Cufflinks make Error (differential.o failed)

[Sebastiano]

hi all

I am trying to install cufflinks using Cygwin in Win7.
I installed correctly the boost library, the Eigen library and samtools and i'm at the point at which i run the "make" command from the cufflinks-2.1.1 folder.

the ./configure command works fine and gets to the end without errors, however, when i run "make" this is what i get:

$ make
make  all-recursive
make[1]: Entering directory `/cygdrive/c/cygdrive/c/cufflinks-2.1.1'
Making all in src
make[2]: Entering directory `/cygdrive/c/cygdrive/c/cufflinks-2.1.1/src'
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I../src  -I/usr/local/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3  -DNDEBUG  -pthread -I/cygdrive/c/cygdrive/c/Boost//include/boost-1_53 -I/cygdrive/c/Users/se24553/SAM_tools//include -I/cygdrive/c/Users/se24553/SAM_tools/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
g++: unrecognized option '-pthread'
In file included from differential.h:29:0,
                 from differential.cpp:21:
replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&)’:
replicates.h:208:50: warning: unused variable ‘s2’
In file included from differential.cpp:21:0:
differential.h: In constructor ‘FPKMContext::FPKMContext(double, double, double, double, const CountPerReplicateTable&, double, const FPKMPerReplicateTable&, double, double, double, AbundanceStatus, const StatusPerReplicateTable&, const std::vector<double>&, double)’:
differential.h:172:21: warning: ‘FPKMContext::status’ will be initialized after
differential.h:167:29: warning:   ‘StatusPerReplicateTable FPKMContext::status_per_rep’
differential.h:132:2: warning:   when initialized here
differential.cpp: In member function ‘void TestLauncher::perform_testing(std::vector<boost::shared_ptr<SampleAbundances> >&)’:
differential.cpp:230:31: warning: unused variable ‘s2’
differential.cpp: In member function ‘void TestLauncher::record_tracking_data(std::vector<boost::shared_ptr<SampleAbundances> >&)’:
differential.cpp:258:31: warning: unused variable ‘s2’
In file included from /cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/math/special_functions/math_fwd.hpp:27:0,
                 from /cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/math/special_functions/sign.hpp:17,
                 from /cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/lexical_cast.hpp:167,
                 from /cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/math/special_functions/gamma.hpp:24,
                 from differential.cpp:16:
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/math/tools/promotion.hpp: At global scope:
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/math/tools/promotion.hpp: In instantiation of ‘boost::math::tools::promote_args<long double, float, float, float, float, float>’:
differential.cpp:359:60:   instantiated from here
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/math/tools/promotion.hpp:141:1: error: invalid application of ‘sizeof’ to incomplete type ‘boost::STATIC_ASSERTION_FAILURE<false>’
differential.cpp: In function ‘long double trunc_normal_log_likelihood(const std::vector<double>&, double, double)’:
differential.cpp:448:21: error: ‘logl’ was not declared in this scope
differential.cpp: In function ‘SampleDifference test_diffexp(const FPKMContext&, const FPKMContext&)’:
differential.cpp:551:86: warning: comparison between signed and unsigned integer expressions
differential.cpp:559:86: warning: comparison between signed and unsigned integer expressions
differential.cpp:581:86: warning: comparison between signed and unsigned integer expressions
differential.cpp:589:86: warning: comparison between signed and unsigned integer expressions
differential.cpp: In function ‘bool test_js(const AbundanceGroup&, const AbundanceGroup&, double&, double&)’:
differential.cpp:833:101: warning: comparison between signed and unsigned integer expressions
differential.cpp:845:101: warning: comparison between signed and unsigned integer expressions
differential.cpp:871:101: warning: comparison between signed and unsigned integer expressions
differential.cpp:883:101: warning: comparison between signed and unsigned integer expressions
differential.cpp: In function ‘void test_differential(const std::string&, const std::vector<boost::shared_ptr<SampleAbundances> >&, const std::vector<std::pair<unsigned int, unsigned int> >&, Tests&, Tracking&)’:
differential.cpp:1803:79: warning: comparison between signed and unsigned integer expressions
differential.cpp:1804:79: warning: comparison between signed and unsigned integer expressions
differential.cpp:1842:80: warning: comparison between signed and unsigned integer expressions
differential.cpp:1843:80: warning: comparison between signed and unsigned integer expressions
differential.cpp:1880:79: warning: comparison between signed and unsigned integer expressions
differential.cpp:1881:79: warning: comparison between signed and unsigned integer expressions
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/system/error_code.hpp: At global scope:
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/system/error_code.hpp:214:36: warning: ‘boost::system::posix_category’ defined but not used
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/system/error_code.hpp:215:36: warning: ‘boost::system::errno_ecat’ defined but not used
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/system/error_code.hpp:216:36: warning: ‘boost::system::native_ecat’ defined but not used
Makefile:1380: recipe for target `differential.o' failed
make[2]: *** [differential.o] Error 1
make[2]: Leaving directory `/cygdrive/c/cygdrive/c/cufflinks-2.1.1/src'
Makefile:250: recipe for target `all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/cygdrive/c/cygdrive/c/cufflinks-2.1.1'
Makefile:188: recipe for target `all' failed
make: *** [all] Error 2

