[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

Nathan Haigh nathanhaigh at ukonline.co.uk
Wed Dec 1 03:35:38 EST 2004

I'm on WinXP and as far as I remember (or don't remember as the case is), I suspect I mustn't have had too bad a time installing
them! However I can test this out on a clean Win98 (virtual machine) installation more or less immediately and if required on a
clean WinXP installation (a bit more hassle and time required for me to do this as I'll have to install WinXP in a virtual machine).
If all goes smoothly, or has some funny quirks etc, I could write a quick installation guide for BioPerlers if that's any use!

The only possible problem I can see for the moment is that of the XML::Parser. I'm not sure what version is installed with
ActiveState, but if BioPerl requires a later version of this module, it can be a bit of a swine to install if you only use ppm. The
problem is this: if someone tries to update XML-Parser or Compress-Zlib (the latter not used by BioPerl so shouldn't be a problem)
using ppm from ActiveState Perl on Win95 and Win98, it will do one of two things: 1) either will not update those modules at all; or
2) will try to update those modules and fail part way through and screw up those modules! The latter being the worst that can happen
since ppm requires these two modules to function. After this happened with me, I had to do a reinstall of Perl and all the Perl
modules I had. See http://aspn.activestate.com/ASPN/Downloads/ActivePerl/PPM/ for a few details.

I think all the following XML modules are available as ppd files for ppm installs on windows, as I included them in a possible
BioPerlv1.5 ppd file:

I'll have a run though on the Win98 system over the next day or two and let you know how I get on!

BTW, has the problem with the quote line in the BEGIN subs of BioPerl 1.5.0-RC1 been fixed? Or should I just use the latest CVS


> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Hilmar Lapp
> Sent: 01 December 2004 06:18
> To: Chris Mungall
> Cc: Allen Day; Aaron J. Mackey; Bioperl
> Subject: Re: [Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
> On Monday, November 29, 2004, at 01:22  PM, Chris Mungall wrote:
> >> It would still require a working XML parser installation, no?
> >
> > yes - it would require some kind of third-party XML module or modules.
> > I
> > guess this may be slightly problemmatic as these are currently all
> > optional for bioperl, yep?
> Yep.
> To me, it's primarily an issue of cross-platform compatibility, unless
> I'm mistaken and there are reasonable pure-perl XML parsers available.
> In my admittedly cursory picture more or less all XML parsers (or those
> of reasonable speed anyway, if the ones frequently used are any
> indication) are based on the expat library. So far I've managed to
> install those modules on all Linux and MacOSX platforms I've worked
> with, sometimes with little and sometimes with a little more trouble,
> but it remains to be seen whether this is an issue for Windows or not.
> Anybody out there who can report on installing Expat and XML::Parser
> and friends?
> 	-hilmar
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
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