[Bioperl-l] Bioperl 1.0.1 Released

[Peter Kos]

Jason,

you have requested notes on Win installation.
It seems pretty satisfactory for me, but you should know if there are 
serious problems among the failed tests or not.
I include here for your reference the failed tests' output lines as 
the whole stuff is long and the all other tests were OK.
Clustalw and TCoffee are not installed so the error is OK. If you are 
interested why StandAloneBlast gave the same messages, I may play 
with the directories and other settings, otherwise I do not care, as 
I run these things under UNIX.
I do not understand that regex problem though. And the Index thing.

Please let me know if you want me to check out details.
Specs: Win2000Pro, Perl 5.6.1

1.)
t\BlastIndex........FAILED test 3
        Failed 1/13 tests, 92.31% okay
		(I don't know what this means)
2.)
t\Clustalw..........ok 1/10Trailing \ in regex m/^\/ at 
c:/Perl/BIOPER~1.1/blib/lib/Bio/Root/IO.pm line 426.
                        (I don't know what this means)
3.)
t\Clustalw..........dubious
        Test returned status 2 (wstat 512, 0x200)
        after all the subtests completed successfully
                        (It is OK, I do not have Clustalw installed 
on this machine)
4.)
t\consed............FAILED tests 12, 14
        Failed 2/15 tests, 86.67% okay
                        (I don't know what this means, as I know 
consed does not run on Win, so I do not see the whole point in it, 
but you should know)
5.)
t\flat..............DB_File not loaded. This means flat.t test cannot 
be executed. Skipping
t\flat..............ok 7/7No root path(s) specified
 at c:/Perl/BIOPER~1.1/blib/lib/Bio/Root/IO.pm line 613
                        (How can I load DB_File? The same error 
occurred on the SUN. Does it mean that it is not [properly] 
installed?)
6.)
t\game..............XML::Parser::PerlSAX not loaded. This means game 
test cannot be execut...
                        (I may not have it installed, I think)
7.)
t\Index.............------------- EXCEPTION  -------------
MSG: This index file is from version [0.1] - You need to rebuild it 
to use module version [0.2]
STACK Bio::Index::Abstract::_type_and_version 
c:/Perl/BIOPER~1.1/blib/lib/Bio/Index/Abstract.pm:486
STACK Bio::Index::Abstract::open_dbm 
c:/Perl/BIOPER~1.1/blib/lib/Bio/Index/Abstract.pm:407
STACK Bio::Index::Abstract::new 
c:/Perl/BIOPER~1.1/blib/lib/Bio/Index/Abstract.pm:151
STACK Bio::Index::AbstractSeq::new 
c:/Perl/BIOPER~1.1/blib/lib/Bio/Index/AbstractSeq.pm:91
STACK toplevel t\Index.t:30

--------------------------------------
t\Index.............dubious
        Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-12
        Failed 12/12 tests, 0.00% okay
                        (NOW what on Earth is this??? I also had this 
on the SUN)
8.)
t\SearchIO..........XML::Parser::PerlSAX not loaded. This means 
SearchIO::blastxml test
                        (As above. Perhaps not installed.)
9.)
t\StandAloneBlast...ok 1/10Trailing \ in regex m/^\/ at c:/Perl/BI  
OPER~1.1/blib/lib/Bio/Root/IO.pm line 426.
t\StandAloneBlast...dubious
        Test returned status 2 (wstat 512, 0x200)
        after all the subtests completed successfully
                        (I don't know... Blastall is installed. 
Perhaps setenv problem or such)
10.)
t\TCoffee...........ok 4/16Trailing \ in regex m/^\/ at 
c:/Perl/BIOPER~1.1/blib/lib/Bio/Root/IO.pm line 426.
t\TCoffee...........dubious
        Test returned status 2 (wstat 512, 0x200)
        after all the subtests completed successfully
                        (It is OK, I do not have TCoffee installed on 
this machine)
11.)
t\Variation_IO......ok 10/25
The XML-format conversion requires the CPAN modules XML::Twig, 
XML::Writer, and IO::String to be installed on your syste
 Skipping these tests.
12.)
t\XEMBL_DB..........SOAP::Lite and/or XML::DOM not installed. This 
means that Bio::DB::XEMBL module is not usable. Skipp

Failed Test         Status Wstat Total Fail  Failed  List of Failed
------------------------------------------------------------------  
--------------
t\BlastIndex.t                        13    1   7.69%  3
t\Clustalw.t               2   512    10    0   0.00%  ??
t\Index.t                255 65280    12   12 100.00%  1-12
t\StandAloneBlast.t        2   512    10    0   0.00%  ??
t\TCoffee.t                2   512    16    0   0.00%  ??
t\consed.t                            15    2  13.33%  12, 14
4 subtests skipped.
Failed 6/93 test scripts, 93.55% okay. 15/3245 subtests failed, 
99.54% okay.
NMAKE : fatal error U1077: 'C:\Perl\bin\Perl.exe' : return code 
'0xff'
Stop.

best regards
Peter

On Tuesday, June 11, 2002 11:28 PM, Jason Stajich 
[SMTP:jason@cgt.mc.duke.edu] wrote:
>
> 11 June 2002
>
> I am happy to announce the release of Bioperl 1.0.1 - bugfix
> release.
....

> Note that I did not have access to a windows machine so I couldn't
> test
> this myself, please let me know if you have any problems.