[Bioperl-l] Problems with installing Bioperl-ext-1.5.1 on Bioperl-1.5.1

[Chris Fields]

Just to note, we're not actively supporting much of the bioperl-ext  
code, in favor of the BioLib initiative:

http://biolib.open-bio.org/wiki/Main_Page

If you do use bioperl-ext I suggest only using the latest code from  
svn (and that in combination with bioperl-live).

chris

On Apr 9, 2009, at 10:18 PM, Joel Martin wrote:

> Hello,
>  I found that 1.5.1 a pain to install, I recommend the code from
>
> http://www.bioperl.org/wiki/Ext_package#The_latest_code
>
>  anywho, the read is read.pm, the message is something from
> inline::c I think, there's an old bug report about it, if
> you can't use the newer code maybe it will help.
> http://bugzilla.open-bio.org/show_bug.cgi?id=2074
>
> joel
>
>
> On Thu, Apr 09, 2009 at 07:54:21PM -0500, Charles Embry wrote:
>> Hello I am a graduate student at UALR and I am trying to install  
>> the ext package(1.5.1) on bioperl 1.5.1.
>> I get this error when i run the make file.
>>
>> "[root at bioinformatics bioperl-ext-1.5.1]# perl Makefile.PL
>> Writing Makefile for Bio::Ext::Align
>> ERROR from evaluation of /home/stephen/capstone/bioperl-ext-1.5.1/ 
>> Bio/SeqIO/staden/Makefile.PL: Invalid version '' for  
>> Bio::SeqIO::staden::read.
>> Must be of the form '#.##'. (For instance '1.23')
>>  at ./Makefile.PL line 4"
>>
>> This is the first  11 lines of the Makefile.PL for ext package
>>
>> use Inline::MakeMaker;
>> use Config;
>>
>> WriteInlineMakefile(
>>             'NAME'        => 'Bio::SeqIO::staden::read',
>>             'VERSION_FROM'    => './read.pm', # finds $VERSION,
>>             'PREREQ_PM'        => { 'Inline::C' => 0.0,
>>                          'Bio::SeqIO::abi' => 0.0,
>>                        }, # e.g., Module::Name => 1.1,
>>             test                => { TESTS => 'test.pl' },
>>            );
>>
>> What does the error mean?
>>
>> And what version does it refer to? Of what? (staden?)
>> What version of Staden should this be if i am using the  
>> io_lib-1.8.11 , following the INSTALL instructions with bioperl-ext?
>>
>>
>> Thanks you
>> C. Stephen Embry
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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