Bioperl: RE: Makefile problems

Osborne, Brian
Wed, 17 Mar 1999 11:53:13 -0500


Thank you for the note, I'll check it out. Another approach, I think,
is to go the ActiveState route entirely, anotherwords create what
Activestate calls a "package" that automatically installs the module.
However, this might be tied in with ActiveState's product, PerlDirect,
I'm not sure. I haven't heard back from ActiveState, I wrote them
a letter about this.

Thanks again,

Brian O.

-----Original Message-----
From:	David J. Evans []
Sent:	Monday, March 15, 1999 5:01 AM
Subject:	Makefile problems

I'm sure you got the solution to this since 12/98, but if not it's due to
the makefile and nmake - you need to either get nmake or (as I did) copy the
GS port of dmake to your path (complete with the associated subdirectory
with the platform macros) and then edit the makefile to say something like
make = 'dmake'

I've just installed BioPerl on an NT box running build 509 activestate and
things are looking (reasonably) good.  Certainly the standard seq manip
seems OK.

Apologies if you sorted this lot out, I just came across your posting on the
archive.  I know how sometimes I jsut pack up - through lack of time -
rather than get to the bottom of a minor hitch.

Have fun

RE: Bioperl: "port" to NT

Osborne, Brian (
Fri, 11 Dec 1998 18:13:47 -0500

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     Previous message: Gunther Birznieks: "Re: Bioperl: "port" to NT"

To the group,

This is getting so easy I'm embarassed. If
one goes to and gets the most recent Perl
port from and
installs it on NT, then downloads,
unzips, and copies the Bio/ directory to the
newly create C:\Perl\lib, the scripts using
Bioperl just work. That's it.

By that I mean either through Cygnus' bash
or through NT's "Command Prompt".

However, the full 'perl' followed by
'make' gives :

Makefile:738: *** missing separator. Stop.

I'll start to dissect this after the weekend with
my 15 month old son. He could have done this "port"

Brian O.

Brian Osborne
Cadus Pharmaceutical Corporation
777 Old Saw Mill River Rd.
Tarrytown NY USA
TEL 914 467 6291
FAX 914 345 3565

> -----Original Message-----
> From: Gunther Birznieks []
> Sent: Friday, December 11, 1998 5:15 PM
> To:;
> Subject: Re: Bioperl: "port" to NT
> At 01:55 PM 12/11/98 -0800, greg heil wrote:
> >Gunther Birznieks wrote:
> >
> >> Why 5.003? I thought that the latest ActiveState port is at
> > 5.005_02 and comes with the If you used this, maybe
> > you wouldn't have to worry about changing the behavior of some
> > of the "pure" Perl modules so much?
> >
> >i can confirm the ActiveState/Posix, at least as of release 507.
> >
> >The 5.003 part, as i understand it, is to get a _least_ common
> >denominator... So folks in big IS depts would not have to bug
> >powers that be to upgrade their Perl;)
> >
> Hmm. That idea is commendable.
> But isn't that a different goal than doing an NT-port? Perhaps I am
> missing something but it seems to me that by that logic,
> one might as well tell people not to bug their UNIX admin to upgrade
> Perl 5.003 for UNIX either. Instead, just start distributing instructions
> with
> Bioperl for running on older versions of Perl in general.
> In addition, the mechanism for manually placing the Bio hierarchy in
> kind of requires pretty intrusive access to the NT Box anyway.
> It's not that much more intrusive to require upgrading
> to a more recent version of NT Perl especially when the install for
> ActiveState
> Perl is GUI-based these days.
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     Previous message: Gunther Birznieks: "Re: Bioperl: "port" to NT"

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