[Bioperl-l] Having no luck installing bioperl in Fedora Core 3 with Perl 5.8.5

[Stefan Kirov]

Oliver,
I have seen the same error for XML::DOM and I remember I fixed it by 
updating another package, but I don't remember which one. Try to install 
it through the usual .configure/make stuff. You will get a warning 
telling you which module may need an update.  As for GD see this post 
http://www.issociate.de/board/post/153088/problem_installing_GD-2.19.html.
Hope it helps,
Stefan


Oliver Homann wrote:

>Hi,
>
>We just recently purchased a new workstation, and I've been trying with absolutely no success to install bioperl.  I've followed the instructions at bioperl.org, attempting several techniques (installing Bundle::BioPerl or bioperl-1.4.tar.gz via CPAN or installing the latter manually), and continue to encounter a litany of errors.  I've pasted a slightly truncated version of the output from my latest attempt to install Bundle::BioPerl via CPAN... I'm hoping someone can offer me some insight into the nature of my problem.
>
>Thanks!
>Oliver
>
>#####STARTING CPAN GIVES ME THIS ERROR MESSAGE:
>
>
># perl -MCPAN -e shell
>Undefined value assigned to typeglob at (eval 17) line 15, <RC> line 11.
>Warning [/etc/inputrc line 11]:
>  Invalid variable `mark-symlinked-directories'
>
>
>#####TRYING TO INSTALL THE BUNDLE GIVES ME THIS:
>
>
>cpan> install "Bundle::BioPerl"
>
>
>Running install for module XML::DOM
>Running make for T/TJ/TJMATHER/XML-DOM-1.43.tar.gz
>  Is already unwrapped into directory /root/.cpan/build/XML-DOM-1.43
>  Has already been processed within this session
>Running make test
>
>
>PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
>"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
>
>
>t/dom_jp_attr.........FAILED tests 3, 9, 12, 14, 19, 22
>        Failed 6/23 tests, 73.91% okay
>t/dom_jp_cdata........FAILED test 3
>        Failed 1/3 tests, 66.67% okay
>t/dom_jp_example......ok
>t/dom_jp_minus........FAILED test 2
>        Failed 1/2 tests, 50.00% okay
>t/dom_jp_modify.......FAILED test 16
>        Failed 1/16 tests, 93.75% okay
>t/dom_jp_print........FAILED tests 2-3
>        Failed 2/3 tests, 33.33% okay
>
>
>Failed Test       Stat Wstat Total Fail  Failed  List of Failed
>t/dom_jp_attr.t                 23    6  26.09%  3 9 12 14 19 22
>t/dom_jp_cdata.t                 3    1  33.33%  3
>t/dom_jp_minus.t                 2    1  50.00%  2
>t/dom_jp_modify.t               16    1   6.25%  16
>t/dom_jp_print.t                 3    2  66.67%  2-3
>Failed 5/21 test scripts, 76.19% okay. 11/129 subtests failed, 91.47% okay.
>
>
>make: *** [test_dynamic] Error 255
>  /usr/bin/make test -- NOT OK
>Running make install
>  make test had returned bad status, won't install without force
>
>
>Running install for module GD
>Running make for L/LD/LDS/GD-2.19.tar.gz
>  Is already unwrapped into directory /root/.cpan/build/GD-2.19
>  Has already been processed within this session
>Running make test
>
>
>PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
>"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
>t/GD..........Can't load './blib/arch/auto/GD/GD.so' for module GD:
>./blib/arch/auto/GD/GD.so: undefined symbol: gdImageGifAnimAddPtr at
>/usr/lib/perl5/5.8.5/i386-linux-thread-multi/DynaLoader.pm line 230.
> at t/GD.t line 13
>Compilation failed in require at t/GD.t line 13.
>BEGIN failed--compilation aborted at t/GD.t line 13.
>t/GD..........dubious
>        Test returned status 255 (wstat 65280, 0xff00)
>DIED. FAILED tests 1-10
>        Failed 10/10 tests, 0.00% okay
>t/Polyline....Can't load
>'/root/.cpan/build/GD-2.19/blib/arch/auto/GD/GD.so' for module GD:
>/root/.cpan/build/GD-2.19/blib/arch/auto/GD/GD.so: undefined symbol:
>gdImageGifAnimAddPtr at
>/usr/lib/perl5/5.8.5/i386-linux-thread-multi/DynaLoader.pm line 230.
> at /root/.cpan/build/GD-2.19/blib/lib/GD/Polyline.pm line 45
>Compilation failed in require at
>/root/.cpan/build/GD-2.19/blib/lib/GD/Polyline.pm line 45.
>BEGIN failed--compilation aborted at
>/root/.cpan/build/GD-2.19/blib/lib/GD/Polyline.pm line 45.
>Compilation failed in require at t/Polyline.t line 10.
>BEGIN failed--compilation aborted at t/Polyline.t line 10.
>t/Polyline....dubious
>        Test returned status 255 (wstat 65280, 0xff00)
>DIED. FAILED test 1
>        Failed 1/1 tests, 0.00% okay
>
>
>Failed Test  Stat Wstat Total Fail  Failed  List of Failed
>--------------------------------------------------------------------------
>-----t/GD.t        255 65280    10   19 190.00%  1-10
>t/Polyline.t  255 65280     1    2 200.00%  1
>Failed 2/2 test scripts, 0.00% okay. 11/11 subtests failed, 0.00% okay.
>
>
>make: *** [test_dynamic] Error 255
>  /usr/bin/make test -- NOT OK
>Running make install
>  make test had returned bad status, won't install without force
>
>
>Bundle summary: The following items in bundle Bundle::BioPerl had
>installation problems:
>  XML::DOM GD 
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>  
>

-- 
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
USA
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fax +865-576-5332
e-mail: skirov at utk.edu
sao at ornl.gov

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