[Bioperl-guts-l] help with installing bioperl-ext-1.4

srikanth patury s_patury at hotmail.com
Wed Jun 2 13:37:03 EDT 2004


Hi all,

I think i successfully installed the bioperl-core, inline::makemaker, io_lib 
libraries (found answers to all my issues in previous emails on this 
list...) but now i have run into a new issue and i am lost completely....

am trying to install bioperl-ext-1.4 on mac os X


1. perl Makefile.PL LIB=/Users/pats/lib/bioperl            - works fine 
without errors..

2. make        - also runs fine without any errors....

3. make test - fails with the following errors...
sorry for the long email.. am copying the complete 'make test output'
---------------------------------------------------------------------------------------------------------------------
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" 
"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/basic....ok
All tests successful.
Files=1, Tests=1,  0 wallclock secs ( 0.04 cusr +  0.00 csys =  0.04 CPU)
PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" 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 /usr/bin/perl "-MExtUtils::Command::MM" "-e" 
"test_harness(0, '../blib/lib', '../blib/arch')" test.pl
test....dyld: /usr/bin/perl Undefined symbols:
/Users/pats/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle 
undefined reference to _deflate expected to be defined in a dynamic image
/Users/pats/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle 
undefined reference to _deflateEnd expected to be defined in a dynamic image
/Users/pats/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle 
undefined reference to _deflateInit2_ expected to be defined in a dynamic 
image
/Users/pats/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle 
undefined reference to _gzclose expected to be defined in a dynamic image
/Users/pats/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle 
undefined reference to _gzdopen expected to be defined in a dynamic image
/Users/pats/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundlea 
dynamic image
/Users/pats/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle 
undefined reference to _gzread expected to be defined in a dynamic image
/Users/pats/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle 
undefined reference to _gzrewind expected to be defined in a dynamic image
/Users/pats/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle 
undefined reference to _gzwrite expected to be defined in a dynamic image
/Users/pats/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle 
undefined reference to _inflate expected to be defined in a dynamic image
/Users/pats/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle 
undefined reference to _inflateEnd expected to be defined in a dynamic image
/Users/pats/bioperl-ext-1.4/Bio/SeqIO/staden/../blib/arch/auto/Bio/SeqIO/staden/read/read.bundle 
undefined reference to _inflateInit_ expected to be defined in a dynamic 
image
test....dubious
        Test returned status 0 (wstat 5, 0x5)
DIED. FAILED tests 1-94
        Failed 94/94 tests, 0.00% okay
Failed Test Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
test.pl        0     5    94  188 200.00%  1-94
Failed 1/1 test scripts, 0.00% okay. 94/94 subtests failed, 0.00% okay.
make[1]: *** [test_dynamic] Error 2
make: *** [test] Error 2

---------------------------------------------------------------------------------------------------------------------------------

4. was curious and went ahead and ran 'make install'
---------------------
Installing /Users/pats/lib/bioperl/Bio/SeqIO/staden/Makefile.old
Installing /Users/pats/lib/bioperl/Bio/SeqIO/staden/Makefile.PL
Installing /Users/pats/lib/bioperl/Bio/SeqIO/staden/read.pm
Installing /Users/pats/lib/bioperl/Bio/SeqIO/staden/test.pl
Installing /man/man3/Bio::SeqIO::staden::read.3pm
Writing 
/Users/pats/lib/bioperl/darwin-thread-multi-2level/auto/Bio/.packlist
Appending installation info to 
/Users/pats/lib/bioperl/darwin-thread-multi-2level/perllocal.pod

-------------------------------

looked like it worked but when i tried to run a sample script..

i get the following error....
------------------------------
The extension 'Bio::SeqIO::staden::read' is not properly installed in path:
  '/Users/pats/lib/bioperl'

If this is a CPAN/distributed module, you may need to reinstall it on your
system.

To allow Inline to compile the module in a temporary cache, simply remove 
the
Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module.

at test.pl line 0
INIT failed--call queue aborted, <DATA> line 1.

------------------------------

any ideas please....

srikanth

_________________________________________________________________
Looking to buy a house? Get informed with the Home Buying Guide from MSN 
House & Home. http://coldwellbanker.msn.com/



More information about the Bioperl-guts-l mailing list