
    "wget"
    "curl"
    "git"
    "htop"
    
    # Development
    "@Development Tools"
    "python3-devel"
    "nodejs"
    
    # Services
    "httpd"
    "mariadb-server"
    "php"
)

for package in "${PACKAGES[@]}"; do
    sudo dnf install -y "$package"
done
EOF

Compliance and Auditing

# Audit installed packages
sudo dnf history userinstalled > user-installed-packages.txt

# Check for unauthorized packages
dnf list extras

# Verify package integrity
sudo rpm -Va > package-verification.log

# Generate compliance report
cat > compliance-check.sh << 'EOF'
#!/bin/bash
echo "Package Compliance Report"
echo "========================"
echo "Date: $(date)"
echo "Hostname: $(hostname)"
echo ""
echo "Installed Packages: $(dnf list installed | wc -l)"
echo "Available Updates: $(dnf check-update | grep -v "^$" | wc -l)"
echo "Security Updates: $(dnf updateinfo list security | wc -l)"
echo "Extra Packages: $(dnf list extras | wc -l)"
echo ""
echo "Repository Status:"
dnf repolist
echo ""
echo "Recent Changes:"
dnf history | head -20
EOF

Conclusion

DNF package manager provides a robust, efficient, and feature-rich solution for package management in AlmaLinux. From basic package operations to advanced repository management and enterprise deployment strategies, DNF offers the tools necessary for maintaining healthy, secure, and up-to-date systems.

Key takeaways:

  • Master basic DNF commands for daily operations
  • Understand repository and module management
  • Implement security best practices
  • Utilize history and rollback features
  • Optimize performance for your environment
  • Develop troubleshooting skills for common issues

With this comprehensive understanding of DNF, you’re equipped to handle any package management challenge in AlmaLinux environments, ensuring efficient system administration and maintenance.

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