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Re: ssaha build on SUN5.8

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  • anthony.j.cox@talk21.com
    Hi Will/Sheldon, I compiled and tested the software on gcc 3.0.2 (I think). gcc 3.1 wasn t available at the time and I think it s a bit more picky. I don t
    Message 1 of 4 , Oct 16, 2002
      Hi Will/Sheldon,

      I compiled and tested the software on gcc 3.0.2 (I think). gcc 3.1 wasn't available at the time and I think it's a bit more picky. I don't have a Sun to test this on, but I think line 78 in HashTableGeneric.h needs to change to

      push back( string(") ); return back();

      I don't think it likes the lack of a constructor argument for the string.

      Failing that try
      push_back("); return back();
      or
      push_back((string)"); return back();

      Hope that helps, let me know if problems continue.

      Tony Cox



      > Hi Sheldon,
      >
      >Sorry about the delay in replying. Form the errors it looks like there is
      >some library incompatibility. What version of libc are you using? It's not
      >the compiler, the latest ssaha builds fine on gcc3.
      >
      >I've cc'ed Tony Cox on this mail, and he may have some better idea what
      >the problem is.
      >
      >Also, you may want to post to the ssahausers group:
      >
      > <a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/''>http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/'</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/'>http://groups.yahoo.com/group/ssahausers/</a></a>
      >
      >Regards,
      >
      >William
      >
      >
      >
      >---
      >Dr William Spooner whs@...
      >Ensembl Web Developer <a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org''>http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org'</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org'>http://www.ensembl.org</a></a>
      >
      >On Wed, 9 Oct 2002, Sheldon Briand wrote:
      >
      > Hi,
      >
      > I'm trying to build ssaha on a SUN SPARC 5.8 machine. I'm using gcc 3.1
      > and I've run into the following error:
      >
      > In file included from
      > /t3-02/software/external/SSAHA/HashTable/HashTable.h:37,
      > from
      > /t3-02/software/external/SSAHA/Global/GlobalDefinitions.cpp:35:
      > /t3-02/software/external/SSAHA/HashTable/HashTableGeneric.h: In member
      > function
      > `std::string& NameReaderLocal::lastName()':
      > /t3-02/software/external/SSAHA/HashTable/HashTableGeneric.h:78: no
      > matching
      > function for call to `NameReaderLocal::push_back()'
      > /usr/local/include/g++-v3/bits/stl_vector.h:490: candidates are: void
      > std::vector<_Tp, _Alloc>::push_back(const _Tp&) [with _Tp =
      > std::string,
      > _Alloc = std::allocator<std::string>]
      > make: *** [GlobalDefinitions.o] Error 1
      >
      > This occurs when I run a make ssaha. No changes were made to the
      > distributed makefile. Any ideas as to what is occuring here?
      >
      > Thanks,
      > -Sheldon
      >
      >
      > --
      > Sheldon Briand
      > Computer Support
      > Canadian Bioinformatics Resource
      > Halifax, Nova Scotia
      > CANADA
      > email: sheldon@...
      > phone: (902)-426-1677
      >
      >
      >



      --------------------
      talk21 your FREE portable and private address on the net at http://www.talk21.com
    • anthony.j.cox@talk21.com
      Hi Will/Sheldon, I compiled and tested the software on gcc 3.0.2 (I think). gcc 3.1 wasn t available at the time and I think it s a bit more picky. I don t
      Message 2 of 4 , Oct 16, 2002
        Hi Will/Sheldon,

        I compiled and tested the software on gcc 3.0.2 (I think). gcc 3.1 wasn't available at the time and I think it's a bit more picky. I don't have a Sun to test this on, but I think line 78 in HashTableGeneric.h needs to change to

        push back( string("") ); return back();

        I don't think it likes the lack of a constructor argument for the string.

        Failing that try
        push_back(""); return back();
        or
        push_back((string)""); return back();

        Hope that helps, let me know if problems continue.

