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**amarth** · 07-01-2013, 07:51 AM

Check this!!:

cufflinks source install error - SEQanswers

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

Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

Offtopic: Cufflinks runs good on windows?

**Sebastiano** · 07-01-2013, 07:57 AM

**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

Code:

[differential.o] Error 1

**Sebastiano** · 07-01-2013, 09:33 AM

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:

Code:

$ 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** · 07-01-2013, 11:42 AM

It seems, that is an error after the first error

http://stackoverflow.com/questions/5...-error-1-error

Verify you are human — FedoraForum.org

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!

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