[Bioperl-l] Problems with Bioperl-ext package on WinVista?
Yee Man Chan
ymc at yahoo.com
Mon Aug 17 03:34:24 UTC 2009
Hi Chris
Good to hear that it is working and thanks for testing.
As to the release, my thinking is that I do understand that your desire to maintain a high level of quality in BioPerl code base. So if the HMM doesn't meet that standard, I am ok with it being spinned off.
So please pass around the updated code and test it extensively, if no one complains about the new code by the time of release, I would think it should go into the next bioperl-ext release. If people uncover new errors with the new code and the errors can't be fixed on time, then it should be spinned off.
What do you think?
Best Regards,
Yee Man
--- On Sun, 8/16/09, Chris Fields <cjfields at illinois.edu> wrote:
> From: Chris Fields <cjfields at illinois.edu>
> Subject: Re: [Bioperl-l] Problems with Bioperl-ext package on WinVista?
> To: "Yee Man Chan" <ymc at yahoo.com>
> Cc: "Robert Buels" <rmb32 at cornell.edu>, "BioPerl List" <bioperl-l at lists.open-bio.org>
> Date: Sunday, August 16, 2009, 5:53 AM
> That worked! Thanks Yee Man!
>
> chris
>
> ps - let me know how you want to deal with a release.
>
> On Aug 16, 2009, at 4:36 AM, Yee Man Chan wrote:
>
> > Hi Chris
> >
> > Thanks for your suggestions. I think
> it is indeed better to check
> > sum to 1.0 using sprintf. I fixed this in the newly
> committed HMM.pm
> >
> > I also fixed codes that will lead to
> warnings with use warnings.
> >
> > So now the only problem left is that
> "monotonic increasing" error.
> > For that part of the code, I was trying to perform an
> expectation
> > maximization step. Theoretically, the expectation
> should
> > monotonically increase in every step. But I suppose
> this is not
> > necessarily true when double precision floating point
> numbers are
> > involved. I don't know why I used a 1e-100 tolerance
> for this.
> > Therefore I "fixed" it by using the same tolerance to
> terminate the
> > maximization step (ie .000001). I suppose this "fix"
> will make it
> > much more unlikely to throw exception with your 5.10.0
> perl.
> >
> > Can you give that a try again and see
> if it works now.
> >
> > Thank you
> > Yee Man
> >
> >
> >
> > --- On Sat, 8/15/09, Chris Fields <cjfields at illinois.edu>
> wrote:
> >
> >> From: Chris Fields <cjfields at illinois.edu>
> >> Subject: Re: [Bioperl-l] Problems with Bioperl-ext
> package on
> >> WinVista?
> >> To: "Yee Man Chan" <ymc at yahoo.com>
> >> Cc: "Robert Buels" <rmb32 at cornell.edu>,
> "BioPerl List" <bioperl-l at lists.open-bio.org
>
> >> >
> >> Date: Saturday, August 15, 2009, 10:38 PM
> >> Yee,
> >>
> >> I took the liberty of making a few simple changes
> to
> >> Bio::Tools::HMM in svn to point out the problem
> and possible
> >> solutions. Feel free to revert these as
> needed.
> >>
> >> I'm seeing two errors, which appear randomly when
> running
> >> 'make test'. The first is easily fixable,
> the second,
> >> I'm not so sure. I'll let you make the
> decisions on
> >> both.
> >>
> >> 1) There is an assumption in the module
> that, when
> >> adding floating points, you will always get
> 1.0. You
> >> may run into problems: see 'perldoc -q long
> decimals'.
> >> Lines like this (two places in the module):
> >> ...
> >> if ($sum != 1.0) {
> >> $self->throw("Sum of
> >> probabilities for each state must be 1.0; got
> $sum\n");
> >> }
> >> ...
