lernerconsulting

PHP itself has a bug in Zip/Unzip in old versions. Hangs without any error message displayed or in logs. Affects WordPress Update, and Plugin/Theme Updates, and any plugins that use compression (e.g. WP-Super-Cache or BackWPup)

PHP Change Log https://www.php.net/ChangeLog-5.php#5.3.4 says
PHP Version 5.3.4 released 09-Dec-2010 – Fixed crash in zip extract method

What PHP version is on their hosting account?

p.s. PHP versions are numbered so version 5.3.10 is higher than 5.3.9

PHP itself has a bug in Zip/Unzip in old versions. Hangs without any error message displayed or in logs. Affects WordPress Update, and Plugin/Theme Updates, and any plugins that use compression (e.g. WP-Super-Cache or BackWPup)

PHP Change Log https://www.php.net/ChangeLog-5.php#5.3.4 says
PHP Version 5.3.4 released 09-Dec-2010 – Fixed crash in zip extract method

(If you want to convince your web hosting tech support people it’s PHP not a WordPress plugin problem, I put PHP code on https://lcblog.lernerconsult.com/2013-php-unzip-bug-makes-wordpress-updates-hang/ but they should update old versions of PHP anyway…)

@wbwp: What version of PHP do you have? BackWPup Settings /wp-admin/network/admin.php?page=backwpupsettings on the Information tab has “PHP version”.

@alex Hackbunker: Your version of PHP has bugs in the zip/unzip routines, which hangs without any messages or log entries. This affects WordPress Updates, as well as BackWPup (anything that uses PHP’s unzip).

Mark, kazoostudios: Check your PHP version, if older than 5.3.4 you might have this PHP bug.

For BackWPup, change to an archive format with no compression (BackWPup, Jobs, Edit Job, General Tab, Archive Format: TAR; and DB Backup Tab, Dumpfile compression: None; and XML export tab, File compression: none).

Or, have your web hosting provider upgrade PHP… Mine actually had it installed, I just need a configuration change in my .htaccess to use the newer version.

Note: PHP Change Log https://www.php.net/ChangeLog-5.php#5.5.4
PHP Version 5.3.4 released 09-Dec-2010 – Fixed crash in zip extract method

I cover it in more detail in https://lcblog.lernerconsult.com/2013-php-unzip-bug-makes-wordpress-updates-hang/

Compressing all the files of the site, takes a while.
Numerous “WordPress database error MySQL server has gone away for query”
Numerous “Job restart due to inactivity for more than 5 minutes.”

Especially after compressing large files, the program should reconnect to the database…

[INFO] BackWPup version 3.0.13; WordPress version 3.6.1; A project of Inpsyde GmbH developed by Daniel Hüsken
[INFO] This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions.
[INFO] Blog url: https://MYSITE.info/
[INFO] BackWPup job: Full Backup; DBDUMP+FILE+WPEXP+WPPLUGIN
[INFO] BackWPup cron: 0 3 * * 0; Sun, 27 Oct 2013 @ 03:44
[INFO] BackWPup job started from wp-cron
[INFO] PHP ver.: 5.3.24; cgi-fcgi; Linux
[INFO] Maximum script execution time is 3600 seconds
[INFO] MySQL ver.: 5.5.30-cll
[INFO] curl ver.: 7.24.0; OpenSSL/0.9.8b
[INFO] Temp folder is: /home/USERNAME/public_html/uploads/backwpup-ec9bf-temp/
[INFO] Logfile folder is: /home/USERNAME/public_html/wp-content/backwpup-ec9bf-logs/
[INFO] Backup type is: archive
[INFO] Backup file is: /home/USERNAME/logs/backwpup_1_2013-10-27_03-44-40.zip [27-Oct-2013 03:44:40] 1. Try to dump database … 

[ Skipping all the Dump Database Table lines ]

