[Bioperl-l] Installing bioperl 1.2 with cygwin's perl 5.6.1 and fixing the fa iled Index.t tests

[Nash, John]

More on cygwin and bioperl.

1.  Upgrading MakeMaker allows bioperl 1.2 to install properly under
cygwin's perl 5.6.1.

As reported yesterday, I managed to get bioperl 1.2 to install properly
under cygwin using perl 5.8. Unfortunately, I am stuck with perl 5.6.1
because I need Tk, which is not yet fully debugged for cygwin's perl 5.8.
After verifying that bioperl 1.2 worked for perl 5.8, I reinstalled perl
5.6.1.  I upgraded the ExtUtils::MakeMaker module (to 6.05) - it takes more
than a CPAN upgrade to fix this because it's installed in
/lib/perl5/5.6.1/ExtUtils and /lib/perl5/site_perl/5.6.1/ExtUtils.  CPAN
upgrades one copy, but
perl doesn't see the changes, so I removed the latter ExtUtils subdirectory.
One of these days, I'll get the hang of the lib/perl5/5.6.1 vs
/lib/perl5/site_perl/5.6.1 versions of the same modules.

2.  I found out how to fix the failed Index.t tests with the cygwin
distribution - it wasn't my idea, I just did some dedicated surfing
(please refer to:
http://sources.redhat.com/ml/cygwin/1999-02/msg00918.html).

Thus educated, I made the following changes to
/lib/perl5/5.6.1/cygwin_multi/Cwd.pm, but note there is also a Cwd.pm
in /lib/perl5/5.6.1/, which I rm'd:

$ diff /lib/perl5/5.6.1/cygwin-multi/Cwd.pm
/lib/perl5/5.6.1/cygwin-multi/Cwd.pm.orig

450,454c450,453
<         *cwd            = \&_backtick_pwd;
<         *getcwd               = \&_backtick_pwd;
<         *fastgetcwd   = \&_backtick_pwd;
<         *fastcwd      = \&_backtick_pwd;
<         *abs_path     = \&_backtick_pwd;
---
>         *getcwd       = \&cwd;
>         *fastgetcwd   = \&cwd;
>         *fastcwd      = \&cwd;
>         *abs_path     = \&fast_abs_path;

And here are the new test results:

$ perl t/Index.t
1..12
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12 # Bio::DB::FileCache not loaded because one or more of Storable,
DB_File or File::Temp not installed

(File::Temp is installed). I'll poke at SearchIO.t when I can.  Thanks for
the opportunity to learn.

cheers,
John

---
John Nash, PhD, Research Officer, Pathogen Genomics Group, 
Institute for Biological Sciences, National Research Council of Canada
Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
Phone: (613) 990-0990, Fax: (613) 952-9092
Please note:  Due to new Government of Canada standardized Internet "Look
and Feel" policies, my email address is now: john.nash@nrc-cnrc.gc.ca. 

---
John Nash, PhD, Research Officer, Pathogen Genomics Group, 
Institute for Biological Sciences, National Research Council of Canada
Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
Phone: (613) 990-0990, Fax: (613) 952-9092
Please note:  Due to new Government of Canada standardized Internet "Look
and Feel" policies, my email address is now: john.nash@nrc-cnrc.gc.ca.