[Bioperl-l] release timetable

Nathan S. Haigh n.haigh at sheffield.ac.uk
Thu Nov 30 07:50:57 EST 2006


Sendu Bala wrote:
> Nathan S. Haigh wrote:
>> Sendu Bala wrote:
>>> Hilmar Lapp wrote:
>>>  
>>>> Sendu -
>>>>
>>>> what is the timetable in your mind for getting the release out? The 
>>>> NESCent phyloinformatics hackathon is impending and if at all 
>>>> possible I'd really like to see the release be out of the way when 
>>>> it starts so that all new code can simply go the main trunk and has 
>>>> no chance of interfering with the release.
>>>>     
>>>
>>> I'm going to do one final merge from HEAD to branch-1-5-2 and then 
>>> set the final release tags later today, so a) anything done at the 
>>> hackathon won't make any difference, and b) the release should go 
>>> out soon.
>>>
>>> The release will go ahead when I've sorted out the Windows PPM and 
>>> the Change Log (neither of which require code changes on the branch).
>>>
>>> On this schedule I won't be able to implement Conrad's pre-req 
>>> installation order in Build.PL since that would require a 
>>> substantial change to ModuleBuildBioperl.pm and another RC. I'll do 
>>> that after release so that 1.5.3 benefits.
>>>
>>> _______________________________________________
>>>   
>>
>> I've not had the time to test out the new CPAN installation until 
>> now. I've just tried it
>
> 'it' being RC5? On Windows?
>
>
>> on a clan install of ActivePerl 5.8.8.819 and it didn't install:
>> Failed Test     Stat Wstat Total Fail  Failed  List of Failed
>> ------------------------------------------------------------------------------- 
>>
>> t/RemoteBlast.t    9  2304    13    0   0.00%  ??
>> t/rnamotif.t       2   512    72  144 200.00%  1-72
>> 2 tests and 197 subtests skipped.
>>
>> How can I get the test output from CPAN to go to a log file so I can 
>> look at the errors more closely?
>
> I don't know about log files, but you can configure the cmd window to 
> have a large history and then just copy/paste the results.
>
> You can also go into the directory that CPAN extracted the archive to 
> and run the tests there manually.
>
> Please send me the results of those tests.
>
>
>

Hi Sendu,

Installation on a clean install of ActivePerl 5.8.8.819 n WindowsXP:
1) nmake is required for CPAN installations
2) I updated CPAN to the latest version
3) Restarted CPAN and did "o conf prefer_installer MB" and "o conf commit"
4) Restarted CPAN and tried the install of bioperl 1.5.2 RC5. I still 
get the message saying it's using Makefile.PL and not Build.PL - not 
sure why! I'm going to see if updating Module::Build helps. For the time 
being I installed anyway.....
5) towards the end of dependency checking I get this:
-- snip --
Checking if your kit is complete...
Looks good
Warning: prerequisite DB_File 0 not found.
Writing Makefile for Bio
---- Unsatisfied dependencies detected during 
[S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz] -----
    DB_File
Shall I follow them and prepend them to the queue
of modules we are processing right now? [yes]
-- snip --

6) When running the install, DB_File fails to install and that appears 
to be the root of the rnamotif test failing:
-- snip --
t/rnamotif...................Can't locate DB_File.pm in @INC (@INC 
contains: t/lib C:\Perl\cpan
\build\bioperl-1.5.2_005-RC\blib\lib 
C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\arch C:/Perl/
site/lib C:/Perl/lib .) at 
C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SeqFeature/Coll
ection.pm line 133.
BEGIN failed--compilation aborted at 
C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SeqFe
ature/Collection.pm line 133.
Compilation failed in require at 
C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Tools/RNA
Motif.pm line 145.
BEGIN failed--compilation aborted at 
C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Tools
/RNAMotif.pm line 145.
Compilation failed in require at t/rnamotif.t line 27.
BEGIN failed--compilation aborted at t/rnamotif.t line 27.
t/rnamotif...................dubious
        Test returned status 2 (wstat 512, 0x200)
DIED. FAILED tests 1-72
        Failed 72/72 tests, 0.00% okay
-- snip --

7) The RemoteBlast seems to fail due to XML/SAX not being installed:
--s nip
t/RemoteBlast................ok 10/13Bio::SearchIO: blastxml cannot be found
Exception
------------- EXCEPTION  -------------
MSG: Failed to load module Bio::SearchIO::blastxml. Can't locate 
XML/SAX.pm in @INC (@INC conta
ins: t C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib 
C:\Perl\cpan\build\bioperl-1.5.2_005-RC
\blib\arch C:/Perl/site/lib C:/Perl/lib .) at 
C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/
Bio\SearchIO\blastxml.pm line 112.
BEGIN failed--compilation aborted at 
C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio\Searc
hIO\blastxml.pm line 112.
Compilation failed in require at 
C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Root/Root
.pm line 425.

STACK Bio::Root::Root::_load_module 
C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/Root/R
oot.pm:427
STACK (eval) 
C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SearchIO.pm:397
STACK Bio::SearchIO::_load_format_module 
C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/S
earchIO.pm:396
STACK Bio::SearchIO::new 
C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib\lib/Bio/SearchIO.pm:176
STACK Bio::Tools::Run::RemoteBlast::retrieve_blast 
C:\Perl\cpan\build\bioperl-1.5.2_005-RC\blib
\lib/Bio/Tools/Run/RemoteBlast.pm:603
STACK toplevel t/RemoteBlast.t:185
--------------------------------------

For more information about the SearchIO system please see the SearchIO docs.
This includes ways of checking for formats at compile time, not run time
Use of uninitialized value in numeric lt (<) at t/RemoteBlast.t line 187.
Can't locate object method "new" via package "Bio::SearchIO::blastxml" 
at C:\Perl\cpan\build\bi
operl-1.5.2_005-RC\blib\lib/Bio/SearchIO.pm line 177.
t/RemoteBlast................dubious
        Test returned status 9 (wstat 2304, 0x900)
        after all the subtests completed successfully
-- snip --

HTH,
Nath




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