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Alias (5735)

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Wednesday October 21, 2009
07:25 PM

Testing Needed: Strawberry October 2009 BioPerl support

[ #39783 ]

(This is a copy of an email to the BioPerl mailing list)

Dear BioPeople

Since we added a "Live Support Chat" link to the frontpage of the Strawberry Perl website ( http://strawberryperl.com/ ) we've noticed that one of the main types of visitors that we see in the IRC channel ( #win32 on irc.perl.org ) is biologists trying to install various
things.

As a result, for the October 2009 release of Strawberry Perl, we've prioritised adding support for CPAN-installation of BioPerl.

Changes include a major improvement to crypto support which provides OpenSSL and support for https:// URLs, we now ship Postgres and MySQL DBI drivers in the default installation, and we have added Berkely DB support (which previously prevented us meeting the dependencies for the BioPerl distribution).

I'm happy to report that we now believe we are in a position to officially support the installation of BioPerl on Strawberry Perl.

Prior to the official release next week, we would appreciate testing from the BioPerl community.

Release candidate installers for the October release are available at the following URLs

http://strawberryperl.com/download/strawberry-perl-5.10.1.0.msi

http://strawberryperl.com/download/strawberry-perl-5.8.9.3.msi

Once installed, run Start -> Program Files -> Strawberry Perl -> CPAN Client

From the CPAN client command line, run "install BioPerl" and select
the default options.

Once installed, you should be able to do anything you do normally with a BioPerl install.

Assuming all goes well in this release, for the next release January 2010 we plan to also produce a "Strawberry Perl Professional" distribution that will bundle BioPerl as part of the default installation, as well as a Perl IDE and other useful packages.

Success or failure of the release candidate can be reported either here [the BioPerl list] or to #win32 on irc.perl.org.

Adam K

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  • It's a little touchy, but it does work using perl 5.10.1 (haven't tried 5.8.9 yet). Getting some warnings about missing DLLs during the test phase, primarily expat or libxml-related (not sure why).

    Also getting tons of 'Subroutine X redefined' warnings, which are pretty harmless but it would be nice to track down why they're popping up. These also occur when testing BioPerl with ActivePerl.

    • I think I know why the "missing DLL's" message pops up... Sometimes the Strawberry installer needs a log-out/log-back-in (a reboot works just as well) to register the path entries it adds to the environment - which it needs to find the dll's. I don't know how to determine when it happens, I just know that it happens.

      I noticed the "Subroutine redefined" errors, too. :)

      --
      The new Strawberry Perl for Windows has been released! Check http://strawberryperl.com for it.
      • I think I know why the "missing DLL's" message pops up... Sometimes the Strawberry installer needs a log-out/log-back-in (a reboot works just as well) to register the path entries it adds to the environment - which it needs to find the dll's. I don't know how to determine when it happens, I just know that it happens.

        Okay, good. May be worth a retry then.

        I noticed the "Subroutine redefined" errors, too. :)

        This also pops up via one of the CPAN Tester reports [perl.org]

  • I think the links should have an extra dash in "strawberry-perl":

    http://strawberryperl.com/download/strawberry-perl-5.10.1.0.msi [strawberryperl.com]

    http://strawberryperl.com/download/strawberry-perl-5.8.9.3.msi [strawberryperl.com]

    • The links were corrected, but unfortunately use.perl always grabs the first version of the article, before the corrections.