[galaxy-dev] [galaxy-user] Help need in troubleshooting cufflinks
carlos.borroto at gmail.com
Mon Dec 19 10:49:56 EST 2011
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:
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,
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: *** [differential.o] Error 1
> make: Leaving directory `/home/binet/Downloads/cufflinks-1.2.0/src'
> make: *** [all-recursive] Error 1
> make: 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
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