[Bioperl-l] Trouble install Bioperl-Ext-1.4 & dpAlign

[Aaron J. Mackey]

The resolution was that Yee had altered the API in Bio::Tools::dpAlign 
without regard to the expected arguments in bioperl-ext-1.4

You'll need to grab a CVS version of Bio/Tools/dpAlign.pm, to replace 
the one from bioperl 1.4

-Aaron

On Aug 4, 2004, at 1:58 AM, Michal Galdzicki wrote:

> I'm having the same problem discussed in June by jany (janynannan at
> yahoo.co.uk) and Aaron J Mackey.
> (http://bioperl.org/pipermail/bioperl-l/2004-June/016154.html,
> http://bioperl.org/pipermail/bioperl-l/2004-June/016153.html)
>
> Could anyone point me to the solution.
>
> During an install bioperl-ext-1.4 in Redhat9 with dpAlign.
> The following error comes up on 'make test' (and later when skipped in
> use dpAlign):
>
> #########################################################
> PERL_DL_NONLAZY=1 /usr/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl
> 1..9
> # Running under perl version 5.008 for linux
> # Current time local: Wed Aug  4 01:15:51 2004
> # Current time GMT:   Wed Aug  4 05:15:51 2004
> # Using Test.pm version 1.23
> Not enough arguments for Bio::Ext::Align::Align_Protein_Sequences at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/dpAlign.pm line 300, near
> "'blosum62')"
> Not enough arguments for Bio::Ext::Align::Align_Protein_Sequences at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/dpAlign.pm line 355, near
> "'blosum62')"
> Compilation failed in require at test.pl line 15.
> BEGIN failed--compilation aborted at test.pl line 15.
> make: *** [test_dynamic] Error 255
>
> ###########################################################
>
> Thank you,
> Michal Galdzicki
>
> ps. sorry if you received this twice
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--
Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania       email:  amackey at pcbi.upenn.edu
415 S. University Avenue         office: 215-898-1205
Philadelphia, PA  19104-6017     fax:    215-746-6697