[Bioperl-l] Windows Testing

Fri, 20 Dec 2002 15:42:02 -0500 (EST)

On Fri, 20 Dec 2002, Paul Boutros wrote:

> I looked into the point made by Pierre Far about the current Windows ppm
> install routine not working with PERL 5.8.0.  I updated the text below to
> take that into account.
>

Note that the way it was setup works for perl 5.6.1 and PPM - the only
windows setup I had access to.  So I'm not sure the suggestion about the
adding the architecture is exactly right.  It would require adding a
second entry to the ppm file I believe.  I can't really help test this
stuff so I've no idea what is the right way with different mixing and
matching of windows and active state versions.

> Also, on a more general note, am I mistaken in noting that the ppm install
> of Bioperl doesn't include these directories?
> /test
> /doc
> /examples
> /models
> /scripts
> /t

Exactly, if you want them, you get to things the old-fashioned way and
download the zipfile.  Same thing happens when you install pkg with CPAN.

>
> =========================================================================
> BioPerl on Windows
> ==================
>
> 1.0 Installation
> 1.1 PERL on Windows
> 1.2 External Modules
> 1.3 Installing Bioperl
> 1.3.1 ActiveState for PERL 5.6.1
> 1.3.2 ActiveState for PERL 5.8.0
> 1.3.3 Download Archive
> 1.3.4 If All Else Fails...
> 2.0 Windows Specific Behaviour
> 2.1 Subroutine <name> redefined at location <location> warnings
> 2.2 Consed
>
> 1.0 Installation
> ================
>
> Windows installation of BioPerl requires three steps:
> i)   installation of PERL
> ii)  installation of external modules
> iii) installation of BioPerl itself
>
> I'll quickly summarize my findings on each of those below.
>
> 1.1 PERL on Windows
> ===================
>
> There are lots of ways of installing PERL on a Windows machine.  Probably
> the easiest and most common is to get the most recent build from
> ActiveState.  You can also build PERL yourself (which requires a C
> compiler) or download one of the other binary distributions.  Regardless
> of which way you choose to go, if have a functioning PERL build higher
> than version 5 or so you can procede to the next step.
>
> The PERL source for building it yourself is available from CPAN
> (http://www.cpan.org), as are a few binary distributions.
>
> ActiveState is a software company (http://www.activestate.com) that
> provides free builds of PERL for windows users.  They are currently
> (December 2002) providing a very stable build of PERL 5.6.1 while a beta
> version of PERL 5.8.0 is also available.  I suggest that you stick to the
> production version of 5.6.1 because: a) it is easier to install the
> external modules for 5.6.1 and b) I find 5.8.0 beta a bit unstable at the
> moment.
>
> 1.2 External Modules
> ====================
>
> The installation documents supply a very comprehensive list of external
> dependencies (i.e. see http://www.bioperl.org/Core/external.shtml).  You
> do not need to install external modules for the parts of BioPerl that you
> do not intend using.  That being said, if you don't know what to install,
> try to install all externals.
>
> If you are using ActiveState, I recommend first attempting to download
> your external modules via the ActiveState Perl Package Manager (PPM).  To
> use it, just go to a command-prompt and type ppm while connected to the
> internet.  The software will connect to a repository of available modules
> that you can install.  For example, to install IO::String you would type:
> "install IO::String"
>
> If you are using ActiveState 5.8.0, you will find that some external
> modules are not yet available via ppm.  In that case you will have to
> download them directly from cpan (http://www.cpan.org) and follow the
> specific build procedures for each module.  This is one major reason for
> avoiding the ActiveState 5.8.0 beta version.
>
> 1.3 Installing BioPerl
> ======================
>
> You have two main choices for installing BioPerl.  If you are using
> ActiveState you can use ppm to install with the commands:
>
> 1.3.1 ActiveState For PERL 5.6.1
> ================================
>
> PPM> set repository bioperl http://bioperl.org/DIST/
> PPM> search bioperl             (shows available bioperl versions)
> PPM> install bioperl		(will install the default version)
>
> 1.3.2 ActiveState For PERL 5.8.0
> ================================
>
> ppm> repository add bioperl http://bioperl.org/DIST
> ppm> search bioperl		(shows available bioperl versions)
>
> This last command returns a numbered list of the available bioperl
> versions.
> Select the number of the version you wish to install and type:
>
> ppm> install <number>
>
> 1.3.3 Download Archive
> ======================
>
> You can download BioPerl as a compressed archive from:
> http://www.bioperl.org/Core/Latest/index.shtml
> This archive can be uncompressed with WinZip (or most other Zip
> utilities).
>
> Don't worry if you get a warning saying something like "Archive contains
> only one file!  Extract and decompress?".  This is just a variation in how
> UNIX and Windows software likes to compress files.  Choose yes, and all
> will be well.
>
> You will need access to a make utility to utilize this approach.
>
> 1.3.4. If All Else Fails....
> ============================
>
> The BioPerl directory tree should be extracted intact (i.e. ensure "Use
> Folder Names" is selected in WinZip) and must be placed so that it is in
> your @INC path.  It may be easier to extract the directory tree to another
> location and moving the \Bio directory to \perl\site\lib
>
> This approach will not install compiled versions of any modules in the
> package, and isn't recommended.
>
> 1.4 Testing Installation
> ========================
>
> It is possible to test your BioPerl installation on windows with "make
> test", although this requires having a copy of make utility available on
> your system.  If you used ppm to install, this step will not be possible
> as activestate doesn't install this information.
>
> 2.0 Windows-Specific Behaviour
> ==============================
>
> Items of windows-specific behaviour are listed below.
>
> 2.1 Subroutine <name> redefined at <location> Warnings
> ======================================================
>
> BioPerl does not get along particularly nicely with the PERL -w flag on
> windows systems.  The sample script below shows what happens with many
> scripts:
>
> test.pl
> ###############################################
> use Bio::ClusterIO;
> my $stream = Bio::ClusterIO->new(
> 		'-file'		=> $ARGV[0],
> 		'-format'	=> 'UniGene',
> 		);
> ###############################################
>
> c:\> perl -w test.pl Hs.Data
> Subroutine new redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line
> 222.
> Subroutine unigene_id redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm
> line 284.
> Subroutine title redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line
> 306.
> Subroutine gene redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line
> 327.
> Subroutine cytoband redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm
> line 345.
> Subroutine mgi redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm line
> 362.
> Subroutine locuslink redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm
> line 390.
> Subroutine gnm_terminus redefined at
> C:/Perl/site/lib/Bio\Cluster\UniGene.pm line 420.
> Subroutine scount redefined at C:/Perl/site/lib/Bio\Cluster\UniGene.pm
> line 436.
> <and many more like this>
>
> These warnings messages are basically the result of the windows version of
> PERL being more cautious than other versions.  These are only warnings
> messages, and can safely be ignored.  For production code, you can remove
> the -w flag and you will not receive these warnings.
>
> 2.2 Consed
> ==========
> The consed module cannot be run under Windows.
> =========================================================================
>
>
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu