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Old 01-17-2012, 08:14 AM   #1
mrbirdy857
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Location: georgia

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Default Compile cufflinks in MacOSX10.7 (Lion)--error in make

Hello,

I am trying to compile cufflinks and have ran into some problems. I have built Boost (version 1.48.0), and copied/installed all the bam/sam items as instructed by the cufflinks website. The configuration of cufflinks runs just fine. However, when I try to make, I get the below output which ends in errors. Does anybody have any clues as to what the problem might be? I am running MacOSX 10.7.2 (Lion)


make all-recursive
Making all in src
if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT differential.o -MD -MP -MF ".deps/differential.Tpo" -c -o differential.o differential.cpp; \
then mv -f ".deps/differential.Tpo" ".deps/differential.Po"; else rm -f ".deps/differential.Tpo"; exit 1; fi
In file included from abundances.h:22,
from differential.cpp:17:
bundles.h: In constructor ‘BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)’:
bundles.h:363: warning: ‘BundleFactory::_curr_bundle’ will be initialized after
bundles.h:209: warning: ‘boost::random::uniform_01<boost::random::mersenne_twister_engine<unsigned int, 32ul, 624ul, 397ul, 31ul, 2567483615u, 11ul, 4294967295u, 7ul, 2636928640u, 15ul, 4022730752u, 18ul, 1812433253u>, double> BundleFactory::_zeroone’
bundles.h:213: warning: when initialized here
In file included from differential.cpp:17:
abundances.h: In constructor ‘AbundanceGroup::AbundanceGroup(const std::vector<boost::shared_ptr<Abundance>, std::allocator<boost::shared_ptr<Abundance> > >&)’:
abundances.h:448: warning: ‘AbundanceGroup::_iterated_exp_count_covariance’ will be initialized after
abundances.h:443: warning: ‘boost::numeric::ublas::matrix<double, boost::numeric::ublas::basic_row_major<long unsigned int, long int>, boost::numeric::ublas::unbounded_array<double, std::allocator<double> > > AbundanceGroup::_count_covariance’
abundances.h:302: warning: when initialized here
In file included from /usr/local/include/boost/graph/named_graph.hpp:17,
from /usr/local/include/boost/graph/adjacency_list.hpp:45,
from differential.h:24,
from differential.cpp:18:
/usr/local/include/boost/multi_index/hashed_index.hpp: At global scope:
/usr/local/include/boost/multi_index/hashed_index.hpp:1254: error: ‘boost::BOOST_FOREACH’ has not been declared
In file included from differential.h:29,
from differential.cpp:18:
replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&)’:
replicates.h:141: warning: unused variable ‘s2’
differential.cpp: In member function ‘void TestLauncher:erform_testing(std::vector<boost::shared_ptr<SampleAbundances>, std::allocator<boost::shared_ptr<SampleAbundances> > >&)’:
differential.cpp:112: warning: unused variable ‘s2’
differential.cpp: In function ‘void sample_abundance_worker(const std::string&, SampleAbundances&, HitBundle*, bool, bool)’:
differential.cpp:1073: warning: comparison between signed and unsigned integer expressions
make[2]: *** [differential.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2


Thanks for any help!
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Old 01-17-2012, 01:34 PM   #2
peromhc
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Location: Durham, NH

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Default

see http://seqanswers.com/forums/showthread.php?t=16637
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Old 01-19-2012, 04:49 AM   #3
mrbirdy857
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Join Date: Jan 2012
Posts: 3
Default Thanks a million!

That is perfect, thanks.
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