[Debian-med-packaging] Bug#1077454: Bug#1077454: bioperl-run: t/SABlastPlus.t failure

[Aaron M. Ucko]

Étienne Mollier <emollier at debian.org> writes:

> Thanks for the additional input, naively I would think the undef
> could have to do with a subtle change in makeblastdb output, but

AFAICT, the relevant change is in blastdbcmd error output and the
following patch suffices (perhaps with a line break thrown in):

--- a/lib/Bio/Tools/Run/StandAloneBlastPlus.pm
+++ b/lib/Bio/Tools/Run/StandAloneBlastPlus.pm
@@ -1106,7 +1106,7 @@ sub check_db {
 	$self->factory->no_throw_on_crash(1);
 	$self->factory->_run();
 	$self->factory->no_throw_on_crash(0);
-	return 0 if ($self->factory->stderr =~ /No alias or index file found/);
+	return 0 if ($self->factory->stderr =~ /No alias or index file found|Database memory map file error/);
 	return 1;
     }
     return;

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?amu@monk.mit.edu