[Bioperl-l] problem with bioperl-ext

[Joel Martin]

You should be using the latest from svn, 1.4 is very old and 1.5.1 on 
the bioperl site still has troubles.
but svn co svn://code.open-bio.org/bioperl/bioperl-ext/trunk bioperl-ext
is timing out for me, perhaps it's down?  I have a version that 
eliminates a few compiler warnings.
if you want it.  It's due to be replaced with BioLib, but I'm not aware 
that it's happened yet.

Joel

bioperl list is giving me trouble, maybe it works from this address.
 
Tom Keller wrote:
> Been struggling to get the bioperl-ext modules to install. I've got the staden libraries:
> $ ll /usr/local/lib/ | grep read
> -rwxr-xr-x   1 root  wheel   265K Apr  9 11:19 libstaden-read.1.1.0.dylib
> lrwxr-xr-x   1 root  wheel    26B Apr  9 11:19 libstaden-read.1.dylib -> libstaden-read.1.1.0.dylib
> -rw-r--r--   1 root  wheel   810K Apr  9 11:19 libstaden-read.a
> lrwxr-xr-x   1 root  wheel    26B Apr  9 11:19 libstaden-read.dylib -> libstaden-read.1.1.0.dylib
> -rwxr-xr-x   1 root  wheel   886B Apr  9 11:19 libstaden-read.la
>
> Here are the test results:
> $ sudo make test
> PERL_DL_NONLAZY=1 /opt/local/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/basic.t .. ok
> All tests successful.
> Files=1, Tests=1,  0 wallclock secs ( 0.01 usr +  0.01 sys =  0.02 CPU)
> Result: PASS
> PERL_DL_NONLAZY=1 /opt/local/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl<http://test.pl>
> 1..2
> ok 1
>
> 2..2
> Testing bp_sw with a protein alignment...
>
> ProteinSW Matrix calculation: [      0] Cells  0%
> one         1        WLGQRNLVSSTGGNLLNVWLKDW
>                      W+G RN+V     NLLNVW +DW
> two         1        WMGNRNVV-----NLLNVWFRDW
>
>
> ok 2
> PERL_DL_NONLAZY=1 /opt/local/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, '../blib/lib', '../blib/arch')" test.pl<http://test.pl>
> test.pl<http://test.pl> .. Had problems bootstrapping Inline module 'Bio::SeqIO::staden::read'
>
> Can't load '/Users/kellert/Downloads/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle' for module Bio::SeqIO::staden::read: dlopen(/Users/kellert/Downloads/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle, 2): Symbol not found: _fread_reading
>   Referenced from: /Users/kellert/Downloads/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle
>   Expected in: flat namespace
>  in /Users/kellert/Downloads/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle at /System/Library/Perl/5.10.0/darwin-thread-multi-2level/DynaLoader.pm line 207, <DATA> line 1.
>  at /Library/Perl/5.10.0/Inline.pm line 527
>
>
>  at test.pl<http://test.pl> line 0
> INIT failed--call queue aborted, <DATA> line 1.
> test.pl<http://test.pl> .. Dubious, test returned 2 (wstat 512, 0x200)
> Failed 94/94 subtests
>
> Test Summary Report
> -------------------
> test.pl<http://test.pl> (Wstat: 512 Tests: 0 Failed: 0)
>   Non-zero exit status: 2
>   Parse errors: Bad plan.  You planned 94 tests but ran 0.
> Files=1, Tests=0,  0 wallclock secs ( 0.01 usr  0.01 sys +  0.09 cusr  0.02 csys =  0.13 CPU)
> Result: FAIL
> Failed 1/1 test programs. 0/0 subtests failed.
> make[1]: *** [test_dynamic] Error 2
> make: *** [subdirs-test] Error 2
>
>
> I'm running OS X 10.6.3, the rest of Bioperl is 1.6.
> Suggestions greatly appreciated.
>
> Tom
> kellert at ohsu.edu<mailto:kellert at ohsu.edu>
> 503-494-2442
>
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