[Bioperl-l] Problems with Bioperl-ext package on WinVista?
Chris Fields
cjfields at illinois.edu
Sun Aug 16 05:38:46 UTC 2009
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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