Bioperl: Problems installing v0.6 pre2

[Kutbuddin Doctor]

Hi, 

I am having some trouble getting Bio.perl modules running in the new
version.

My main problem is that the "new" method is not defined when I try to
do things using DB::GenBank, DB::GenPept, and even Bio::Seq .

Perhaps (likely!) it goes back to some problems I had during installation. 
The 'perl Makefile.PL' ran fine, albeit, I did not have AceDB (I don't use
it). The 'make' also did not complain.

However, in the 'make test':
-> the make stalls (virtually no cpu usage) during the test of blast.
(it seems from the errors that $GNU_PATH was not being detected so that
gunzip was not functioning).
So, I changed the value of $GNU_PATH to where gunzip was. Then did make
again. It seems to do the right thing (no changes except in
Bio/Root/Utilities.pm)

-> again it "stalls" leaving a process as "sleep"ing control-C => gives
the following message:  
-------------------- EXCEPTION -------------------- 
MSG: Failed to gunzip/uncompress file t/blast.report.gz: No such file or
directory 
NOTE: Confirm current $GNU_PATH: /usr/local/bin/ 
TECH: Edit $GNU_PATH in Bio::Root::Utilities.pm if necessary.  
CONTEXT: Error in object
Bio::Root::Utilities "Static Utilities object" SCRIPT: t/Blast.t STACK: 
Bio::Root::Utilities::uncompress(501) 
Bio::Root::IOManager::uncompress_file(989) 
Bio::Root::Object::uncompress_file(1978) main::t/Blast.t(89)
---------------------------------------------------

I manually gunzip the file, edited out the compress/uncompress lines in
the Blast.t file and ran 'make test' again.

this results in the following.. (pls excuse the format problems)

PERL_DL_NONLAZY=1 /usr/bin/perl -I./blib/arch -I./blib/lib
-I/usr/local/lib/perl5/sun4-solaris/5.00404 -I/usr/local/lib/perl5 -e 'use
Test::Harness qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
t/Annotation........ok 
t/Blast.............FAILED tests 24-28
        Failed 5/29 tests, 82.76% okay 
t/CodonTable........ok
t/DB................Warning: Couldn't connect to Genbank with
          Bio::DB::GenBank.pm! 
{Probably no network access. 
 Skipping Test Warning: Couldn't connect to Genbank with
Bio::DB::GenPept.pm! Probably no network access ok 
t/HSP...............ok
t/HTML..............ok t/Index.............ok t/PrimarySeq........ok
t/Range.............ok t/RangeI............ok t/RestrictionEnzyme.ok
t/Sbjct.............ok t/Seq...............ok t/SeqAnal...........ok
t/SeqFeature........ok t/SeqIO.............ok t/Sigcleave.........ok
t/SimpleAlign.......ok t/UnivAln...........ok t/WWW...............ok
t/exception.........ok 
t/hmmer.............ok 
Failed Test  Status Wstat Total Fail  Failed  List of failed
-------------------------------------------------------------------------------
t/Blast.t                    29    5  17.24%  24-28 
Failed 1/22 test scripts, 95.45% okay. 5/144 subtests failed, 96.53% okay.
*** Error code 29
make: Fatal error: Command failed for target `test_dynamic'

#

It seems rather suspect that It could not make a connection to GenBank!
I tried it immediatly after with netscape -OK.
I tried the qserver with:
http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/qserver.cgi?
DB=n&REQUEST_TYPE=LIST_OF_GIS&FORMAT=1&HTML=FALSE
&SAVETO=FALSE&NOHEADER=TRUE&UID= blah,blah,blah...

And it worked fine.

As for the test dynamic - I decided not to fool outside of my ken.

The result - inability to use the "new" method for
Bio::DB::GenBank
Bio::DB::GenPept
Bio::Seq

My system is a Sun workstation running SunOS 5.7

thanks in advance,

Kutbuddin Doctor


(Last thing..
can I just do an make and install the old version on top of the new to
revert back properly? I noticed that some of the files still think that
the Makefile thinks it is installing Bio v 0.05.1 )


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