Not sure if it should matter, but I'm using the Stretch testing branch.
A notice is thrown but the script seems to complete successfully. Also, the same notice appears subsequently in the web UI when viewing Special:SiteMatrix.
vagrant@vagrantstretch:/vagrant/mediawiki/extensions/ReadingLists/maintenance$ mwscript extensions/ReadingLists/maintenance/populateProjectsFromSiteMatrix.php --wiki=wiki
PHP Notice: Undefined index: name in /vagrant/mediawiki/extensions/SiteMatrix/includes/SiteMatrix.php on line 95
PHP Stack trace:
PHP 1. {main}() /var/www/w/MWScript.php:0
PHP 2. require_once() /var/www/w/MWScript.php:95
PHP 3. require_once() /vagrant/mediawiki/extensions/ReadingLists/maintenance/populateProjectsFromSiteMatrix.php:104
PHP 4. MediaWiki\Extensions\ReadingLists\Maintenance\PopulateProjectsFromSiteMatrix->execute() /vagrant/mediawiki/maintenance/doMaintenance.php:94
PHP 5. SiteMatrix->__construct() /vagrant/mediawiki/extensions/ReadingLists/maintenance/populateProjectsFromSiteMatrix.php:40
Notice: Undefined index: name in /vagrant/mediawiki/extensions/SiteMatrix/includes/SiteMatrix.php on line 95
Call Stack:
0.0002 365896 1. {main}() /var/www/w/MWScript.php:0
0.0054 421552 2. require_once('/vagrant/mediawiki/extensions/ReadingLists/maintenance/populateProjectsFromSiteMatrix.php') /var/www/w/MWScript.php:95
0.0088 698552 3. require_once('/vagrant/mediawiki/maintenance/doMaintenance.php') /vagrant/mediawiki/extensions/ReadingLists/maintenance/populateProjectsFromSiteMatrix.php:104
0.2158 10824560 4. MediaWiki\Extensions\ReadingLists\Maintenance\PopulateProjectsFromSiteMatrix->execute() /vagrant/mediawiki/maintenance/doMaintenance.php:94
0.2177 10867712 5. SiteMatrix->__construct() /vagrant/mediawiki/extensions/ReadingLists/maintenance/populateProjectsFromSiteMatrix.php:40
populating...
inserted 10 projects