[Bioperl-l] Bio::SeqIO::staden::read problem

[Aaron J. Mackey]

Mark, you were the last person to comment/uncomment this line in CVS  
(the log says "to get CGI to work").  Can you clarify?  Was this under  
mod_perl?  All of the read.pm-requiring SeqIO formats should load  
staden/read.pm themselves, why do we need SeqIO to do it?

Thanks,

-Aaron

On Dec 20, 2004, at 7:32 AM, Aaron J. Mackey wrote:

>
> You should comment out line 316 of /usr/lib/perl5/5.8.0/Bio/SeqIO.pm  
> to read:
>
>  sub BEGIN {
>  #    eval { require Bio::SeqIO::staden::read; };
>  }
>
> This is one of those things that we can't seem to agree on (some  
> installations seem to require this eval, other's fail when we use it).
>
> -Aaron
>
> On Dec 17, 2004, at 11:39 PM, xuying wrote:
>
>> all output is in the attached file "out.make.ext".
>>>
>>>
>>> xuying wrote:
>>>
>>>> Running make install
>>>> make[1]: Entering directory  
>>>> `/root/.cpan/build/bioperl-ext-1.4/Bio/Ext/Align'
>>>> make[1]: Leaving directory  
>>>> `/root/.cpan/build/bioperl-ext-1.4/Bio/Ext/Align'
>>>> make[1]: Entering directory  
>>>> `/root/.cpan/build/bioperl-ext-1.4/Bio/SeqIO/staden'
>>>> make[1]: Leaving directory  
>>>> `/root/.cpan/build/bioperl-ext-1.4/Bio/SeqIO/staden'
>>>> Installing /usr/share/man/man3/Bio::SeqIO::staden::read.3pm
>>>> Writing  
>>>> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi/auto/Bio/ 
>>>> .packlist
>>>> Appending installation info to  
>>>> /usr/lib/perl5/5.8.0/i386-linux-thread-multi/perllocal.pod
>>>>   /usr/bin/make install  -- OK
>>>
>>> No, this doesn't look entirely correct; more files should be listed  
>>> as
>>> being installed/written to.  From within the CPAN shell, type "look
>>> Bio::SeqIO::staden" to drop into a subshell, then do a make clean,  
>>> and
>>> start over with perl Makefile.PL, make, make test, make install;  
>>> send me
>>> all the output.
>>>
>>> -Aaron
>>>
>>>
>>
>> = = = = = = = = = = = = = = = = = = = =
>> 			
>>
>> 　　　　　　　　致
>> 礼！
>>
>> 				
>> 　　　　　　　　xuying
>> 　　　　　　　　xuying at sibs.ac.cn
>> 　　　　　　　　　　2004-12-18
>>
>> <out.make.ext>_______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> --
> Aaron J. Mackey, Ph.D.
> Dept. of Biology, Goddard 212
> University of Pennsylvania       email:  amackey at pcbi.upenn.edu
> 415 S. University Avenue         office: 215-898-1205
> Philadelphia, PA  19104-6017     fax:    215-746-6697
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
--
Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania       email:  amackey at pcbi.upenn.edu
415 S. University Avenue         office: 215-898-1205
Philadelphia, PA  19104-6017     fax:    215-746-6697