Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 805

[hyphaltip]

This warning has shown up for years --

https://github.com/bioperl/bioperl-live/blob/2b53e22cd3f61961ea9ac7707537a01e4bf75a73/lib/Bio/DB/IndexedBase.pm#L804

I don't remember the exact logic intended but should the return be inside the eval to avoid the ambiguity? Here's my proposed solution - anyone want to look and test - it seems to run okay when I change locally and am trying out in some limited tests.

    eval {
      return $self->_fhcache( File::Spec->catfile($self->{dirname}, $file));
    } or $self->throw( "Can't open file $file" );

[cjfields]

Seems like the logic is to die if the File::Spec->catfile($self->{dirname}, $file) call is performed; notably $@ isn't checked. I'm guessing it's okay to return from inside an eval, but I would do it something like the below, which is more explicit about the intent:

# completely untested
my $fh = eval {
     $self->_fhcache( File::Spec->catfile($self->{dirname}, $file));
    };
$self->throw( "Can't open file $file: $@" ) if $@;
return $fh;

[alanhoyle]

I am seeing this warning as well. It occurs for me when the current version of VEP (103.1) is installed using Bioconda, and VEP throws the warning at startup every time.

[hyphaltip]

This warning has been around for years. No one has dug in to fix though I think. Should be harmless but let’s fix it ...

On Fri, Apr 23, 2021 at 8:06 AM Alan Hoyle @.***> wrote:

I am seeing this warning as well. It occurs for me when the current version of VEP (103.1) is installed using Bioconda, and VEP throws the warning at startup every time.

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