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21Re: ssaha build on SUN5.8

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  • anthony.j.cox@talk21.com
    Oct 16, 2002
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      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
      > > >
      > > >
      > > >
      > >
      > >
      > >
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      >
      >
      > --------------------
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