[27-Oct-2013 03:44:48] Database dump done!
[27-Oct-2013 03:44:49] 1. Trying to make a list of folders to back up …
[27-Oct-2013 03:45:01] 3018 folders to back up.
[27-Oct-2013 03:45:01] 1. Trying to create a WordPress export to XML file …
[27-Oct-2013 03:45:01] Added XML export "USERNAME-Consulting-Dashboard.wordpress.2013-10-27.xml.gz" with 6.47 kB to backup file list.
[27-Oct-2013 03:45:02] 1. Trying to generate a file with installed plugin names …
[27-Oct-2013 03:45:02] Added plugin list file "USERNAME-Consulting-Dashboard.pluginlist.2013-10-27.txt.gz" with 754.00 B to backup file list.
[27-Oct-2013 03:45:02] 1. Trying to create backup archive …
[27-Oct-2013 03:45:02] Compression method is ZipArchive
[27-Oct-2013 19:00:14 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[27-Oct-2013 19:00:14 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[27-Oct-2013 19:09:22 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[27-Oct-2013 19:09:22 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[27-Oct-2013 19:19:49 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[27-Oct-2013 19:19:49 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[27-Oct-2013 19:27:51 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[27-Oct-2013 19:27:51 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[27-Oct-2013 19:33:40 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[27-Oct-2013 19:33:40 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[27-Oct-2013 19:37:43 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[27-Oct-2013 19:37:43 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[27-Oct-2013 19:46:31 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[27-Oct-2013 19:46:31 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[27-Oct-2013 19:54:31 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[27-Oct-2013 19:54:31 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[27-Oct-2013 20:06:49 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[27-Oct-2013 20:06:49 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[27-Oct-2013 20:10:35 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[27-Oct-2013 20:10:35 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[27-Oct-2013 20:21:17 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[27-Oct-2013 20:21:17 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[27-Oct-2013 20:36:03 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[27-Oct-2013 20:36:03 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[27-Oct-2013 20:43:33 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[27-Oct-2013 20:43:33 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[27-Oct-2013 20:57:46 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[27-Oct-2013 20:57:46 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[27-Oct-2013 21:12:11 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[27-Oct-2013 21:12:11 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[27-Oct-2013 21:30:04 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[27-Oct-2013 21:30:04 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[27-Oct-2013 20:20:01] WARNING: Job restart due to inactivity for more than 5 minutes.
[27-Oct-2013 21:04:54] WARNING: Job restart due to inactivity for more than 5 minutes.
[27-Oct-2013 21:16:42] WARNING: Job restart due to inactivity for more than 5 minutes.
[27-Oct-2013 21:16:43] Job has done with warnings in 63124 seconds. Please resolve them for correct execution.

I have the “Restart the job” setting checked.
I have a newer version of PHP so zip compression now works (see https://lcblog.lernerconsult.com/2013-php-unzip-bug-makes-wordpress-updates-hang/ )

MySQL connection needs to be re-made after making .zip of website folders.

[INFO] BackWPup version 3.0.13; WordPress version 3.6.1; A project of Inpsyde GmbH developed by Daniel Hüsken
[INFO] This program comes with ABSOLUTELY NO WARRANTY. This is free software, and you are welcome to redistribute it under certain conditions.
[INFO] Blog url: https://lernerconsulting.info/
[INFO] BackWPup job: Full Backup; DBDUMP+FILE+WPEXP+WPPLUGIN [INFO] BackWPup cron: 0 3 * * 0; Sun, 20 Oct 2013 @ 03:16 [
INFO] BackWPup job started from wp-cron
[INFO] PHP ver.: 5.3.24; cgi-fcgi; Linux
[INFO] Maximum script execution time is 3600 seconds
[INFO] MySQL ver.: 5.5.30-cll [
INFO] curl ver.: 7.24.0; OpenSSL/0.9.8b
[INFO] Temp folder is: /home/*****/public_html/uploads/backwpup-ec9bf-temp/
[INFO] Logfile folder is: /home/*****/public_html/wp-content/backwpup-ec9bf-logs/
[INFO] Backup type is: archive
[INFO] Backup file is: /home/*****/logs/backwpup_1_2013-10-20_03-16-03.zip
[20-Oct-2013 03:16:03] 1. Try to dump database …
[20-Oct-2013 03:16:08] Connected to database *****_wrdp1 on localhost 

... removed "Dump database table" lines ...

