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Old 08-03-2013, 05:41 AM   #1
letusgo
Member
 
Location: china

Join Date: Aug 2011
Posts: 17
Unhappy Trinity make jellyfish error

Dear All,
i downloaded trinityrnaseq_r2013-02-25.tgz. when i used "make" after "tar zxf" it, there were some errors appeared just like that:

CXX jellyfish/libjellyfish_la-parse_read.lo
./jellyfish/divisor.hpp:31: error: '__int128' does not name a type
./jellyfish/divisor.hpp: In constructor 'jellyfish::divisor64::divisor64(uint64_t)':
./jellyfish/divisor.hpp:39: error: class 'jellyfish::divisor64' does not have any field named 'm_'
./jellyfish/divisor.hpp:39: error: expected primary-expression before 'unsigned'
./jellyfish/divisor.hpp:39: error: expected `)' before 'unsigned'
./jellyfish/divisor.hpp:41: error: expected `)' at end of input
./jellyfish/divisor.hpp:41: error: expected `{' at end of input
./jellyfish/divisor.hpp: In constructor 'jellyfish::divisor64::divisor64()':
./jellyfish/divisor.hpp:46: error: class 'jellyfish::divisor64' does not have any field named 'm_'
./jellyfish/divisor.hpp: In member function 'uint64_t jellyfish::divisor64::divide(uint64_t) const':
./jellyfish/divisor.hpp:52: error: 'm_' was not declared in this scope
./jellyfish/divisor.hpp:56: error: '__int128' does not name a type
./jellyfish/divisor.hpp:57: error: 'n_' was not declared in this scope
./jellyfish/divisor.hpp: In member function 'uint64_t jellyfish::divisor64::remainder(uint64_t) const':
./jellyfish/divisor.hpp:66: error: 'm_' was not declared in this scope
./jellyfish/divisor.hpp: In member function 'void jellyfish::divisor64::division(uint64_t, uint64_t&, uint64_t&) const':
./jellyfish/divisor.hpp:81: error: 'm_' was not declared in this scope
./jellyfish/divisor.hpp: In member function 'uint64_t jellyfish::divisor64::m() const':
./jellyfish/divisor.hpp:107: error: 'm_' was not declared in this scope
make[2]: *** [jellyfish/libjellyfish_la-parse_read.lo] Error 1
make[2]: Leaving directory `/disk3/anhong/test/biosoft/trinityrnaseq_r2013-02-25/trinity-plugins/jellyfish-1.1.6'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/disk3/anhong/test/biosoft/trinityrnaseq_r2013-02-25/trinity-plugins/jellyfish-1.1.6'
make: *** [all] Error 2

how can i fix it

best wish
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Old 08-05-2013, 12:27 PM   #2
gt1
Junior Member
 
Location: Cambridge, UK

Join Date: Jul 2013
Posts: 9
Default

Quote:
Originally Posted by letusgo View Post
Dear All,
i downloaded trinityrnaseq_r2013-02-25.tgz. when i used "make" after "tar zxf" it, there were some errors appeared just like that:

CXX jellyfish/libjellyfish_la-parse_read.lo
./jellyfish/divisor.hpp:31: error: '__int128' does not name a type
./jellyfish/divisor.hpp: In constructor 'jellyfish::divisor64::divisor64(uint64_t)':
./jellyfish/divisor.hpp:39: error: class 'jellyfish::divisor64' does not have any field named 'm_'
./jellyfish/divisor.hpp:39: error: expected primary-expression before 'unsigned'
./jellyfish/divisor.hpp:39: error: expected `)' before 'unsigned'
./jellyfish/divisor.hpp:41: error: expected `)' at end of input
./jellyfish/divisor.hpp:41: error: expected `{' at end of input
./jellyfish/divisor.hpp: In constructor 'jellyfish::divisor64::divisor64()':
./jellyfish/divisor.hpp:46: error: class 'jellyfish::divisor64' does not have any field named 'm_'
./jellyfish/divisor.hpp: In member function 'uint64_t jellyfish::divisor64::divide(uint64_t) const':
./jellyfish/divisor.hpp:52: error: 'm_' was not declared in this scope
./jellyfish/divisor.hpp:56: error: '__int128' does not name a type
./jellyfish/divisor.hpp:57: error: 'n_' was not declared in this scope
./jellyfish/divisor.hpp: In member function 'uint64_t jellyfish::divisor64::remainder(uint64_t) const':
./jellyfish/divisor.hpp:66: error: 'm_' was not declared in this scope
./jellyfish/divisor.hpp: In member function 'void jellyfish::divisor64::division(uint64_t, uint64_t&, uint64_t&) const':
./jellyfish/divisor.hpp:81: error: 'm_' was not declared in this scope
./jellyfish/divisor.hpp: In member function 'uint64_t jellyfish::divisor64::m() const':
./jellyfish/divisor.hpp:107: error: 'm_' was not declared in this scope
make[2]: *** [jellyfish/libjellyfish_la-parse_read.lo] Error 1
make[2]: Leaving directory `/disk3/anhong/test/biosoft/trinityrnaseq_r2013-02-25/trinity-plugins/jellyfish-1.1.6'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/disk3/anhong/test/biosoft/trinityrnaseq_r2013-02-25/trinity-plugins/jellyfish-1.1.6'
make: *** [all] Error 2

how can i fix it

best wish
The __int128 type is an extension of the C language supported/introduced by recent versions of the GNU C compiler. As far as I can see it was introduced in GCC 4.6. You probably need a newer compiler to compile this code.
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