The example docker-compose.yml uses a bind mount for the MariaDB data directory:

services:
  mariadb:
    volumes:
      # You generally only ever need to map this one volume.
      # This maps it to a "bookstack_db_data" folder in the same
      # directory as this compose config file.
      - ./bookstack_db_data:/config

On Windows, this bind-mount path resolves to a case-insensitive filesystem (NTFS). MariaDB detects this at startup and automatically forces lower_case_table_names=2, logging:

[Warning] Setting lower_case_table_names=2 because file system for /config/databases/ is case insensitive

This cannot be overridden via my.cnf — MariaDB ignores the setting when its filesystem detection takes precedence.

lower_case_table_names=2 is a partially broken mode. InnoDB's TRUNCATE TABLE implementation internally tries to rename the .ibd tablespace file, which fails under this mode, producing:

[ERROR] InnoDB: Cannot rename './bookstack/joint_permissions.ibd' to
'./bookstack/#sql-ib70.ibd' because the source file does not exist.

This causes BookStack's migration 2023_01_24_104625_refactor_joint_permissions_storage to fail with:

SQLSTATE[HY000]: General error: 1030 Got error 194 "Tablespace is missing for a table"
SQL: truncate table `joint_permissions`

BookStack becomes unreachable on every fresh install on Windows. The error is not obvious — the containers appear to start successfully. Only after the first login you will see an "Unknown Error" page.

Fix

Replace the MariaDB bind mount with a named Docker volume. Docker named volumes reside on the Linux VM filesystem inside Docker Desktop's WSL2 backend, which is case-sensitive. MariaDB initialises correctly and migrations complete without error.

services:
  mariadb:
    volumes:
      - bookstack_db_data:/config   # named volume, not a host path

volumes:
  bookstack_db_data:

Suggested documentation changes

Add a callout/warning in the comments along the lines of:

Windows users: Do not bind-mount the MariaDB data directory to a Windows host path (e.g. ./bookstack_db_data:/config). Use a named Docker volume instead. Bind-mounting to a Windows filesystem forces MariaDB into lower_case_table_names=2 mode, which causes InnoDB errors and breaks database migrations.

Tested with

AI Disclaimer: The analysis and description of this issue were developed with the assistance of an AI tool (GitHub Copilot). However, the issue itself is real and was encountered and verified by me on an actual Windows installation. The root cause, error messages, and fix have all been confirmed through hands-on testing.

I followed the link on https://www.bookstackapp.com/docs/admin/installation/ which led me here.

here are the steps i followed

1. Create an empty directory and cd into it
2. Create empty directories for the volumes mkdir bookstack_db_data and mkdir bookstack_app_data
3. Create the file docker-compose.yml as linked above
4. Paste in the file contents as linked above. Change only row 37 APP_KEY with the output from the command docker run -it --rm --entrypoint /bin/bash lscr.io/linuxserver/bookstack:latest appkey
5. Run docker-compose up -d

resulting error (logs from bookstack container)

  SQLSTATE[HY000] [2002] Operation timed out (Connection: mysql, SQL: select exists (select 1 from information_schema.tables where table_schema = 'bookstack' and table_name = 'migrations' and table_type in ('BASE TABLE', 'SYSTEM VERSIONED')) as `exists`)
  at /app/www/vendor/laravel/framework/src/Illuminate/Database/Connection.php:825
    821▕                     $this->getName(), $query, $this->prepareBindings($bindings), $e
    822▕                 );
    823▕             }
    824▕ 
  ➜ 825▕             throw new QueryException(
    826▕                 $this->getName(), $query, $this->prepareBindings($bindings), $e
    827▕             );
    828▕         }
    829▕     }
      +38 vendor frames 
  39  /app/www/artisan:35
      Illuminate\Foundation\Console\Kernel::handle()

No visible errors from mariadb.

Not sure if i'm missing anything but I would expect the example to work as-is.
using synology dsm fwiw

I'll therefore close this off since re-running the script worked okay, but I'll keep this in mind if I get further reports, or if there's specific errors to address.

I also had issues with DOMAIN=$1 which also caused it to error out. I cannot remember what the error was though.

Also, if you still have it, please share the install log from the original failed attempt (Should be in the same directory as where you originally ran the script from).

I don't think changes in Ubuntu should need those changes, but there could environmental elements which lead to differences, so it would be good to know those to properly plan for them in future.

Changed these sections
#Get the domain from the arguments (Requested later if not set)
if [ -z "${1-}" ]; then
read -rp "Enter your domain (or press Enter to use IP $CURRENT_IP): " DOMAIN
DOMAIN=${DOMAIN:-$CURRENT_IP}
else
DOMAIN=$1
fi

#Install core system packages
function run_package_installs() {
apt update
apt install -y git unzip apache2 curl mysql-server php8.3
php8.3-fpm php8.3-curl php8.3-mbstring php8.3-ldap php8.3-xml php8.3-zip php8.3-gd php8.3-mysql
}

#Set up database
function run_database_setup() {
#Ensure database service has started
systemctl start mysql.service
systemctl enable mysql.service
sleep 3

Todo

• Fix mysql commands to suit mariadb (User create command)
• Swap out composer install/usage to system cli download-vendor command