> >>
> >> won't work as expected (note I added a simple
> diagnostic,
> >> just print out the 'bad' sum). With perl
> 5.8.8, this
> >> appears to work fine, but this is what I get with
> perl 5.10
> >> (64-bit):
> >>
> >> pyrimidine1:HMM cjfields$ make test
> >> PERL_DL_NONLAZY=1 /opt/perl/bin/perl "-Iblib/lib"
> >> "-Iblib/arch" test.pl
> >> Baum-Welch Training
> >> ===================
> >> Initial Probability Array:
> >> 0.499978 0.500022
> >> Transition Probability Matrix:
> >> 0.499978 0.500022
> >> 0.499978 0.500022
> >> Emission Probability Matrix:
> >> 0.133333 0.143333
> >> 0.163333 0.123333
> >> 0.143333 0.293333
> >> 0.133333 0.143333
> >> 0.163333 0.123333
> >> 0.143333 0.293333
> >>
> >> Log Probability of sequence 1: -521.808
> >> Log Probability of sequence 2: -426.057
> >>
> >> Statistical Training
> >> ====================
> >> Initial Probability Array:
> >> 1 0
> >> Transition Probability Matrix:
> >>
> >> ------------- EXCEPTION -------------
> >> MSG: Sum of probabilities for each from-state must
> be 1.0;
> >> got 0.999999999999999976
> >>
> >> STACK Bio::Tools::HMM::transition_prob
> >>
> /Users/cjfields/bioperl/bioperl-live/Bio/Tools/HMM.pm:499
> >> STACK toplevel test.pl:82
> >> -------------------------------------
> >>
> >> make: *** [test_dynamic] Error 255
> >>
> >> I'm assuming this needs to simply be rounded up
> to
> >> 1.0. That could be accomplished with
> something like
> >> 'if (sprintf("%.2f", $sum) != 1.0) {...}'
> >>
> >> 2) The second error is a little stranger. I
> have been
> >> randomly getting this:
> >>
> >> pyrimidine1:HMM cjfields$ make test
> >> PERL_DL_NONLAZY=1 /opt/perl/bin/perl "-Iblib/lib"
> >> "-Iblib/arch" test.pl
> >> Baum-Welch Training
> >> ===================
> >> S should be monotonic increasing!
> >> make: *** [test_dynamic] Error 255
> >>
> >> When I add strict and warnings pragmas to
> Bio::Tools::HMM
> >> (with a little additional cleanup to get things
> running), I
> >> get an additional warning (arrow):
> >>
> >> pyrimidine1:HMM cjfields$ make test
> >> PERL_DL_NONLAZY=1 /opt/perl/bin/perl "-Iblib/lib"
> >> "-Iblib/arch" test.pl
> >> Argument "FL" isn't numeric in numeric lt (<)
> at
> >>
> /Users/cjfields/bioperl/bioperl-live/Bio/Tools/HMM.pm line
> >> 188. <----
> >> Baum-Welch Training
> >> ===================
> >> S should be monotonic increasing!
> >> make: *** [test_dynamic] Error 255
> >>
> >> So something is not being converted as expected.
> >>
> >> chris
> >>
> >> On Aug 15, 2009, at 11:32 PM, Yee Man Chan wrote:
> >>
> >>> When are you going to release 1.6? Maybe let
> me work
> >> on it before it releases. If it doesn't resolve
> the problem,
> >> then we can think about other alternatives.
> >>>
> >>> Also, please show me the latest errors you
> have for
> >> 5.10.0.
> >>>
> >>> Thanks
> >>> Yee Man
> >>>
> >>> --- On Sat, 8/15/09, Chris Fields <cjfields at illinois.edu>
> >> wrote:
> >>>
> >>>> From: Chris Fields <cjfields at illinois.edu>
> >>>> Subject: Re: [Bioperl-l] Problems with
> Bioperl-ext
> >> package on WinVista?
> >>>> To: "Yee Man Chan" <ymc at yahoo.com>
> >>>> Cc: "Robert Buels" <rmb32 at cornell.edu>,
> >> "BioPerl List" <bioperl-l at lists.open-bio.org>
> >>>> Date: Saturday, August 15, 2009, 7:05 PM
> >>>> I'm still seeing the same errors on
> >>>> Mac OS X for 64-bit perl 5.10.0. Mac
> OS X,
> >> native perl
> >>>> (v5.8.8) passes fine now (as well as perl
> 5.8.8
> >> on
> >>>> dev.open-bio.org).
