update stuck from D5.3 to D6 at system_update_6021

After getting the problem with Drupal 6 beta 3, I downloaded the Nov 29 6.x-dev build but still encountered the same problem. I'll keep an eye out for the nightly builds.

Here's some more facts if it offers anymore help. My original DB data was from D4.7.8 updated to D5.3 and then cleaned up to remove some unused modules and tables. And now I'm taking that D5.3 to update it to D6. Would that have any effect?

I couldn't check the logs because it never stopped. The progress bar was not doing anything for 30 minutes. That seemed long enough for me to manually stop it and retry again with the same result happening again.

Here it is

I was finally able to get some errors after hitting to the previous page. This is from the system.install,v 1.199 2007/11/29 12:02:06 goba

* user warning: Duplicate column name 'converted' query: update_sql /* jxxx : update_sql */ ALTER TABLE menu ADD `converted` TINYINT unsigned NOT NULL DEFAULT 0 in /drupal/includes/database.mysql-common.inc on line 297.
* user warning: Table 'menu_custom' already exists query: update_sql /* jxxx : update_sql */ CREATE TABLE menu_custom ( `menu_name` VARCHAR(32) NOT NULL DEFAULT '', `title` VARCHAR(255) NOT NULL DEFAULT '', `description` TEXT DEFAULT NULL, PRIMARY KEY (menu_name) ) /*!40100 DEFAULT CHARACTER SET UTF8 */ in /drupal/includes/database.inc on line 451.
* user warning: Duplicate entry 'navigation' for key 1 query: system_update_6021 /* jxxx : system_update_6021 */ INSERT INTO menu_custom (menu_name, title, description) VALUES ('navigation', 'Navigation', 'The navigation menu is provided by Drupal and is the main interactive menu for any site. It is usually the only menu that contains personalized links for authenticated users, and is often not even visible to anonymous users.') in /drupal/modules/system/system.install on line 2246.
* user warning: Duplicate entry 'primary-links' for key 1 query: system_update_6021 /* jxxx : system_update_6021 */ INSERT INTO menu_custom (menu_name, title, description) VALUES ('primary-links', 'Primary links', 'Primary links are often used at the theme layer to show the major sections of a site. A typical representation for primary links would be tabs along the top.') in /drupal/modules/system/system.install on line 2246.
* user warning: Duplicate entry 'secondary-links' for key 1 query: system_update_6021 /* jxxx : system_update_6021 */ INSERT INTO menu_custom (menu_name, title, description) VALUES ('secondary-links', 'Secondary links', 'Secondary links are often used for pages like legal notices, contact details, and other secondary navigation items that play a lesser role than primary links') in /drupal/modules/system/system.install on line 2246.

chx,

I just tried your safeguard.patch but that had no effect.

Yes, the safer_stop.patch worked but there was an error

user warning: Unknown column 'updated' in 'where clause' query: system_update_6021 /* jxxx : system_update_6021 */ SELECT * FROM menu WHERE updated = 0 in /drupal/modules/system/system.install on line 2350.

I looked carefully at your patch

if (!db_result(db_query('SELECT * FROM {menu} WHERE updated = 0'))) {

Looking at the menu table, there's no updated column. Did you mean converted column?

After successful update, I tried to go back and check it if indeed finished all the upgrades but I get this warning causing incorrect rendering of all the pages on my website.

* warning: tempnam() [function.tempnam]: open_basedir restriction in effect. File() is not within the allowed path(s): (/home/badfscom/:/usr/lib/php:/usr/local/lib/php:/tmp) in /drupal/includes/file.inc on line 756.
* The file could not be created.
* warning: array_key_exists() [function.array-key-exists]: The first argument should be either a string or an integer in /drupal/modules/system/system.module on line 854.
* warning: array_map() [function.array-map]: Argument #2 should be an array in /drupal/modules/system/system.module on line 856.
* warning: array_keys() [function.array-keys]: The first argument should be an array in /drupal/includes/theme.inc on line 1769.
* warning: Invalid argument supplied for foreach() in /drupal/includes/theme.inc on line 1769.

I just did the Drupal 6 beta 4 upgrade completely again and everything went smoothly with the upgrade. I solved my problem in #12. I didn't have the tmp directory in my new install directory that drupal needed to create the theme files.