I think that the error is towards the end where it says

Makefile:1380: recipe for target `differential.o' failed
make[2]: *** [differential.o] Error 1
make[2]: Leaving directory `/cygdrive/c/cygdrive/c/cufflinks-2.1.1/src'
Makefile:250: recipe for target `all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/cygdrive/c/cygdrive/c/cufflinks-2.1.1'
Makefile:188: recipe for target `all' failed
make: *** [all] Error 2

I googled the "differential.o" error but i can't seem to find an answer

any suggestion would be awesome!

thanks!

Seb

[amarth]

Check this!!:

http://seqanswers.com/forums/showthread.php?t=16637

Offtopic: Cufflinks runs good on windows?

[Sebastiano]

**edited post**
I did try to use the "do" trick from the src folder and followed the instructions.

however, i still get the same error

[differential.o] Error 1

[Sebastiano]

quick update...
i tried to follow also the instructions ehre

http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007893.html

but now the error i get is the following:

$ make
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I../src  -I/usr/local/include  -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -D_FILE_OFFSET_BITS=64 -O3  -DNDEBUG  -pthread -I/cygdrive/c/cygdrive/c/Boost//include/boost-1_53 -I/cygdrive/c/Users/se24553/SAM_tools//include -I/cygdrive/c/Users/se24553/SAM_tools/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
g++: unrecognized option '-pthread'
In file included from /cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/multi_index/hashed_index.hpp:22:0,
                 from /cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/graph/named_graph.hpp:17,
                 from /cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/graph/adjacency_list.hpp:45,
                 from clustering.h:19,
                 from clustering.cpp:10:
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/foreach_fwd.hpp:32:2: error: ‘pait’ in namespace ‘std’ does not name a type
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/foreach_fwd.hpp:36:5: error: expected unqualified-id before ‘typedef’
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/foreach_fwd.hpp:57:23: error: ‘boost::foreach::in_range’ has not been declared
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/foreach_fwd.hpp:58:23: error: ‘boost::foreach::tag’ has not been declared
In file included from /cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/graph/named_graph.hpp:17:0,
                 from /cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/graph/adjacency_list.hpp:45,
                 from clustering.h:19,
                 from clustering.cpp:10:
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/multi_index/hashed_index.hpp:1254:19: error: ‘boost::foreach::tag’ has not been declared
In file included from common.h:24:0,
                 from hits.h:21,
                 from abundances.h:23,
                 from clustering.h:38,
                 from clustering.cpp:10:
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/foreach.hpp:170:42: error: ‘boost::foreach::tag’ has not been declared
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/foreach.hpp:174:72: error: ‘boost::foreach::tag’ has not been declared
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/foreach.hpp:178:81: error: ‘boost::foreach::tag’ has not been declared
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/foreach.hpp:182:76: error: ‘boost::foreach::tag’ has not been declared
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/foreach.hpp:186:59: error: ‘boost::foreach::tag’ has not been declared
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/foreach.hpp:196:36: error: ‘boost::foreach::tag’ has not been declared
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/system/error_code.hpp:214:36: warning: ‘boost::system::posix_category’ defined but not used
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/system/error_code.hpp:215:36: warning: ‘boost::system::errno_ecat’ defined but not used
/cygdrive/c/cygdrive/c/Boost//include/boost-1_53/boost/system/error_code.hpp:216:36: warning: ‘boost::system::native_ecat’ defined but not used
Makefile:1380: recipe for target `clustering.o' failed
make: *** [clustering.o] Error 1

..my head starts hurting..

[amarth]

It seems, that is an error after the first error

http://stackoverflow.com/questions/5535548/make-error-1-error

http://forums.fedoraforum.org/showthread.php?t=266446

As far as i understood, Error 1 comes within the "if " part of the makefile. Try to remove that "-pthread" and tell what happens!