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Old 01-05-2012, 10:14 AM   #1
peromhc
Senior Member
 
Location: Durham, NH

Join Date: Sep 2009
Posts: 108
Thumbs down cufflinks source install error

I am having problems with a source install of cufflinks: Seems to be Boost related, but, configure does not show error

Using Boost 1.48.0 and Cufflinks 1.3.0.

Here are the relevant lines from configure
Code:
checking for boostlib >= 1.38.0... yes
checking for bamlib... yes
checking build system type... x86_64-unknown-linux-gnu
checking whether the Boost::Thread library is available... yes
...
-- cufflinks 1.3.0 Configuration Results --
  C++ compiler:        g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3  -DNDEBUG  -pthread -I/home/matthew/local/include/boost-1_48 -I/usr/local/include 
  GCC version:         gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1
  Host System type:    x86_64-unknown-linux-gnu
  Install prefix:      /home/matthew/software
  Install eprefix:     ${prefix}
when making, however, I get errors

Code:
matthew@macmanes:~/cufflinks-1.3.0$ make
make  all-recursive
make[1]: Entering directory `/home/matthew/cufflinks-1.3.0'
Making all in src
make[2]: Entering directory `/home/matthew/cufflinks-1.3.0/src'
if g++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3  -DNDEBUG  -pthread -I/home/matthew/local/include/boost-1_48 -I/usr/local/include -MT clustering.o -MD -MP -MF ".deps/clustering.Tpo" -c -o clustering.o clustering.cpp; \
	then mv -f ".deps/clustering.Tpo" ".deps/clustering.Po"; else rm -f ".deps/clustering.Tpo"; exit 1; fi
In file included from abundances.h:22:0,
                 from clustering.h:38,
                 from clustering.cpp:10:
bundles.h: In constructor ‘BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)’:
bundles.h:363:9: warning: ‘BundleFactory::_curr_bundle’ will be initialized after [-Wreorder]
bundles.h:209:39: 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> > BundleFactory::_zeroone’ [-Wreorder]
bundles.h:213:2: warning:   when initialized here [-Wreorder]
In file included from clustering.h:38:0,
                 from clustering.cpp:10:
abundances.h: In constructor ‘AbundanceGroup::AbundanceGroup(const std::vector<boost::shared_ptr<Abundance> >&)’:
abundances.h:448:27: warning: ‘AbundanceGroup::_iterated_exp_count_covariance’ will be initialized after [-Wreorder]
abundances.h:443:27: warning:   ‘boost::numeric::ublas::matrix<double> AbundanceGroup::_count_covariance’ [-Wreorder]
abundances.h:302:2: warning:   when initialized here [-Wreorder]
if g++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -m64 -O3  -DNDEBUG  -pthread -I/home/matthew/local/include/boost-1_48 -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:22:0,
                 from differential.cpp:17:
bundles.h: In constructor ‘BundleFactory::BundleFactory(boost::shared_ptr<HitFactory>, BundleMode)’:
bundles.h:363:9: warning: ‘BundleFactory::_curr_bundle’ will be initialized after [-Wreorder]
bundles.h:209:39: 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> > BundleFactory::_zeroone’ [-Wreorder]
bundles.h:213:2: warning:   when initialized here [-Wreorder]
In file included from differential.cpp:17:0:
abundances.h: In constructor ‘AbundanceGroup::AbundanceGroup(const std::vector<boost::shared_ptr<Abundance> >&)’:
abundances.h:448:27: warning: ‘AbundanceGroup::_iterated_exp_count_covariance’ will be initialized after [-Wreorder]
abundances.h:443:27: warning:   ‘boost::numeric::ublas::matrix<double> AbundanceGroup::_count_covariance’ [-Wreorder]
abundances.h:302:2: warning:   when initialized here [-Wreorder]
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:112:31: warning: unused variable ‘s2’ [-Wunused-variable]
differential.cpp: In function ‘void sample_abundance_worker(const string&, SampleAbundances&, HitBundle*, bool, bool)’:
differential.cpp:1073:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
make[2]: *** [differential.o] Error 1
make[2]: Leaving directory `/home/matthew/cufflinks-1.3.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/matthew/cufflinks-1.3.0'
Any ideas about this?
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