===> Tue Jun 28 12:40:20 BST 2016 Starting it
===> Tue Jun 28 12:40:20 BST 2016 Configuring it
configure.php: $Id: configure.php 337463 2015-08-14 23:54:15Z cmb $
PHP version: 5.3.3

Checking for source directory... /local/src/phpdoc-all/doc-base
Checking for output filename... /local/src/phpdoc-all//doc-base/2016-06-28-12-it.xml
Checking whether to include CHM... no
Checking for PHP executable... /usr/bin/php
Checking for language to build... it
Checking whether the language is supported... yes
Checking for partial build... no
Checking whether to enable detailed XML error messages... no
Checking libxml version... 2.7.6
Checking whether to enable detailed error reporting (may segfault)... yes
Checking whether to optimize out the DTD (performance gain, but segfaults)... no
Generating /local/src/phpdoc-all/doc-base/manual.xml... done
Generating /local/src/phpdoc-all/doc-base/install-unix.xml... done
Generating /local/src/phpdoc-all/doc-base/install-win.xml... done
Generating /local/src/phpdoc-all/doc-base/developer.template.xml... done
Generating /local/src/phpdoc-all/doc-base/scripts/file-entities.php... done
Iterating over extension specific version files... OK
Saving it... OK
Creating file /local/src/phpdoc-all/doc-base/entities/file-entities.ent... done
Checking for if we should generate a simplified file... no
Checking whether to save an invalid .manual.xml... no
Loading and parsing manual.xml... done.
Validating manual.xml...  Namespace default prefix was not found
 Namespace default prefix was not found
failed.

The document didn't validate, here are the errors I got:
(If this isn't enough information, try again with --enable-xml-details)
 Element warning namespace name for default namespace does not match the DTD
 Element simpara namespace name for default namespace does not match the DTD

Eyh man. No worries. Happ shittens. Try again after fixing the errors above.
=============> Something happenend when snapshotting it
Failed completely
=============> Please have a look!
=============> Something happenend when snapshotting it
Failed configuring it
=============> Please have a look!
===> Tue Jun 28 12:41:44 BST 2016 Cleaning /local/src/phpdoc-all//doc-base/2016-06-28-12-it.xml