From @schwern

Package namespace installed latest in CPAN file
AutoLoader undef 5.56 CHIPS/perl5.004_05.tar.gz
Could not eval '
  package ExtUtils​::MakeMaker​::_version;
  no strict;

  local $VERSION;
  $VERSION=undef; do {
  $VERSION = _version();
  }; $VERSION
  ' in /home/schwern/lib/perl5/site_perl/5.005/Bio/Index/EMBL.pm​: Undefined subroutine &ExtUtils​::MakeMaker​::_version​::_version called at (eval 234) line 7, <FH> chunk 103.

Lovely, ain't it?

The failure comes because Bio​::Index​::EMBL does the following​:

sub _version {
  return 0.1;
}
$VERSION = _version();

And parse_version() only sees "$VERSION = _version();". As
Bio​::Index​::EMBL​::_version hasn't been loaded, the eval fails. Now, I
have no idea how to improve parse_version to fix this, but I -do- know
that it shouldn't -die- upon failing to eval.

I've switched the eval to a warning and added a smidge more
documentation to parse_version. I've also mentioned this to the
bioperl developers and recommended they alter the way they set $VERSION
so that parse_version can see it.

*** lib/ExtUtils/MM_Unix.pm 1999/07/19 01​:37​:56
--- lib/ExtUtils/MM_Unix.pm 1999/07/19 01​:56​:40
***************
*** 2564,2570 ****
 
  =item parse_version
 
! parse a file and return what you think is $VERSION in this file set to
 
  =cut
 
--- 2564,2571 ----
 
  =item parse_version
 
! parse a file and return what you think is $VERSION in this file set to.
! It will return undef if it can't figure out what $VERSION is.
 
  =cut
 
***************
*** 2592,2598 ****
  };
  local($^W) = 0;
  $result = eval($eval);
! die "Could not eval '$eval' in $parsefile​: $@​" if $@​;
  $result = "undef" unless defined $result;
  last;
  }
--- 2593,2599 ----
  };
  local($^W) = 0;
  $result = eval($eval);
! warn "Could not eval '$eval' in $parsefile​: $@​" if $@​;
  $result = "undef" unless defined $result;
  last;
  }