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

Wed Apr 27 16:44:43 EDT 2005

Hi Oliver,

My advice to you, as someone who has been working and developing on FC3
for several months is to not use it.  I've had many problems with it,
some related to SELinux (until I gave up on it and turned it off) and
other things a well (including apache and mod_perl).  My suggestion
would be to use FC2, especially since there is an rpm for bioperl 1.5
built by Allen Day available on biopackages.net.

Scott

On Wed, 2005-04-27 at 13:33 -0700, 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 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.org
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory