Package: libbio-eutilities-perl
Followup-For: Bug #1093338
X-Debbugs-Cc: carandraug+...@gmail.com
I'm an upstream developer of Bio::EUtilities. As you remark, this bug
is weird because nothing seems to have changed.
I've tried to reproduce it on a container of Debian Trixie but all
tests are OK. Can you help me reproduce this bug?
If I'm reading the logs correctly, the following perl code should be
enough to trigger the bug:
use Bio::Tools::EUtilities;
my $eutil = Bio::Tools::EUtilities->new(-eutil => 'elink', -file =>
't/data/eutils/elink_acheck.xml');
my @databases = $eutil->get_databases; # this line should trigger the bug
N.B.: Bio::EUtilities uses XML::Simple which is an API layer for a
series of underlying XML parsers. Which parser gets used is dependent
on env vars and on what's available in the system. The error message
"choice/seq contains no opening bracket" seems to come from
XML/SAX/PurePerl/DTDDecls.pm from the the XML::SAX::PurePerl parser
(part of Debian's libxml-sax-perl package).
Many thanks
David
