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Old 11-11-2009, 07:58 AM   #1
scozza
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Location: Colorado

Join Date: Jan 2009
Posts: 16
Default TopHat/Cufflinks on OpenSolaris?

The latest version (1.0.12) of TopHat split off the gene expression functionality into Cufflinks. While I could get TopHat 1.0.10 to compile on OpenSolaris 10 I can't get either TopHat or Cufflinks to compile. Has anyone tried to get 1.0.12 to run on OpenSolaris and succeeded? If so could you please let me know what you did to accomplish that. I realize that officially it isn't supported on that platform but it is the best platform I have available to me and TopHat had been working.

I've included some of the pertinent compilation errors just in case someone can recognize what is wrong. Thanks for any help.

-steve

TopHat compilation error:

g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -m64 -O3 -DNDEBUG -I./SeqAn-1.1 -Wall -g -m64 -O3 -DNDEBUG -MT segment_juncs.o -MD -MP -MF .deps/segment_juncs.Tpo -c -o segment_juncs.o segment_juncs.cpp
segment_juncs.cpp: In function ‘void store_read_extensions(MerExtensionTable&, int, int, const std::string&, bool)’:
segment_juncs.cpp:346: warning: comparison between signed and unsigned integer expressions
segment_juncs.cpp: At global scope:
segment_juncs.cpp:1534: error: expected ‘,’ or ‘...’ before numeric constant
segment_juncs.cpp: In constructor ‘PODSplice::PODSplice(uint32_t, uint64_t, uint64_t)’:
segment_juncs.cpp:1535: error: ‘J’ was not declared in this scope

=================

Cufflinks compilation error:
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wall -Wno-strict-aliasing -g -gdwarf-2 -m64 -O3 -DNDEBUG -pthread -I/data/mccombie/cozzas/boost_1_39_0/include -MT assemble.o -MD -MP -MF .deps/assemble.Tpo -c -o assemble.o assemble.cpp
In file included from /datafc/zfsdata/mccombie/cozzas/bin/../lib/gcc/i386-pc-solaris2.11/4.4.0/../../../../include/c++/4.4.0/backward/hash_set:59,
from /data/mccombie/cozzas/boost_1_39_0/include/boost/graph/adjacency_list.hpp:25,
from assemble.cpp:32:
/datafc/zfsdata/mccombie/cozzas/bin/../lib/gcc/i386-pc-solaris2.11/4.4.0/../../../../include/c++/4.4.0/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
In file included from assemble.cpp:42:
transitive_closure.h:39: error: reference to ‘uint16_t’ is ambiguous
/usr/include/sys/int_types.h:94: error: candidates are: typedef short unsigned int uint16_t
/data/mccombie/cozzas/boost_1_39_0/include/boost/cstdint.hpp:219: error: typedef short unsigned int boost::uint16_t
transitive_closure.h:39: error: reference to ‘uint16_t’ is ambiguous
/usr/include/sys/int_types.h:94: error: candidates are: typedef short unsigned int uint16_t
/data/mccombie/cozzas/boost_1_39_0/include/boost/cstdint.hpp:219: error: typedef short unsigned int boost::uint16_t
transitive_closure.h:39: error: ‘uint16_t’ does not name a type
transitive_closure.h:42: error: ‘v_id_size_type’ was not declared in this scope
transitive_closure.h:42: error: template argument 1 is invalid
...
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