> >>>>
> >>>> I'm wondering if this is a problem with my
> local
> >> perl
> >>>> build. I'm very tempted to push the
> >> HMM-related code
> >>>> into a separate distribution (bioperl-hmm)
> and
> >> make a CPAN
> >>>> release out of it so it gets wider testing
> via
> >> CPAN testers;
> >>>> it would just require a minimum bioperl
> 1.6
> >> installation for
> >>>> Bio::Tools::HMM and any related modules.
> >> Yee, would
> >>>> that be okay with you?
> >>>>
> >>>> chris
> >>>>
> >>>> On Aug 15, 2009, at 8:23 PM, Yee Man Chan
> wrote:
> >>>>
> >>>>>
> >>>>> I just committed HMM.xs and typemap to
> SVN.
> >> Can you
> >>>> test it to confirm it works in 64-bit
> machines?
> >>>>>
> >>>>> Thanks
> >>>>> Yee Man
> >>>>>
> >>>>> --- On Sat, 8/15/09, Chris Fields
> <cjfields at illinois.edu>
> >>>> wrote:
> >>>>>
> >>>>>> From: Chris Fields <cjfields at illinois.edu>
> >>>>>> Subject: Re: [Bioperl-l] Problems
> with
> >> Bioperl-ext
> >>>> package on WinVista?
> >>>>>> To: "Robert Buels" <rmb32 at cornell.edu>
> >>>>>> Cc: "Yee Man Chan" <ymc at yahoo.com>,
> >>>> "BioPerl List" <bioperl-l at lists.open-bio.org>
> >>>>>> Date: Saturday, August 15, 2009,
> 12:11 PM
> >>>>>> I'm not sure, but it makes more
> sense
> >>>>>> to commit these changes directly.
> >> Yee, need
> >>>> us to set
> >>>>>> you up with a commit bit? If
> so,
> >> fill out
> >>>> the
> >>>>>> information on this page:
> >>>>>>
> >>>>>> http://www.bioperl.org/wiki/SVN_Account_Request
> >>>>>>
> >>>>>> and forward it to support at open-bio.org.
> >>>>>> I'll sponsor you.
> >>>>>>
> >>>>>> chris
> >>>>>>
> >>>>>> On Aug 15, 2009, at 11:44 AM,
> Robert Buels
> >> wrote:
> >>>>>>
> >>>>>>> The usual procedure for
> developing
> >> code is to
> >>>> exchange
> >>>>>> code via commits to a version
> control
> >>>> system. Yee, do
> >>>>>> you know how to use Subversion?
> Does Yee
> >> need a
> >>>> commit bit?
> >>>>>>>
> >>>>>>> Rob
> >>>>>>>
> >>>>>>> Yee Man Chan wrote:
> >>>>>>>> Hi Chris
> >>>>>>>> I
> find
> >> that there is a
> >>>> memory
> >>>>>> access bug in my code. Attached is
> the
> >> fixed
> >>>> HMM.xs. This
> >>>>>> file together with the simpler
> typemap
> >> should fix
> >>>> all
> >>>>>> problems. (I hope..)
> >>>>>>>> Please
> let
> >> me know if it
> >>>> works
> >>>>>> for you.
> >>>>>>>> Sorry for the bug...
> >>>>>>>> Yee Man
> >>>>>>>> --- On Fri, 8/14/09, Chris
> Fields
> >> <cjfields at illinois.edu>
> >>>>>> wrote:
> >>>>>>>>> From: Chris Fields
> <cjfields at illinois.edu>
> >>>>>>>>> Subject: Re:
> [Bioperl-l]
> >> Problems
> >>>> with
> >>>>>> Bioperl-ext package on WinVista?
