[Bioperl-l] Installation error, please help!

[Brian Osborne]

Darson,

I don't think missing GD, AcePerl, or Graph::Directed will affect a query of
Unigene, I don't think that's the cause of your problem.

In order to diagnose why your scripts fails you will have to show us the
code itself and the exact error message that you see when you try to run the
script.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of darson
Sent: Thursday, March 13, 2003 8:16 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Installation error, please help!

Hello,
My OS: Linux Redhat 7.3
       Perl:ver. 5.6.1
I downloaded the Bioperl-1.2 from website, unzip and tar -xvf. Then I
proceed with "perl Makefile.PL"
output result below:
Generated sub tests. go make show_tests to see available subtests
Do you want to run the BioDBGFF tests (requires a mysql database) y/n [n] n

External Module Ace, Aceperl,
is not installed on this computer.
  The Bio::DB::Ace in Bioperl needs it for access of ACeDB database

External Module GD, Graphical Drawing Toolkit,
is not installed on this computer.
  The Bio::Graphics in Bioperl needs it for Rendering Sequences and Features

External Module Graph::Directed, Generic Graph data stucture and algorithms,
is not installed on this computer.
  The Bio::Ontology::SimpleOntologyEngine in Bioperl needs it for Ontology
Engine implementation for
the GO parser.....

but I've tried to install the three modules above and all failed, are they
vital to most other modules?
When I run "make test", the result presents below:
t/XXXXX......ok(many test seemed ok)
.....
t/Variation_IO......dubious
Test returned status 0 (wstat 11, 0xb)
DIED. FAILED tests 13-25
Failed 13/25 tests, 48.00% okay
t/XXXXX.......ok
.........
Failed Test      Status Wstat Total Fail  Failed  List of Failed
----------------------------------------------------------------------------
----
t/Variation_IO.t    0    11    25   13  52.00%  13-25
4 subtests skipped.
Failed 1/134 test scripts, 99.25% okay. 13/5938 subtests failed, 99.78%
okay.
make: *** [test_dynamic] Error 29

Finally it reports a failure of installation, anyway I tried to run "make
install".
It reports:
Writing /usr/lib/perl5/site_perl/5.6.1/i386-linux/auto/Bio/.packlist
Appending installation info to /usr/lib/perl5/5.6.1/i386-linux/perllocal.pod

It seems that it is successful of installation. But when I tried to run some
perl script to work, it always reports that "Can't locate XXX::XXX(module
name) from @INC, The @INC includes ......"  something like that.  Therefore,
my question is : 1. Whether the failed test modules influence other modules?
2. I am struggleing to querr the Unigene ID from giving the ACC (via the
Hs.data file--human unigene data file from NCBI FTP site, any suggestions or
guides would be appreciated? Thanks
           Best regards,

Darson  2003/03/13


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