Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • errors during installing mira on suse 10

    I’m trying to comply mira 3.4.1 on a cluster computer with suse 10 Linux system. We’ve upgraded boost and flex to the latest version before complying. Since I do not have the administrator authority, necessary libs were installed under $Home/bin.
    The locations of the newly-installed libs were informed using option switches as listed below: “./configure --prefix=/public/home/zhaozengfang/software/mira --with-boost=/public/home/zhaozengfang/software/boost148/ --with-boost-libdir=/public/home/zhaozengfang/software/boost148/lib/ --with-tcmalloc-dir=/public/home/zhaozengfang/software/gperf/lib --enable-64=yes --enable-mirastatic”. It seems OK for this step. The system reported that everything looks good.
    However, during make step, several errors occurred. I failed to install mira on the MPI computer. The error message were given:

    ##########################
    g++ -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"3.4.0.1\" -DPACKAGE_STRING=\"mira\ 3.4.0.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"3.4.0.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DDEVELOPMENTVERSION=0 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I. -I../../src -DPUBLICQUIET -DAJ_Linux64 -I/public/home/zhaozengfang/software/mira/include -O3 -funroll-loops -I/public/home/zhaozengfang/software/expat/include -pthread -I/public/home/zhaozengfang/software/boost148//include -MT exp_flexer.o -MD -MP -MF .deps/exp_flexer.Tpo -c -o exp_flexer.o exp_flexer.cc
    exp_flexer.cc:325:25: error: no ?.nt EXPFlexLexer::yywrap()?.member function declared in class ?.XPFlexLexer?
    exp_flexer.cc: In member function ?.irtual int EXPFlexLexer::yylex()?.
    exp_flexer.cc:1313:19: error: ?.ywrap?.was not declared in this scope
    exp_flexer.cc: In member function ?.nt EXPFlexLexer::yyinput()?.
    exp_flexer.cc:1732:20: error: ?.ywrap?.was not declared in this scope
    make[2]: *** [exp_flexer.o] Error 1
    make[2]: Leaving directory `/public/home/zhaozengfang/software/mira-3.4.0.1/src/io'
    make[1]: *** [all-recursive] Error 1
    make[1]: Leaving directory `/public/home/zhaozengfang/software/mira-3.4.0.1/src'
    make: *** [all-recursive] Error 1
    ###########################

    There may be something wrong for flex. I’ve tried my best to fix the problem including add the new libs into environmental variables, but still failed.
    The config.log were attached, I’m grateful if you can give me some help.
    Attached Files

  • #2
    You might want to consult the MIRA mailing list. http://chevreux.org/mira_mailinglists.html


    Comment


    • #3
      Thanks a lot for the information

      Comment


      • #4
        It would have been nice to cross link your email and this thread:


        Originally posted by qingdaoalbert View Post
        There may be something wrong for flex.
        Yes.

        Comment


        • #5
          Thanks a lot for the advices, the problem has been resolved following the information from http://www.freelists.org/post/mira_t...my-configlog,7

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Current Approaches to Protein Sequencing
            by seqadmin


            Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
            04-04-2024, 04:25 PM
          • seqadmin
            Strategies for Sequencing Challenging Samples
            by seqadmin


            Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
            03-22-2024, 06:39 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 04-11-2024, 12:08 PM
          0 responses
          30 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 10:19 PM
          0 responses
          32 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 09:21 AM
          0 responses
          28 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-04-2024, 09:00 AM
          0 responses
          52 views
          0 likes
          Last Post seqadmin  
          Working...
          X