> >>>>>>>>> To: "Yee Man Chan"
> <ymc at yahoo.com>
> >>>>>>>>> Cc: "Robert Buels"
> <rmb32 at cornell.edu>,
> >>>>>> "Jonny Dalzell" <jdalzell03 at qub.ac.uk>,
> >>>>>> "BioPerl List" <Bioperl-l at lists.open-bio.org>
> >>>>>>>>> Date: Friday, August
> 14, 2009,
> >> 8:31
> >>>> AM
> >>>>>>>>> Yee Man,
> >>>>>>>>>
> >>>>>>>>> I tested this out
> locally
> >> (perl 5.8.8
> >>>> 32-bit,
> >>>>>> perl 5.10.0
> >>>>>>>>> 64-bit) and on
> >> dev.open-bio.org (which
> >>>> is perl
> >>>>>> 5.8.8,
> >>>>>>>>> appears to be
> 32-bit).
> >> The patch
> >>>> results
> >>>>>> in cleaning
> >>>>>>>>> up warnings for 5.10.0
> but
> >> results in
> >>>> similar
> >>>>>> warnings for
> >>>>>>>>> 5.8.8 (linux or OS
> X).
> >>>>>>>>>
> >>>>>>>>> On OS X perl 5.8.8,
> this
> >> sometimes
> >>>> passes
> >>>>>> (note the first
> >>>>>>>>> attempt fails, the
> second
> >> succeeds),
> >>>> so it's
> >>>>>> not entirely a
> >>>>>>>>> 32-bit issue:
> >>>>>>>>>
> >>>>>>>>> http://gist.github.com/167860
> >>>>>>>>>
> >>>>>>>>> OS X and perl 5.10.0,
> this
> >> always
> >>>> fails as the
> >>>>>> previous
> >>>>>>>>> gist shows, but
> demonstrates
> >> similar
> >>>> behavior
> >>>>>> (multiple
> >>>>>>>>> attempts to test get
> >> different
> >>>> responses):
> >>>>>>>>>
> >>>>>>>>> http://gist.github.com/167542
> >>>>>>>>>
> >>>>>>>>> On linux, everything
> passes
> >> with or
> >>>> w/o the
> >>>>>> patched files
> >>>>>>>>> (patched files have
> warnings
> >> as
> >>>> indicated
> >>>>>> above):
> >>>>>>>>>
> >>>>>>>>> Specs for all three
> perl
> >> executables
> >>>> (they
> >>>>>> vary a bit):
> >>>>>>>>>
> >>>>>>>>> http://gist.github.com/167883
> >>>>>>>>>
> >>>>>>>>> chris
> >>>>>>>>>
> >>>>>>>>> On Aug 14, 2009, at
> 3:27 AM,
> >> Yee Man
> >>>> Chan
> >>>>>> wrote:
> >>>>>>>>>
> >>>>>>>>>> Ah.. I find that
> the
> >> typemap can
> >>>> become as
> >>>>>> simple as
> >>>>>>>>> this
> >>>>>>>>>>
> =====================
> >>>>>>>>>> TYPEMAP
> >>>>>>>>>> HMM *
> >> T_PTROBJ
> >>>>>>>>>>
> =====================
> >>>>>>>>>>
> >>>>>>>>>> Then the generated
> HMM.c
> >> will have
> >>>> a
> >>>>>> function called
> >>>>>>>>> INT2PTR to do the
> pointer
> >> conversion.
> >>>> I
> >>>>>> believe this should
> >>>>>>>>> solve the warnings.
> >>>>>>>>>> Attached are the
> updated
> >> HMM.xs
> >>>> and
> >>>>>> typemap. Can
> >>>>>>>>> someone with a 64-bit
> machine
> >> give it
> >>>> a try?
> >>>>>>>>>> Thank you
> >>>>>>>>>> Yee Man
> >>>>>>>>>> --- On Thu,
> 8/13/09, Chris
> >> Fields
> >>>> <cjfields at illinois.edu>
> >>>>>>>>> wrote:
> >>>>>>>>>>> From: Chris
> Fields
> >> <cjfields at illinois.edu>
> >>>>>>>>>>> Subject: Re:
> >> [Bioperl-l]
> >>>> Problems with
> >>>>>> Bioperl-ext
> >>>>>>>>> package on WinVista?
