[Bioperl-l] Bio::Ext::Align?

jmf jeanmarc.frigerio at gmail.com
Tue Oct 18 08:43:51 EDT 2011


Hi
I agree that it'd be nice to see it revived. I made a patch to the Bio/
Ext/Align/Makefile.PL to make the compiler happy, just by changing:

 'MYEXTLIB'  => 'libs/libsw$(LIB_EXT)',
to
'MYEXTLIB'  => '\'-fPIC libs/libsw$(LIB_EXT)\'',

Thanks Dave for the topic !

Chris can you correct the file or should I submit the patch (I don't
know where ?)

On 2 sep, 17:20, Jack Tanner <i... at hotmail.com> wrote:
> I also see that someone's forked it on Github and made some packaging fixes.
>
> It'd be nice to see it revived.
>
> On 9/2/2011 9:00 AM, Fields, Christopher J wrote:
>
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>
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>
>
> > I think, if this is actively being used, we should split it away from bioperl-ext and release it on its own.  Otherwise I worry about the long-term support for it/
>
> > chris
>
> > On Sep 2, 2011, at 3:44 AM, Dave Messina wrote:
>
> >> As it happens, a colleague of mine needed Bio::Ext::Alignfor hhrpred:
> >>http://toolkit.tuebingen.mpg.de/hhpred
>
> >> He got it working thus:
> >> Hi Dave,
> >> thanks a lot. i made it work. The error i got later on was:
> >> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object;
> >> recompile with -fPIC
>
> >> the solution is:
> >> perl Makefile.PL PREFIX=<path to installation>  /fftwsingle --enable-shared --with-pic --enable-single
> >> <edit Makefile to add -fPIC to CFLAGS>
> >> make
> >> make install
> >>http://forums.fedoraforum.org/showthread.php?t=232607
>
> >> Dave
>
> >> On Fri, Sep 2, 2011 at 06:31, Fields, Christopher J<cjfie... at illinois.edu>  wrote:
> >> Yes, it's essentially deprecated (unmaintained).  I don't know of anyone who has packaged that up in a while, if ever.
>
> >> chris
>
> >> On Sep 1, 2011, at 10:49 PM, Jack Tanner wrote:
>
> >>> I'd like to run Bio::Ext::Align, from bioperl-ext. Seems like a pretty quiet codebase these days... Is it dead?
>
> >>> Does anyone have a spec file for building an SRPM for it for RHEL 6?
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