wp core update "Warning: Failed to create directory '/var/www/.wp-cli/cache/': mkdir(): Permission denied."

[Danrancan]

Bug Report

• Yes, I reviewed the contribution guidelines.
• [ X Yes, more specifically, I reviewed the guidelines on how to write clear bug reports.

Describe the current, buggy behavior

I am trying to upgrade my wordpress installation from the wp cli. From the ssh terminal I move into the wordpress directory in /var/www/example.com. Then I execute the following command:

wp plugin deactivate --all
Plugin 'tinymce-advanced' deactivated.
Plugin 'akismet' deactivated.
Plugin 'autoptimize' deactivated.
Plugin 'classic-widgets' deactivated.
Plugin 'contact-form-manager' deactivated.
Plugin 'webp-converter-for-media' deactivated.
Plugin 'duplicate-page' deactivated.
Plugin 'emails-verification-for-woocommerce' deactivated.
Plugin 'envato-market' deactivated.
Plugin 'hcode-addons' deactivated.
Plugin 'mime-types-plus' deactivated.
Plugin 'newsletter-manager' deactivated.
Plugin 'nginx-helper' deactivated.
Plugin 'one-user-avatar' deactivated.
Plugin 'woo-stripe-payment' deactivated.
Plugin 'seo-by-rank-math' deactivated.
Plugin 'seo-by-rank-math-pro' deactivated.
Plugin 'real-media-library-lite' deactivated.
Plugin 'redis-cache' deactivated.
Plugin 'simple-cloudflare-turnstile' deactivated.
Plugin 'revslider' deactivated.
Plugin 'social-media-auto-publish' deactivated.
Plugin 'woocommerce' deactivated.
Plugin 'woocommerce-paypal-payments' deactivated.
Plugin 'woocommerce-services' deactivated.
Plugin 'js_composer' deactivated.
Plugin 'wp-mail-smtp' deactivated.
Plugin 'amazon-s3-and-cloudfront' deactivated.
Success: Deactivated 28 of 28 plugins.

Then I attempt to update wordpress from the wp cli:

Danran@mail:/var/www/example.com$ wp core update
Updating to version 6.6.1 (en_US)...
Warning: Failed to create directory '/var/www/.wp-cli/cache/': mkdir(): Permission denied.
Downloading update from https://downloads.wordpress.org/release/wordpress-6.6.1-no-content.zip...
Unpacking the update...
PHP Warning:  copy(/var/www/example.com/wp-config-sample.php): Failed to open stream: Permission denied in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 309
Warning: copy(/var/www/example.com/wp-config-sample.php): Failed to open stream: Permission denied in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 309
PHP Warning:  chmod(): No such file or directory in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 173
Warning: chmod(): No such file or directory in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 173
PHP Warning:  chmod(): No such file or directory in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 173
Warning: chmod(): No such file or directory in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 173
PHP Warning:  copy(/var/www/example.com/wp-config-sample.php): Failed to open stream: Permission denied in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 309
Warning: copy(/var/www/example.com/wp-config-sample.php): Failed to open stream: Permission denied in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 309
PHP Warning:  chmod(): No such file or directory in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 173
Warning: chmod(): No such file or directory in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 173
PHP Warning:  copy(/var/www/example.com/wp-config-sample.php): Failed to open stream: Permission denied in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 309
Warning: copy(/var/www/example.com/wp-config-sample.php): Failed to open stream: Permission denied in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 309
PHP Warning:  chmod(): No such file or directory in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 173
Warning: chmod(): No such file or directory in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 173
PHP Warning:  chmod(): No such file or directory in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 173
Warning: chmod(): No such file or directory in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 173
PHP Warning:  copy(/var/www/example.com/wp-config-sample.php): Failed to open stream: Permission denied in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 309
Warning: copy(/var/www/example.com/wp-config-sample.php): Failed to open stream: Permission denied in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 309
PHP Warning:  chmod(): No such file or directory in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 173
Warning: chmod(): No such file or directory in /var/www/example.com/wp-admin/includes/class-wp-filesystem-direct.php on line 173
Error: Could not copy file. "wp-config-sample.php"

NOW, I am stuck with a broken/botched Wordpress installation. When I go to www.example.com, it says "Critical Error", on a blank white page.

Describe how other contributors can replicate this bug

• Just go to your wordpress directory and execute wp core update
• the error condition: I don't know what this means.

// You can also use code snippets if needed.

Describe what you would expect as the correct outcome

I expect wordpress to be updated correctly without problems.

Let us know what environment you are running this on
Ubuntu 22.04 Server for Raspberry Pi 4 (aarch64)
Nginx v1.27.0 Mainline
MariaDB 10.11.8
PHP v8.1.2

Danran@mail:/var/www/example.com$ wp cli info
OS:	Linux 5.15.0-1055-raspi #58-Ubuntu SMP PREEMPT Sat May 4 03:52:40 UTC 2024 aarch64
Shell:	/usr/sbin/nologin
PHP binary:	/usr/bin/php8.1
PHP version:	8.1.2-1ubuntu2.18
php.ini used:	/etc/php/8.1/cli/php.ini
MySQL binary:	/usr/bin/mysql
MySQL version:	mysql  Ver 15.1 Distrib 10.11.8-MariaDB, for debian-linux-gnu (aarch64) using  EditLine wrapper
SQL modes:
WP-CLI root dir:	phar://wp-cli.phar/vendor/wp-cli/wp-cli
WP-CLI vendor dir:	phar://wp-cli.phar/vendor
WP_CLI phar path:	/var/www/example.com
WP-CLI packages dir:
WP-CLI cache dir:	/var/www/.wp-cli/cache
WP-CLI global config:
WP-CLI project config:
WP-CLI version:	2.10.0

How can I fix this so I no longer have a botched update installation? I have backups.