[Bioperl-l] New Fink Bioperl dependency installer, etc.

[Hilmar Lapp]

I used CPAN, but not BioPerl::Bundle (I just installed the various 
dependencies; I work on the cvs HEAD). It does try to update Perl at 
some point, but you can interrupt that step (that's what I did: ^C) 
and it just carries on with the other modules. As far as I can tell, 
it works.

The problem with LWP is still there, it did override my system head 
(do you happen to know where I can get the original one? Can you 
send me yours?)

I tried to install some perl packages and their dependencies with 
Fink, but wasn't very happy with the results. E.g., some packages 
(GD for example, MySQL) required C-libs to be available; first, Fink 
didn't have the required versions, and second after installing it 
myself it didn't appreciate the stuff being there now. That was all 
2 months ago, so things may be different by now.

	-hilmar

On Wednesday, September 4, 2002, at 08:29  AM, Steven Cannon wrote:

> I've been maintaining a site describing my Bioperl install 
> experiences on Mac OS X 
> ( http://www.tc.umn.edu/~cann0010/Bioperl_OSX_install.html ), and 
> would like to keep it up to date by getting feedback from other OS 
> X users. In particular, there are two install options that I would 
> like to hear more about: the CPAN.pm BioPerl::Bundle, and a new 
> Fink Bioperl dependency installer by Christopher Dithi (Thanks! - 
> this should be an ideal solution for OS X).
>
> There is an OS X - specific problem with CPAN (see below). The Fink 
> "bioperl-pm" is currently in the "unstable" branch, meaning that it 
> needs more testing. I would also like to know whether the new 
> version of the OS (10.2) causes any problems, either in existing or 
> new installations. Here's what I say on my page -- and I'll update 
> this as I hear other peoples' experiences with CPAN or Fink.
> ===
>  There are at least three quite distinct options for installing the 
> BioPerl dependencies on OS X. You can 1) do it "from scratch," 
> following the instructions on this page, or 2) you can use the 
> CPAN.pm module and BioPerl::Bundle, which should install almost all 
> of the dependencies nearly automatically, or 3) you can try the new 
> Fink bioperl-pm package, which also should install almost all of 
> the dependencies nearly automatically. Unfortunately, none of these 
> options is entirely without a certain amount of hassle and risk. In 
> order, here are the options in more detail:
>
> 1) Doing the installations manually gives you the most control, but 
> there are a few pitfalls here and there (particularly, see the note 
> about "HEAD" below, under "LWP.")
>
> 2) CPAN.pm is a wonderful creation, but I have been frustrated by 
> it on OS X. In particular, the last time I tried to install CPAN.pm 
> itself (in July, 2002), it tried to update my version of Perl to 
> 5.80 -- which would seem like a virtuous thing, but the Perl 
> reinstallation process itself was long and arduous, and didn't work 
> for me (it caused me no problems with the default installation, but 
> 5.80 didn't "take.") And then when I tried to use it to install 
> BioPerl::Bundle, it tried AGAIN (and without asking or giving me 
> the option to refuse) to install 5.80. That said, the dependencies 
> did install correctly. However, unless someone knows how to 
> circumvent this problem, I can't recommend BioPerl::Bundle on OS X. 
> (And if someone knows a way around this problem, please let me 
> know! Actually, to investigate, try 
> http://www.scriptdigital.com/divers/frontiermonitor.html -- which 
> looks like a solution).
>
> 3) The Fink option should be the best solution, because the Fink 
> package manager is explicitly designed for OS X. It also installs 
> everything in its own private directory (/sw), so there is 
> essentially no danger of overwriting important Unix utilities and 
> libraries. The bioperl-pm package is new, and I haven't tested it, 
> so I (and the package maintainer, Christopher Dithi) would be 
> interested to hear how it goes. As of August, 2002, the Fink 
> bioperl-pm is in the "unstable" branch, meaning that it has not 
> been well tested. You can help!
> ===
> - Steven Cannon
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------