Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • letusgo
    Member
    • Aug 2011
    • 17

    #1

    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
  • gt1
    Junior Member
    • Jul 2013
    • 9

    #2
    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.

    Comment

    Latest Articles

    Collapse

    • kinpict.com
      Reply to 16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
      by kinpict.com
      The part about this topic feels surprisingly grounded, and the details on the page is the bit that made me slow down. I’d keep <a href="https://kinpict.com/">ai family photo generator</a> bookmarked for later.
      Today, 06:37 PM
    • SEQadmin2
      16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
      by SEQadmin2





      NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...
      10-30-2026, 06:46 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by SEQadmin2, 11-12-2026, 07:59 AM
    0 responses
    27 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 11-05-2026, 09:25 AM
    0 responses
    35 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 11-03-2026, 11:54 AM
    2 responses
    56 views
    0 reactions
    Last Post kinpict.com  
    Started by SEQadmin2, 10-28-2026, 09:57 AM
    0 responses
    175 views
    0 reactions
    Last Post SEQadmin2  
    Working...