[galaxy-dev] [galaxy-user] Help need in troubleshooting cufflinks

[Carlos Borroto]

Hi Vijay,

I ran into this error also, which by the way is not a galaxy issue but
cufflinks and more specific is a Boost's bug.

In my case it was caused because I was using the last version of Boost
and there is a bug on that version causing the problem. You could
apply this patch to boost:
https://svn.boost.org/trac/boost/changeset/75540

If you are by any chance using Mac OS X, I would recommend using
Homebrew (http://mxcl.github.com/homebrew/) to install cufflinks.
Homebrew will take care of installing any dependency needed by
cufflinks, for example Boost. In Homebrew Boost have been patched to
resolve this issue.

Hope it helps,
Carlos
PS: I'm copying galaxy-dev list, as this is an issue with a local install.

On Wed, Dec 14, 2011 at 4:15 AM, Vijay  T <vijay.t at elogic.co.in> wrote:
> Hi Team,
>
> This is Vijay from ELogic Technologies Pvt Ltd, Bangalore, India.
>
> 1. Using Galaxy local
> 2. NA
> 3. Galaxy was downloaded using the tar files
> 4. NA
> 5. When i tried to install Cufflinks into my system i am getting the following error.
>
> In file included from hits.h:21:0,
>                 from abundances.h:20,
>                 from differential.cpp:17:
> common.h: At global scope:
> common.h:25:25: error: ‘boost::BOOST_FOREACH’ has not been declared
> In file included from differential.h:29:0,
>                 from differential.cpp:18:
> replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&)’:
> replicates.h:141:50: warning: unused variable ‘s2’ [-Wunused-variable]
> differential.cpp: In member function ‘void TestLauncher::perform_testing(std::vector<boost::shared_ptr<SampleAbundances> >&)’:
> differential.cpp:111:31: warning: unused variable ‘s2’ [-Wunused-variable]
> differential.cpp: In function ‘void sample_abundance_worker(const string&, SampleAbundances&, HitBundle*, bool, bool)’:
> differential.cpp:704:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
> make[2]: *** [differential.o] Error 1
> make[2]: Leaving directory `/home/binet/Downloads/cufflinks-1.2.0/src'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/home/binet/Downloads/cufflinks-1.2.0'
> make: *** [all] Error 2
>
>
>   Even i have tried with various versions of cufflinks but i am getting the same error.
> Please kindly help me in getting out of this error.
>
>
> Thanks and Regards
>
> Vijay
>
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