Re: [Inchworm-users] compilation problem

[Brian J H. <bh...@br...>]

Fantastic!  Thanks for checking!

I'll run some tests on this new version and hopefully release it later today
or tomorrow.  There are a couple things this new version does, such as:

-removes error-containing kmers for cleaner output
-defaults to a kmer of 26 to avoid artifacts related to palindromic kmers.
(should give improved results with non-strand-specific RNA-Seq data)


Best,

-b



On Fri, Feb 18, 2011 at 9:32 AM, Fabrice Legeai <fab...@ir...>wrote:

>  Hi Brian,
>
> It worked perfectly. Thanks !
>
> Fabrice
>
> Le 18/02/2011 15:21, Brian J Haas a écrit :
>
>  Hi Fabrice,
>>
>> Thanks for the info.  I hadn't experienced that error on our centos linux
>> nor mac osx.  I did update the code to rectify the error, and I took the
>> Werror out of the compilation.
>>
>> Could you do me a big favor and see if the latest code under SVN builds
>> properly? If so, I'll plan for a new release shortly.   You can pull the
>> code like so:
>>
>> svn co https://inchworm.svn.sourceforge.net/svnroot/inchworm inchworm
>>
>> and hopefully, just do the configure / make / make install
>>
>> Thanks!
>>
>> -brian
>>
>>
>> On Fri, Feb 18, 2011 at 4:38 AM, Fabrice Legeai<fab...@ir...
>> >wrote:
>>
>>   Hi,
>>>
>>> I've installed the 01-20-2010 version of inchwom
>>> on a linux Redhat (2.6.18-194.11.4.el5 x86_64).
>>> But while compiling I got the following error :
>>>
>>> g++ -DHAVE_CONFIG_H -I. -I.. -Wall -Werror
>>> -Wno-deprecated -MT IRKE.o -MD -MP -MF
>>> .deps/IRKE.Tpo -c -o IRKE.o IRKE.cpp
>>> cc1plus: warnings being treated as errors
>>> IRKE.cpp: In member function ‘void
>>> IRKE::populate_Kmers_from_fasta(const
>>> std::string&, bool)’:
>>> IRKE.cpp:126: warning: converting to ‘unsigned
>>> int’ from ‘double’
>>> IRKE.cpp: In member function ‘void
>>> IRKE::compute_sequence_assemblies(KmerCounter&,
>>> float, unsigned int, unsigned int, bool,
>>> std::string)’:
>>> IRKE.cpp:492: warning: converting to ‘unsigned
>>> int’ from ‘double’
>>> make[2]: *** [IRKE.o] Error 1
>>> make[2]: Leaving directory
>>> `/partage/tmp/inchworm_01-20-2010/src'
>>> make[1]: *** [all-recursive] Error 1
>>> make[1]: Leaving directory
>>> `/partage/tmp/inchworm_01-20-2010'
>>> make: *** [all] Error 2
>>>
>>> I achieved to compile by removing the -Werror from
>>> the configure.ac and src/Makefile.in, but I am not
>>> sure that it is the good option. Would you please
>>> check ?
>>>
>>> Best regards,
>>>
>>> Fabrice Legeai
>>> AphidBase
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
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>>>
>>>
>>
>>
>


-- 
-- 
Brian J. Haas
Manager, Bioinformatics Outreach, Genome Annotation and Analysis
The Broad Institute
http://broad.mit.edu/~bhaas