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

[Oliver Homann]

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