[20-Oct-2013 03:16:17] Dump database table "wp_users"
[20-Oct-2013 03:16:17] Added database dump "lernerc3_wrdp1.sql.gz" with 5.36 MB to backup file list
[20-Oct-2013 03:16:17] Database dump done!
[20-Oct-2013 03:16:17] 1. Trying to make a list of folders to back up …
[20-Oct-2013 03:16:40] 3585 folders to back up.
[20-Oct-2013 03:16:40] 1. Trying to create a WordPress export to XML file …
[20-Oct-2013 03:16:40] Added XML export "Lerner-Consulting-Dashboard.wordpress.2013-10-20.xml.gz" with 4.60 kB to backup file list.
[20-Oct-2013 03:16:41] 1. Trying to generate a file with installed plugin names …
[20-Oct-2013 03:16:41] Added plugin list file "Lerner-Consulting-Dashboard.pluginlist.2013-10-20.txt.gz" with 754.00 B to backup file list.
[20-Oct-2013 03:16:41] 1. Trying to create backup archive …
[20-Oct-2013 03:16:41] Compression method is ZipArchive 

***** Notice the long time (13 hours) to compress all the files *****

[20-Oct-2013 16:56:26 America/Chicago] WordPress database error MySQL server has gone away for query SELECT meta_value FROM wp3_sitemeta WHERE meta_key = 'ms_files_rewriting' AND site_id = 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data, BackWPup_Option::get, BackWPup_Option::defaults, wp_upload_dir, get_site_option
[20-Oct-2013 16:56:26 America/Chicago] WordPress database error MySQL server has gone away for query SELECT 1 made by require_once('wp-load.php'), require_once('wp-config.php'), require_once('wp-settings.php'), do_action('init'), call_user_func_array, BackWPup_Cron::cron_active, BackWPup_Job::start_http, BackWPup_Job->run, BackWPup_Job->create_archive, BackWPup_Job->update_working_data
[20-Oct-2013 14:56:26] WARNING: mysql_error() expects parameter 1 to be resource, boolean given
[20-Oct-2013 16:56:26 America/Chicago] PHP Warning: mysql_error() expects parameter 1 to be resource, boolean given in /home/*****/public_html/wp-includes/wp-db.php on line 1206 

... removed duplicate "line 1206" messages and "WARNING: mysql_error() expects parameter 1 to be resource, boolean given" messages ...

[20-Oct-2013 17:10:45 America/Chicago] PHP Warning: mysql_error() expects parameter 1 to be resource, boolean given in /home/*****/public_html/wp-includes/wp-db.php on line 1206
[20-Oct-2013 16:58:22] WARNING: Job restart due to inactivity for more than 5 minutes.
[20-Oct-2013 17:22:20] WARNING: Job restart due to inactivity for more than 5 minutes.
[20-Oct-2013 17:33:48] WARNING: Job restart due to inactivity for more than 5 minutes.
[20-Oct-2013 17:33:48] Job has done with warnings in 51465 seconds. Please resolve them for correct execution.

With PHP 5.4.8, and you not mentioning “WordPress Update hangs”, I would say you do not have the PHP Zip/Unzip problem.

When I’ve gotten “MySQL server has gone away for query” is when I’ve gotten “Job restart due to inactivity”, but you don’t say you’ve gotten that error.

No other ideas.

WP-Super-Cache (and WordPress Updates, and BackWPUp) works with compression after talking to my hosting provider; they already had a newer PHP installed, a .htaccess configuration change switched me to the newer PHP.

See https://lcblog.lernerconsult.com/2013-php-unzip-bug-makes-wordpress-updates-hang/ for PHP code demonstrating the bug is in PHP not WordPress. (WordPress should test if PHP Unzip has this bug!)

There are older versions of PHP that have bugs with zip/unzip, hang with no error messages — and make WordPress Update fail, make BackWPup compression fail, anything using zip/gzip.

https://lcblog.lernerconsult.com/2013-php-unzip-bug-makes-wordpress-updates-hang/ has PHP code that demonstrates the bug isn’t in WordPress or BackWPUp (if your version of PHP has the bug).

BackWPUp works with compression after talking to my hosting provider, a .htaccess configuration change switched me to a newer PHP.

Update on my earlier post:

There are (older) versions of PHP that have bugs with zip/unzip, hang with no error messages — and make WordPress Update fail, make BackWPup compression fail, anything using zip/gzip. https://lcblog.lernerconsult.com/2013-php-unzip-bug-makes-wordpress-updates-hang/ has PHP code that demonstrates the bug isn’t in WordPress.

BackWPUp works with compression after talking to my hosting provider; they already had a newer PHP installed, a .htaccess configuration change switched me to the newer PHP.

Does WordPress Update work successfully?

What version of PHP do you have? There are (older) versions of PHP that have bugs with zip/unzip, hang with no error messages — and make WordPress Update fail, make BackWPup compression fail, anything using zip/gzip. https://lcblog.lernerconsult.com/2013-php-unzip-bug-makes-wordpress-updates-hang/ has PHP code that demonstrates the bug isn’t in WordPress.

Obviously a temporary workaround is disable BackWPUp compression, if this is the problem.

What other symptoms are there, perhaps with WordPress or other plugins?

Other symptoms with BackWPUp? Are you getting “WordPress database error MySQL server has gone away for query” messages?

Do you have BackWPup configured to use compression (zip, gzip, tar)?

Does WordPress Update work successfully?

What version of PHP do you have? There are (older) versions of PHP that have bugs with zip/unzip, hang with no error messages — and make WordPress Update fail, make BackWPup compression fail, anything using zip/gzip. https://lcblog.lernerconsult.com/2013-php-unzip-bug-makes-wordpress-updates-hang/ has PHP code that demonstrates the bug isn’t in WordPress.

I no longer saw the “inactivity” warning after disabling BackWPup compression. Obviously the fix for this is 1) you update PHP if you have a version that has this bug or 2) WordPress itself test for the bug and use a WP version of zip/unzip or 3) don’t use BackWPUp with compression.

BackWPUp works with compression after talking to my hosting provider; they already had a newer PHP installed, a .htaccess configuration change switched me to the newer PHP.

The 500 Server Error is probably “Premature end of script headers” (a PHP error message, only visible if are logging 500 errors; I’ve seen it with truncated files, and with too-restrictive file permissions.)

WordPress 3.6.1, Multi-Site, WP Super Cache 1.3.2
This seems to work:

Configured to use PHP caching, Cache Test (on WPSuperCache “Easy” tab): Successful.
Add “Compress pages so they’re served more quickly to visitors. (Recommended)” on Advanced tab.

Fetching [URL] to prime cache: OK
Fetching first copy of [URL]: OK (1.html)
Fetching second copy of [URL]: OK (2.html)
One or more page requests failed:
Page 1: 500 (Internal Server Error)
Page 2: 500 (Internal Server Error)
The pages do not match! Timestamps differ or were not found!

Uncheck “Compress pages so they’re served more quickly to visitors. (Recommended)” on Advanced tab.
Cache Test successful

[note: On my server, WordPress Update hangs, WordPress plugin update hangs, and PHP Unzip hangs e.g. $zip->extractTo($path.’/folder’) or copy(“zip://”.$zipFullPath.’#’.$filename, $destPath.$destName); ]

[Note: in PHP error pages, log $_SERVER[‘REDIRECT_ERROR_NOTES’] to see if there is any error message.]

Got it as soon as I turned on Debug (via wp-config.php)
Have had AIOSP for a long time, and updated settings.

I have BackWPup version 3.0.13; WordPress version 3.6 in Multi-Site mode.

With TAR compression, database backup works, for all the multi-site tables. That is the most important feature.

With other compressions, database backup gives errors, seems to be with the PHP ZIP functions; i.e. getting the database data from MySQL works, combining and compressing the data into a .zip file, in any of the compressed formats, hangs and times out.

I have only tried backing up my web site (non-database) files with compression; of course bigger files fail being made into zip file as well.

p.s. The email report says “WARNING: mysqli::mysqli(): Headers and client library minor version mismatch. Headers:50162 Library:50530” which is programmer-ese for “oh, you have newer Library software than is required for this program to work, good”. [Author: reword it as “Your server meets the Library version requirements for this plugin”?]

You may see (if you have enabled warnings at the “strict” level): “STRICT NOTICE: is_a(): Deprecated. Please use the instanceof operator”, which is programmer-ese for “that’s the old way of saying it, here’s the new way to say it, a few years from now we won’t understand the old way”; in English, you can ignore that unless you’re the programmer.

George
https://lcblog.lernerconsult.com/