> >>>>>>>>>>> To: "Yee Man
> Chan"
> >> <ymc at yahoo.com>
> >>>>>>>>>>> Cc: "Robert
> Buels"
> >> <rmb32 at cornell.edu>,
> >>>>>>>>> "Jonny Dalzell" <jdalzell03 at qub.ac.uk>,
> >>>>>>>>> "BioPerl List" <Bioperl-l at lists.open-bio.org>
> >>>>>>>>>>> Date:
> Thursday, August
> >> 13,
> >>>> 2009, 5:31
> >>>>>> PM
> >>>>>>>>>>> (just to point
> out to
> >>>> everyone, Yee
> >>>>>>>>>>> Man's contact
> >> information was
> >>>> in the
> >>>>>> POD)
> >>>>>>>>>>>
> >>>>>>>>>>> Yee Man,
> >>>>>>>>>>>
> >>>>>>>>>>> I have the
> output in
> >> the below
> >>>> link:
> >>>>>>>>>>>
> >>>>>>>>>>> http://gist.github.com/167542
> >>>>>>>>>>>
> >>>>>>>>>>> There are
> similar
> >> problems
> >>>> popping up
> >>>>>> on 32- and
> >>>>>>>>> 64-bit
> >>>>>>>>>>> perl 5.10.0,
> Mac OS X
> >> 10.5.
> >>>>>> Haven't had time
> >>>>>>>>> to debug
> >>>>>>>>>>> it
> unfortunately.
> >>>>>>>>>>>
> >>>>>>>>>>> I think we
> should
> >> seriously
> >>>> consider
> >>>>>> spinning this
> >>>>>>>>> code off
> >>>>>>>>>>> into it's own
> >> distribution
> >>>> for
> >>>>>> CPAN. It's
> >>>>>>>>>>> unfortunately
> >> bit-rotting away
> >>>> in
> >>>>>>>>> bioperl-ext. If
> you
> >>>>>>>>>>> want to
> continue
> >> supporting it
> >>>> I can
> >>>>>> help set that
> >>>>>>>>> up.
> >>>>>>>>>>> chris
> >>>>>>>>>>>
> >>>>>>>>>>> On Aug 13,
> 2009, at
> >> 6:58 PM,
> >>>> Yee Man
> >>>>>> Chan wrote:
> >>>>>>>>>>>
> >>>>>>>>>>>> Hi
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >> So is
> >>>> this
> >>>>>> an HMM only
> >>>>>>>>> problem? Or does
> >>>>>>>>>>> it apply to
> other
> >> bioperl-ext
> >>>>>> modules?
> >>>>>>>>>>>>
> >> What
> >>>>>> exactly are the
> >>>>>>>>> compilation errors
> >>>>>>>>>>> for HMM? I
> believe my
> >>>> implementation
> >>>>>> is just a
> >>>>>>>>> simple one
> >>>>>>>>>>> based on
> Rabiner's
> >> paper.
> >>>>>>>>>>>> http://www.google.com/url?sa=t&source=web&ct=res&cd=1&url=http%3A%2F%2Fwww.cs.ubc.ca%2F
>
> >>>>>>>>>>>>
> ~murphyk%2FBayes
> >>>>>>>>>>>>
> %2Frabiner.pdf&ei=QqiESvClHNCfkQXbh8mWBw&rct=j&q=rabiner
>
> >>>>>>>>>>>>
> +hmm&usg=AFQjCNHeXLhTHmuKUXKKCHYSs58TxVGfZg
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >> I
> >>>> don't
> >>>>>> think I did
> >>>>>>>>> anything fancy that
> >>>>>>>>>>> makes it
> machine
> >> dependent or
> >>>> non-ANSI
> >>>>>> C.
