Description:
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I've tested this problem and it is duplicable on Ubuntu 10.04 and FreeBSD 8, both with 5.3.2 installed (from apt-get/ports).  I also did a build of 5.3.2 from source to test this and it failed in the same way.

The problem comes when you try to create a table in a newly created database when using the SQLite3 class.  The empty db is created without error and when you then try to create a table, you get the following error:

PHP Warning:  SQLite3::exec(): disk I/O error in php shell code on line 1

This is the same error in all builds on all OSes.

Test script:
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$ php -a

php > $s = new SQLite3('/home/jdeiman/tmp/php.db',  SQLITE3_OPEN_CREATE);
php > $ret = $s->exec('CREATE table testing (id integer)');
PHP Warning:  SQLite3::exec(): disk I/O error in php shell code on line 1