        Tony Cox



        > Hi Sheldon,
        >
        >Sorry about the delay in replying. Form the errors it looks like there is
        >some library incompatibility. What version of libc are you using? It's not
        >the compiler, the latest ssaha builds fine on gcc3.
        >
        >I've cc'ed Tony Cox on this mail, and he may have some better idea what
        >the problem is.
        >
        >Also, you may want to post to the ssahausers group:
        >
        > <a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/''>http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/'</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/'>http://groups.yahoo.com/group/ssahausers/</a></a>
        >
        >Regards,
        >
        >William
        >
        >
        >
        >---
        >Dr William Spooner whs@...
        >Ensembl Web Developer <a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org''>http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org'</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org'>http://www.ensembl.org</a></a>
        >
        >On Wed, 9 Oct 2002, Sheldon Briand wrote:
        >
        > Hi,
        >
        > I'm trying to build ssaha on a SUN SPARC 5.8 machine. I'm using gcc 3.1
        > and I've run into the following error:
        >
        > In file included from
        > /t3-02/software/external/SSAHA/HashTable/HashTable.h:37,
        > from
        > /t3-02/software/external/SSAHA/Global/GlobalDefinitions.cpp:35:
        > /t3-02/software/external/SSAHA/HashTable/HashTableGeneric.h: In member
        > function
        > `std::string& NameReaderLocal::lastName()':
        > /t3-02/software/external/SSAHA/HashTable/HashTableGeneric.h:78: no
        > matching
        > function for call to `NameReaderLocal::push_back()'
        > /usr/local/include/g++-v3/bits/stl_vector.h:490: candidates are: void
        > std::vector<_Tp, _Alloc>::push_back(const _Tp&) [with _Tp =
        > std::string,
        > _Alloc = std::allocator<std::string>]
        > make: *** [GlobalDefinitions.o] Error 1
        >
        > This occurs when I run a make ssaha. No changes were made to the
        > distributed makefile. Any ideas as to what is occuring here?
        >
        > Thanks,
        > -Sheldon
        >
        >
        > --
        > Sheldon Briand
        > Computer Support
        > Canadian Bioinformatics Resource
        > Halifax, Nova Scotia
        > CANADA
        > email: sheldon@...
        > phone: (902)-426-1677
        >
        >
        >



        --------------------
        talk21 your FREE portable and private address on the net at http://www.talk21.com
      • anthony.j.cox@talk21.com
        Sorry Sheldon, there was a typo in my previous post. I noticed it just as I pressed send , I cancelled the mail, corrected it and sent a revised version, but
        Message 3 of 4 , Oct 16, 2002
          Sorry Sheldon, there was a typo in my previous post. I noticed it just as I pressed "send", I cancelled the mail, corrected it and sent a revised version, but somehow two mails seem to have been sent out, both containing the mistake. Sorry about that. Annyyyyway, the three possibilities to try are:

          push back( string("") ); return back();
          push_back(""); return back();
          push_back((string)""); return back();