> >>>>>>>>>>>> Yee Man
> >>>>>>>>>>>>
> >>>>>>>>>>>> --- On
> Thu,
> >> 8/13/09, Chris
> >>>> Fields
> >>>>>> <cjfields at illinois.edu>
> >>>>>>>>>>> wrote:
> >>>>>>>>>>>>> From:
> Chris
> >> Fields
> >>>> <cjfields at illinois.edu>
> >>>>>>>>>>>>>
> Subject: Re:
> >>>> [Bioperl-l]
> >>>>>> Problems with
> >>>>>>>>> Bioperl-ext
> >>>>>>>>>>> package on
> WinVista?
> >>>>>>>>>>>>> To:
> "Robert
> >> Buels"
> >>>> <rmb32 at cornell.edu>
> >>>>>>>>>>>>> Cc:
> "Jonny
> >> Dalzell"
> >>>> <jdalzell03 at qub.ac.uk>,
> >>>>>>>>>>> "BioPerl List"
> <Bioperl-l at lists.open-bio.org>,
> >>>>>>>>>>> "Yee Man Chan"
> <ymc at yahoo.com>
> >>>>>>>>>>>>> Date:
> >> Thursday, August
> >>>> 13,
> >>>>>> 2009, 3:18 PM
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> On Aug
> 13,
> >> 2009, at
> >>>> 4:37 PM,
> >>>>>> Robert Buels
> >>>>>>>>> wrote:
> >>>>>>>>>>>>>>
> Jonny
> >> Dalzell
> >>>> wrote:
> >>>>>>>>>>>>>>>
> Is it
> >>>> ridiculous of me
> >>>>>> to expect
> >>>>>>>>> ubuntu to
> >>>>>>>>>>> take
> >>>>>>>>>>>>> care
> of this
> >> for
> >>>> me? How
> >>>>>> do
> >>>>>>>>>>>>>>>
> I go
> >> about
> >>>> compiling
> >>>>>> the HMM?
> >>>>>>>>>>>>>>
> Yes.
> >> This is
> >>>> a very
> >>>>>> specialized
> >>>>>>>>> thing
> >>>>>>>>>>> that
> >>>>>>>>>>>>> you're
> doing,
> >> and
> >>>> Ubuntu does
> >>>>>> not have
> >>>>>>>>> the
> >>>>>>>>>>> resources to
> >>>>>>>>>>>>>
> package every
> >> single
> >>>> thing.
> >>>>>>>>>>>>>>
> >> Unfortunately, it
> >>>> looks
> >>>>>> like
> >>>>>>>>> bioperl-ext
> >>>>>>>>>>> package is
> >>>>>>>>>>>>> not
> >> installable under
> >>>> Ubuntu
> >>>>>> 9.04 anyway,
> >>>>>>>>> which is
> >>>>>>>>>>> what I'm
> >>>>>>>>>>>>>
> running.
> >> For
> >>>> others on
> >>>>>> this list,
> >>>>>>>>> if
> >>>>>>>>>>> somebody is
> >>>>>>>>>>>>>
> interested in
> >> doing
> >>>>>> maintaining it, I'd be
> >>>>>>>>> happy
> >>>>>>>>>>> to help out
> >>>>>>>>>>>>> by
> testing on
> >>>> Debian-based
> >>>>>> Linux
> >>>>>>>>> platforms.
> >>>>>>>>>>> We need to
> >>>>>>>>>>>>>
> clarify this
> >>>> package's
> >>>>>> maintenance status:
> >>>>>>>>> if
> >>>>>>>>>>> there is
> >>>>>>>>>>>>>
> nobody
> >> interested in
> >>>>>> maintaining it, I
> >>>>>>>>> would
> >>>>>>>>>>> recommend
> that
> >>>>>>>>>>>>>
> bioperl-ext be
> >> removed
> >>>> from
> >>>>>> distribution.
