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Re: Problem Installing BioPerl

by Itatsumaki (Friar)
on Apr 11, 2004 at 21:35 UTC ( #344289=note: print w/replies, xml ) Need Help??

in reply to Problem Installing BioPerl

As noted above, you didn't give much detail so it's hard to give good advice. Three basic things come to mind. One: you can't generally install just one part of BioPerl in isolation -- you have to install the entire suite because of all the inter-dependencies. In fact, when you say the "module for GUI" I'm not too sure what you're thinking of? Bio::Graphics maybe?

Two, what exactly are the tests that are failing? The identity of the failed tests (and what module they are against) will help you decide if this is something to worry about or not.

Three, if you are having problems, try asking at the bioperl help group ( If this is a verifiable bug I'm sure they'd want to fix the problems.


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Re: ^2 Problem Installing BioPerl
by Sameet (Beadle) on Apr 11, 2004 at 07:15 UTC
    I have tried using installing BioPerl using CPAN. But it somehow passes 99% of the tests, but ultimately the result i get it a message "cannot force install"

    Can it be helped. Following is the error message that i received

    Running make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/seqcanvas.... Can't locate in @INC (@INC contains: /root/.cpan/build/bioperl-gui/blib/lib /root/.cpan/build/bioperl-gui/blib/arch /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 . /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0 .) at t/seqcanvas.t line 3. BEGIN failed--compilation aborted at t/seqcanvas.t line 3. t/seqcanvas....dubious Test returned status 2 (wstat 512, 0x200) FAILED--1 test script could be run, alas--no output ever seen make: *** [test_dynamic] Error 2 /usr/bin/make test -- NOT OK Running make install make test had returned bad status, won't install without force

    janitored by ybiC: Re-parented into related thread, balanced <code> tags around longish error message, minor format tweaks for legibility

      For future reference, if you've already asked the question, please update or reply to your previous question. (You might not have seen it because it wasn't approved yet, but visit Sameet and click on your posting history and you can find it.)

      About this question, if it passed 99% of the tests, then it failed 1% of the tests. That means that it does not work as the author intended and it will be buggy for you. Therefore you should track down the error (eg run the test suite, figure out what is failing, and contact the author). Hopefully it can get fixed in short order. (You might be able to figure the test out and come up with a fix yourself. Authors really enjoy getting a bug report and patch together in the same email. Been there, done that, and it is a pleasant surprise.)

      Should you wish to have a known buggy install of partially working software, you can always force install Foo using CPAN to force it to install despite errors.

      Again, I don't recommend doing that though.

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