[Bioperl-l] error during installation

[Peng Du]

Thank you for all your replies.

So,what do you suggest me do if I want to do alignment with external tools like clustawl or dpalign? In the current distribution of BioPerl, ext package is still required to do this, I am afraid.
Thank you. 

Sent from my iPhone

On 2012/06/17, at 2:43, "Fields, Christopher J" <cjfields at illinois.edu> wrote:

> On Jun 16, 2012, at 3:50 AM, Leon Timmermans wrote:
> 
>> On Sat, Jun 16, 2012 at 5:28 AM, Du, Peng <du at ibio.jp> wrote:
>>> Hi everybody,
>>> 
>>> I am a newbie, I encountered a problem while installing bioperl-ext.
>>> The error message is :
>>> 
>>> 
>>> /usr/bin/ld: libs/libsw.a(aln.o): relocation R_X86_64_32 against
>>> `.rodata.str1.8' can not be used when making a shared object;
>>> recompile with -fPIC
>>> libs/libsw.a: could not read symbols: Bad value
>>> collect2: ld returned 1 exit status
>>> 
>>> I googled some solutions, but all of them are confusing, could you
>>> tell me where exactly should I add the -fPIC? In the makefile under
>>> the bioperl-ext-1.4 directory?  I tried to add this to the CCCDLFLAGS,
>>> CCDLFLAGS, LDDLFLAGS and LDFLAGS in that file. But it still doesn't
>>> work.
>>> f
>>> Could you tell me what to do or where could I find the answer?
>>> 
>>> Thank you very much.
>>> 
>>> Best Regards,
>>> Peng
>> 
>> You should not install it in the first place. BioPerl-ext has been
>> partly merged into the main Bioperl distribution, and partly spun off
>> into its own dists (Bio::Tools::HMM, not released yet AFAIK). You
>> should just install the former, or help release the latter.
>> 
>> Leon
> 
> 
> For all intents and purposes I would consider all parts (past and present) of bioperl-ext deprecated, unless we can find someone willing to take them on.  And, with that in mind, frankly I would be much more amenable to supporting XS (or similar) interfaces to common bioinformatics libraries (Bio::DB::Sam as an example) than ones specifically designed with bioperl in mind.  The latter (bioperl-ext) have significantly bit-rotted to the point I'm not sure whether they would be worth keeping around.
> 
> chris