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
when making, however, I get errors
Any ideas about this?
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: ${prefix}
Code:
matthew@macmanes:~/cufflinks-1.3.0$ 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'
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