          Tony Cox

          > Hope that helps, let me know if problems continue.
          >
          > Tony Cox
          >
          >
          >
          > > Hi Sheldon,
          > >
          > >Sorry about the delay in replying. Form the errors it looks like there is
          > >some library incompatibility. What version of libc are you using? It's not
          > >the compiler, the latest ssaha builds fine on gcc3.
          > >
          > >I've cc'ed Tony Cox on this mail, and he may have some better idea what
          > >the problem is.
          > >
          > >Also, you may want to post to the ssahausers group:
          > >
          > > <a Target='_new' Href='<a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/'''>http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/''</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/''>http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/'</a></a<a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/''>http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/'</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/'>http://groups.yahoo.com/group/ssahausers/</a></a</a>
          > >
          > >Regards,
          > >
          > >William
          > >
          > >
          > >
          > >---
          > >Dr William Spooner whs@...
          > >Ensembl Web Developer <a Target='_new' Href='<a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org'''>http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org''</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org''>http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org'</a></a<a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org''>http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org'</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org'>http://www.ensembl.org</a></a</a>
          > >
          > >On Wed, 9 Oct 2002, Sheldon Briand wrote:
          > >
          > > Hi,
          > >
          > > I'm trying to build ssaha on a SUN SPARC 5.8 machine. I'm using gcc 3.1
          > > and I've run into the following error:
          > >
          > > In file included from
          > > /t3-02/software/external/SSAHA/HashTable/HashTable.h:37,
          > > from
          > > /t3-02/software/external/SSAHA/Global/GlobalDefinitions.cpp:35:
          > > /t3-02/software/external/SSAHA/HashTable/HashTableGeneric.h: In member
          > > function
          > > `std::string& NameReaderLocal::lastName()':
          > > /t3-02/software/external/SSAHA/HashTable/HashTableGeneric.h:78: no
          > > matching
          > > function for call to `NameReaderLocal::push_back()'
          > > /usr/local/include/g++-v3/bits/stl_vector.h:490: candidates are: void
          > > std::vector<_Tp, _Alloc>::push_back(const _Tp&) [with _Tp =
          > > std::string,
          > > _Alloc = std::allocator<std::string>]
          > > make: *** [GlobalDefinitions.o] Error 1
          > >
          > > This occurs when I run a make ssaha. No changes were made to the
          > > distributed makefile. Any ideas as to what is occuring here?
          > >
          > > Thanks,
          > > -Sheldon
          > >
          > >
          > > --
          > > Sheldon Briand
          > > Computer Support
          > > Canadian Bioinformatics Resource
          > > Halifax, Nova Scotia
          > > CANADA
          > > email: sheldon@...
          > > phone: (902)-426-1677
          > >
          > >
          > >
          >
          >
          >
          > --------------------
          > talk21 your FREE portable and private address on the net at <a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://www.talk21.com'>http://www.talk21.com</a>
          >
          >
          >



          --------------------
          talk21 your FREE portable and private address on the net at http://www.talk21.com
        • anthony.j.cox@talk21.com
          Hi Sheldon, Another case of the new compiler being fussier I think. In this case it doesn t like default function parameters being specified in the source file
          Message 4 of 4 , Oct 16, 2002
            Hi Sheldon,

            Another case of the new compiler being fussier I think. In this case it doesn't like default function parameters being specified in the source file as well as the header file. I think you just need to remove the "=NULL" from lines 486 and 553 of HashTableGeneric.cpp.

            Looks like it's time for me to download a more up-to-date version of gcc ... (I'm still using 2.96.2)

