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Old 12-16-2012, 08:31 PM   #1
bharat_iyengar
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Location: Delhi, India

Join Date: Dec 2012
Posts: 20
Default problem installing cufflinks

there was no problem configuring Cufflinks v2.02 but when i make it i get an error like this

Code:
make  all-recursive
make[1]: Entering directory `/media/sda8/bharat/genomes/cufflinks-2.0.2'
Making all in src
make[2]: Entering directory `/media/sda8/bharat/genomes/cufflinks-2.0.2/src'
if g++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -m64 -O3  -DNDEBUG  -pthread -I usr/local/include -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
if g++ -DHAVE_CONFIG_H -I. -I. -I..  -I../src  -I/usr/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -m64 -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 hits.h:21:0,
                 from abundances.h:23,
                 from differential.cpp:17:
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:152:50: warning: unused variable 's2' [-Wunused-variable]
In file included from differential.cpp:18:0:
differential.h: In constructor 'FPKMContext::FPKMContext(double, double, double,                                                                                uble, AbundanceStatus, const StatusPerReplicateTable&)':
differential.h:142:21: warning: 'FPKMContext::status' will be initialized after
differential.h:139:29: warning:   'StatusPerReplicateTable FPKMContext::status_p
differential.h:131:2: warning:   when initialized here [-Wreorder]
differential.cpp: In member function 'void TestLauncher::perform_testing(std::ve
differential.cpp:212:31: warning: unused variable 's2' [-Wunused-variable]
differential.cpp: In member function 'void TestLauncher::record_tracking_data(st
differential.cpp:240:31: warning: unused variable 's2' [-Wunused-variable]
differential.cpp: In function 'SampleDifference get_ds_tests(const AbundanceGrou
differential.cpp:790:16: warning: unused variable 'name' [-Wunused-variable]
differential.cpp: In function 'void test_differential(const string&, const std::
differential.cpp:1771:83: warning: comparison between signed and unsigned intege
differential.cpp:1772:83: warning: comparison between signed and unsigned intege
differential.cpp:1814:83: warning: comparison between signed and unsigned intege
differential.cpp:1815:83: warning: comparison between signed and unsigned intege
differential.cpp:1856:83: warning: comparison between signed and unsigned intege
differential.cpp:1857:83: warning: comparison between signed and unsigned intege
make[2]: *** [differential.o] Error 1
make[2]: Leaving directory `/media/sda8/bharat/genomes/cufflinks-2.0.2/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/media/sda8/bharat/genomes/cufflinks-2.0.2'
make: *** [all] Error 2
-----------------------------------------------------------------------

I dont understand where to troubleshoot. All boost1.52 and Eigen libraries are copied in /usr/local/lib

Last edited by bharat_iyengar; 12-16-2012 at 08:36 PM.
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