[mira_talk] Re: Compiling MIRA -> error
- From: "Martin A. Hansen" <mail@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 14 Aug 2009 18:59:29 +0200
OK, I got expat installed but there is still a flex snag - flex not found:
maasha@node1:~/sletmig/mira-3rc2hf2$ make
Making all in src
make[1]: Entering directory `/home/maasha/sletmig/mira-3rc2hf2/src'
Making all in lec
make[2]: Entering directory `/home/maasha/sletmig/mira-3rc2hf2/src/lec'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/home/maasha/sletmig/mira-3rc2hf2/src/lec'
Making all in io
make[2]: Entering directory `/home/maasha/sletmig/mira-3rc2hf2/src/io'
Flexing exp_flexer.flex.C
/bin/sh: flex++: command not found
make[2]: *** [exp_flexer.flex.C] Error 127
make[2]: Leaving directory `/home/maasha/sletmig/mira-3rc2hf2/src/io'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/maasha/sletmig/mira-3rc2hf2/src'
make: *** [all-recursive] Error 1
maasha@node1:~/sletmig/mira-3rc2hf2$ which flex
~/maasha_install/bin/flex
maasha@node1:~/sletmig/mira-3rc2hf2$
Martin
On Fri, Aug 14, 2009 at 6:54 PM, Martin A. Hansen <mail@xxxxxxxxx> wrote:
> OK, I got a bit further until I hit another set of errors, but those is
> probably because there is no expat on the machine I am trying to build on.
> I'll get some expat ...
>
>
> Martin
>
>
> ncbiinfoxml.H:52:19: error: expat.h: No such file or directory
> ncbiinfoxml.C: In member function ‘void NCBIInfoXML::readXMLFile(const
> std::string&, std::list<NCBIInfoXML::ncbitraceelements_t,
> std::allocator<NCBIInfoXML::ncbitraceelements_t> >&)’:
> ncbiinfoxml.C:272: error: ‘XML_Parser’ was not declared in this scope
> ncbiinfoxml.C:272: error: expected `;' before ‘parser’
> ncbiinfoxml.C:275: error: ‘parser’ was not declared in this scope
> ncbiinfoxml.C:275: error: ‘XML_SetUserData’ was not declared in this scope
> ncbiinfoxml.C:278: error: ‘XML_SetElementHandler’ was not declared in this
> scope
> ncbiinfoxml.C:279: error: ‘XML_SetCharacterDataHandler’ was not declared in
> this scope
> ncbiinfoxml.C:285: error: ‘XML_Parse’ was not declared in this scope
> ncbiinfoxml.C:285: error: ‘XML_STATUS_ERROR’ was not declared in this scope
> ncbiinfoxml.C:286: error: ‘XML_GetErrorCode’ was not declared in this scope
> ncbiinfoxml.C:286: error: ‘XML_ErrorString’ was not declared in this scope
> ncbiinfoxml.C:286: error: ‘XML_GetCurrentLineNumber’ was not declared in
> this scope
> ncbiinfoxml.C:290: error: ‘XML_ParserFree’ was not declared in this scope
> make[2]: *** [ncbiinfoxml.o] Error 1
> make[2]: Leaving directory `/home/maasha/sletmig/mira-3rc2hf2/src/io'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/home/maasha/sletmig/mira-3rc2hf2/src'
> make: *** [all-recursive] Error 1
>
>
>
>
>
>
>
> On Fri, Aug 14, 2009 at 6:42 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote:
>
>> On Freitag 14 August 2009 Martin A. Hansen wrote:
>> > Nay, that didn't help. Same error.
>>
>> That's because there should be an additional "/include" at the end of each
>> line and then it should work.
>>
>> Anyway, I recreated an environment similar to yours (don't I just love
>> virtual
>> machines) and have found a way to compile painless for these cases ... I
>> think.
>>
>> Can you please download
>>
>> http://www.chevreux.org/tmp/mira-3rc2hf2.tar.bz2
>>
>> and try to compile that? You shouldn't need to remove old *flex.C there
>> and it
>> should also compile gracefully with your type of flex installation.
>>
>> Please do NOT use the resulting executable as I'm currently busy at
>> another
>> site and I haven't checked whether I took back some changes that I made to
>> debug a few things.
>>
>> If everything compiles ok for you, the changes would make it to rc3 (this
>> week-end, I hope).
>>
>> Regards,
>> Bastien
>>
>>
>> --
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>
>
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