> >>>>>>>>>>> It's not in
> >>>>>>>>>>>>>
> anybody's
> >> interest to
> >>>> have
> >>>>>> unmaintained
> >>>>>>>>> software
> >>>>>>>>>>> out there
> >>>>>>>>>>>>>
> causing
> >> confusion.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> I have
> cc'd
> >> Yee Man
> >>>> Chan for
> >>>>>> this.
> >>>>>>>>> If there
> >>>>>>>>>>> isn't a
> >>>>>>>>>>>>>
> response or
> >> the
> >>>> message
> >>>>>> bounces, we do one
> >>>>>>>>> of two
> >>>>>>>>>>> things:
> >>>>>>>>>>>>> 1)
> consider
> >> it
> >>>> deprecated
> >>>>>> (probably
> >>>>>>>>> safest).
> >>>>>>>>>>>>> 2)
> spin it out
> >> into a
> >>>> separate
> >>>>>> module.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Just
> tried to
> >> comile
> >>>> it myself
> >>>>>> and am
> >>>>>>>>> getting
> >>>>>>>>>>> errors (using
> >>>>>>>>>>>>> 64bit
> perl
> >> 5.10), so I
> >>>> think,
> >>>>>> unless
> >>>>>>>>> someone wants
> >>>>>>>>>>> to take
> >>>>>>>>>>>>> this
> on,
> >> option #1 is
> >>>> best.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>> So
> Jonny,
> >> in
> >>>> short, I
> >>>>>> would say "do
> >>>>>>>>> not use
> >>>>>>>>>>>>>
> bioperl-ext".
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> In
> general,
> >> that's a
> >>>> safe
> >>>>>> bet. We're
> >>>>>>>>> moving
> >>>>>>>>>>> most of
> >>>>>>>>>>>>> our
> C/C++
> >> bindings to
> >>>> BioLib.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> Step
> >> back.
> >>>> What are
> >>>>>> you trying
> >>>>>>>>> to
> >>>>>>>>>>>>>
> accomplish?
> >>>> Chris
> >>>>>> already
> >>>>>>>>> recommended some
> >>>>>>>>>>> alternative
> >>>>>>>>>>>>>
> methods in his
> >> email
> >>>> of 8/11
> >>>>>> on this
> >>>>>>>>>>> subject.
> >> Perhaps
> >>>>>>>>>>>>> we can
> guide
> >> you to
> >>>> some
> >>>>>> software that is
> >>>>>>>>>>> actively
> >>>>>>>>>>>>>
> maintained and
> >> will
> >>>> meet your
> >>>>>> needs.
> >>>>>>>>>>>>>>
> Rob
> >>>>>>>>>>>>>
> Exactly.
> >> Lots of
> >>>> other
> >>>>>> (better
> >>>>>>>>> supported!)
> >>>>>>>>>>> options
> >>>>>>>>>>>>> out
> there.
> >>>> HMMER, SeqAn,
> >>>>>> and
> >>>>>>>>> others.
> >>>>>>>>>>>>> chris
> >>>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>
> >>>>
> >>
> __________________________________________________
> >>>>>>>>>> Do You Yahoo!?
> >>>>>>>>>> Tired of spam?
> >> Yahoo! Mail
> >>>> has the
> >>>>>> best spam
> >>>>>>>>> protection around
> >>>>>>>>>> http://mail.yahoo.com
> >>>>>>>>>
> >>>>>>
> >>>>
> >>
> <HMM.xs><typemap>_______________________________________________
> >>>>>>>>>> Bioperl-l mailing
> list
> >>>>>>>>>> Bioperl-l at lists.open-bio.org
> >>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>>>>
> >>>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> --Robert Buels
> >>>>>>> Bioinformatics Analyst, Sol
> Genomics
> >> Network
> >>>>>>> Boyce Thompson Institute for
> Plant
> >> Research
> >>>>>>> Tower Rd
> >>>>>>> Ithaca, NY 14853
> >>>>>>> Tel: 503-889-8539
> >>>>>>> rmb32 at cornell.edu
> >>>>>>> http://www.sgn.cornell.edu
> >>>>>>
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>
> >>
> >
> >
> >
>
>
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