error in Database

unfortunately this line added to bugs too

[10-Nov-2020 11:33:59 UTC] PHP Notice:  تابع wpdb::prepare به طور<strong>نادرست</strong> فراخوانی شد. آرگومان کوئری wpdb::prepare() باید دارای نگهدارندهٔ مکان (placeholder) باشد. لطفاً برای اطلاعات بیشتر، <a href="https://wordpress.org/support/article/debugging-in-wordpress/">اشکال زدایی در وردپرس</a> را مشاهده کنید. (این پیام در نگارش 3.9.0 افزوده شده است.) in /public_html/wp-includes/functions.php on line 5229
[10-Nov-2020 11:33:59 UTC] خطای You have an error in your SQL syntax; check the manual that corresponds to your MariaDB server version for the right syntax to use near ')' at line 24 در پایگاه‌داده وردپرس برای دستور SELECT COUNT(ID)
			FROM wp_posts
			WHERE
				(
					ID NOT IN (
						SELECT object_id
						FROM wp_yoast_indexable
						WHERE
							link_count IS NOT NULL
							AND object_type = 'post'
					)
					OR
					ID IN (
						SELECT DISTINCT post_id
						FROM wp_yoast_seo_links
						WHERE
							target_indexable_id IS NULL
							AND <code>type</code> = 'internal'
							AND target_post_id IS NOT NULL
							AND target_post_id != 0
					)
				)
				AND post_status = 'publish'
				AND post_type IN ()
			
			 ساخته شده توسط do_action('admin_init'), WP_Hook->do_action, WP_Hook->apply_filters, Yoast\WP\SEO\Integrations\Admin\Background_Indexing_Integration->register_shutdown_indexing, Yoast\WP\SEO\Integrations\Admin\Background_Indexing_Integration->get_unindexed_count, Yoast\WP\SEO\Actions\Indexing\Abstract_Link_Indexing_Action->get_total_unindexed
[10-Nov-2020 11:34:02 UTC] PHP Notice:  تابع wpdb::prepare به طور<strong>نادرست</strong> فراخوانی شد. آرگومان کوئری wpdb::prepare() باید دارای نگهدارندهٔ مکان (placeholder) باشد. لطفاً برای اطلاعات بیشتر، <a href="https://wordpress.org/support/article/debugging-in-wordpress/">اشکال زدایی در وردپرس</a> را مشاهده کنید. (این پیام در نگارش 3.9.0 افزوده شده است.) in /home/timecode/public_html/wp-includes/functions.php on line 5229
[10-Nov-2020 11:34:02 UTC] خطای You have an error in your SQL syntax; check the manual that corresponds to your MariaDB server version for the right syntax to use near ')' at line 24 در پایگاه‌داده وردپرس برای دستور SELECT COUNT(ID)
			FROM wp_posts
			WHERE
				(
					ID NOT IN (
						SELECT object_id
						FROM wp_yoast_indexable
						WHERE
							link_count IS NOT NULL
							AND object_type = 'post'
					)
					OR
					ID IN (
						SELECT DISTINCT post_id
						FROM wp_yoast_seo_links
						WHERE
							target_indexable_id IS NULL
							AND <code>type</code> = 'internal'
							AND target_post_id IS NOT NULL
							AND target_post_id != 0
					)
				)
				AND post_status = 'publish'
				AND post_type IN ()

• This reply was modified 5 years, 6 months ago by RezaY.

@devnihil I did it but again I get the bottom bugs, specially when I want to publish a post:

[11-Nov-2020 14:43:11 UTC] خطای Commands out of sync; you can't run this command now در پایگاه‌داده وردپرس برای دستور SELECT umeta_id FROM wp_usermeta WHERE meta_key = 'tc_yoast_notifications' AND user_id = 1 ساخته شده توسط shutdown_action_hook, do_action('shutdown'), WP_Hook->do_action, WP_Hook->apply_filters, Yoast_Notification_Center->update_storage, array_walk, Yoast_Notification_Center->store_notifications_for_user, update_user_option, update_user_meta, update_metadata

[11-Nov-2020 14:43:11 UTC] خطای Commands out of sync; you can't run this command now در پایگاه‌داده وردپرس برای دستور SHOW FULL COLUMNS FROM <code>wp_usermeta</code> ساخته شده توسط shutdown_action_hook, do_action('shutdown'), WP_Hook->do_action, WP_Hook->apply_filters, Yoast_Notification_Center->update_storage, array_walk, Yoast_Notification_Center->store_notifications_for_user, update_user_option, update_user_meta, update_metadata, add_metadata

I did all your suggestions.
it related to Yoast plugin.
If you google my bug, you will see a lot of users have this problem! and there is not any solution for it!

this error appears when I want to publish posts. I get this message in the post page.

Connection lost. Saving has been disabled until you’re reconnected. We’re backing up this post in your browser, just in case.

after that when I check the debug file these line added to it

[11-Nov-2020 16:32:07 UTC] خطای Commands out of sync; you can't run this command now در پایگاه‌داده وردپرس برای دستور SELECT umeta_id FROM tc_usermeta WHERE meta_key = 'tc_yoast_notifications' AND user_id = 1 ساخته شده توسط shutdown_action_hook, do_action('shutdown'), WP_Hook->do_action, WP_Hook->apply_filters, Yoast_Notification_Center->update_storage, array_walk, Yoast_Notification_Center->store_notifications_for_user, update_user_option, update_user_meta, update_metadata
[11-Nov-2020 16:32:07 UTC] خطای Commands out of sync; you can't run this command now در پایگاه‌داده وردپرس برای دستور SHOW FULL COLUMNS FROM <code>tc_usermeta</code> ساخته شده توسط shutdown_action_hook, do_action('shutdown'), WP_Hook->do_action, WP_Hook->apply_filters, Yoast_Notification_Center->update_storage, array_walk, Yoast_Notification_Center->store_notifications_for_user, update_user_option, update_user_meta, update_metadata, add_metadata

It does not work again.
I have this problem with this version and older verions.
I have 3 websites. with different them. All of them has this error. please google this error you will see lots of people have the same problem.
please consider it!

[16-Nov-2020 11:49:18 UTC] خطای Commands out of sync; you can't run this command now در پایگاه‌داده وردپرس برای دستور SELECT * FROM hvylq_users WHERE user_login = 'fathi' LIMIT 1 ساخته شده توسط shutdown_action_hook, do_action('shutdown'), WP_Hook->do_action, WP_Hook->apply_filters, Yoast_Notification_Center->update_storage, Yoast_Notification_Center->remove_storage, Yoast_Notification_Center->has_stored_notifications, Yoast_Notification_Center->get_stored_notifications, get_current_user_id, wp_get_current_user, _wp_get_current_user, apply_filters('determine_current_user'), WP_Hook->apply_filters, wp_validate_logged_in_cookie, wp_validate_auth_cookie, get_user_by, WP_User::get_data_by

• This reply was modified 5 years, 5 months ago by RezaY.

One of my websites has about 48000 posts on other website have 11000 posts(one author). maybe my problem related to the post that you mentioned. So I will wait for publishing the new version.

• This reply was modified 5 years, 5 months ago by RezaY.