            Tony

            > Hi,
            >
            >Yeah I figured that's what you meant. I tried it and got the following
            >errors laterin the build process(it does proceed much further though):
            >
            >/t3-02/software/external/SSAHA/HashTable/HashTableGeneric.cpp: At global
            >scope:
            >/t3-02/software/external/SSAHA/HashTable/HashTableGeneric.cpp:486: default
            > argument given for parameter 2 of `HashTableGeneric*
            > HashTableFactory::loadHashTable(const std::string&, SourceReaderIndex*
            >= 0)'
            >/t3-02/software/external/SSAHA/HashTable/HashTableGeneric.h:443: after
            >previous
            > specification in `HashTableGeneric*
            >HashTableFactory::loadHashTable(const
            > std::string&, SourceReaderIndex* = 0)'
            >/t3-02/software/external/SSAHA/HashTable/HashTableGeneric.cpp:553: default
            > argument given for parameter 1 of `void
            > HashTableGeneric::loadHashTable(SourceReaderIndex* = 0)'
            >/t3-02/software/external/SSAHA/HashTable/HashTableGeneric.h:261: after
            >previous
            > specification in `virtual void
            > HashTableGeneric::loadHashTable(SourceReaderIndex* = 0)'
            >make: *** [HashTableGeneric.o] Error 1
            >
            >Thanks,
            >-Sheldon
            >
            >
            >
            >Sheldon Briand
            >Computer Support
            >Canadian Bioinformatics Resource
            >Halifax, Nova Scotia
            >CANADA
            >email: sheldon@...
            >phone: (902)-426-1677
            >
            >On Wed, 16 Oct 2002 anthony.j.cox@... wrote:
            >
            > Sorry Sheldon, there was a typo in my previous post. I noticed it just as I pressed "send", I cancelled the mail, corrected it and sent a revised version, but somehow two mails seem to have been sent out, both containing the mistake. Sorry about that. Annyyyyway, the three possibilities to try are:
            >
            > push back( string(") ); return back();
            > push_back("); return back();
            > push_back((string)"); return back();
            >
            > Tony Cox
            >
            > > Hope that helps, let me know if problems continue.
            > >
            > > Tony Cox
            > >
            > >
            > >
            > > > Hi Sheldon,
            > > >
            > > >Sorry about the delay in replying. Form the errors it looks like there is
            > > >some library incompatibility. What version of libc are you using? It's not
            > > >the compiler, the latest ssaha builds fine on gcc3.
            > > >
            > > >I've cc'ed Tony Cox on this mail, and he may have some better idea what
            > > >the problem is.
            > > >
            > > >Also, you may want to post to the ssahausers group:
            > > >
            > > > <a Target='_new' Href='<a Target='_new' Href='<a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/''''>http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/'''</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/'''>http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/''</a></a<a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/'''>http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/''</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/''>http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/'</a></a</a<a Target='_new' Href='<a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/'''>http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/''</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/''>http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/'</a></a<a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/''>http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/'</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://groups.yahoo.com/group/ssahausers/'>http://groups.yahoo.com/group/ssahausers/</a></a</a</a>
            > > >
            > > >Regards,
            > > >
            > > >William
            > > >
            > > >
            > > >
            > > >---
            > > >Dr William Spooner whs@...
            > > >Ensembl Web Developer <a Target='_new' Href='<a Target='_new' Href='<a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org''''>http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org'''</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org'''>http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org''</a></a<a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org'''>http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org''</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org''>http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org'</a></a</a<a Target='_new' Href='<a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org'''>http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org''</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org''>http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org'</a></a<a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org''>http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org'</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://www.ensembl.org'>http://www.ensembl.org</a></a</a</a>
            > > >
            > > >On Wed, 9 Oct 2002, Sheldon Briand wrote:
            > > >
            > > > Hi,
            > > >
            > > > I'm trying to build ssaha on a SUN SPARC 5.8 machine. I'm using gcc 3.1
            > > > and I've run into the following error:
            > > >
            > > > In file included from
            > > > /t3-02/software/external/SSAHA/HashTable/HashTable.h:37,
            > > > from
            > > > /t3-02/software/external/SSAHA/Global/GlobalDefinitions.cpp:35:
            > > > /t3-02/software/external/SSAHA/HashTable/HashTableGeneric.h: In member
            > > > function
            > > > `std::string& NameReaderLocal::lastName()':
            > > > /t3-02/software/external/SSAHA/HashTable/HashTableGeneric.h:78: no
            > > > matching
            > > > function for call to `NameReaderLocal::push_back()'
            > > > /usr/local/include/g++-v3/bits/stl_vector.h:490: candidates are: void
            > > > std::vector<_Tp, _Alloc>::push_back(const _Tp&) [with _Tp =
            > > > std::string,
            > > > _Alloc = std::allocator<std::string>]
            > > > make: *** [GlobalDefinitions.o] Error 1
            > > >
            > > > This occurs when I run a make ssaha. No changes were made to the
            > > > distributed makefile. Any ideas as to what is occuring here?
            > > >
            > > > Thanks,
            > > > -Sheldon
            > > >
            > > >
            > > > --
            > > > Sheldon Briand
            > > > Computer Support
            > > > Canadian Bioinformatics Resource
            > > > Halifax, Nova Scotia
            > > > CANADA
            > > > email: sheldon@...
            > > > phone: (902)-426-1677
            > > >
            > > >
            > > >
            > >
            > >
            > >
            > > --------------------
            > > talk21 your FREE portable and private address on the net at <a Target='_new' Href='<a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://talk21.btopenworld.com/redirect.html?http://www.talk21.com''>http://talk21.btopenworld.com/redirect.html?http://www.talk21.com'</a>><a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://www.talk21.com'>http://www.talk21.com</a></a>
            > >
            > >
            > >
            >
            >
            >
            > --------------------
            > talk21 your FREE portable and private address on the net at <a Target='_new' Href='http://talk21.btopenworld.com/redirect.html?http://www.talk21.com'>http://www.talk21.com</a>
            >
            >
            >



            --------------------
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