[mira_talk] Re: Compiling MIRA 3.0.3 on Mac OS X 10.6 Snow L
- From: Craig Marshall <craig.marshall@xxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 19 Mar 2010 09:02:40 +1300
Hi Peter and Bastien,
We've compiled MIRA3.0.3 (and the whole 3.x.x set of programs) without
problems. We did have problems of these kinds in earlier versions of MIRA and
these related to units of the program and elements of the libraries using the
same names. Bastien fixed these as part of the 3.0.0 upgrade.
One thing to note is that the developer tools are apparently not installed by
default when you upgrade to Snow Leopard and have to be explicitly installed.
That did cause some interesting problems when we first tried to compile MIRA
after upgrading to Snow Leopard, and it might be worth checking in your case.
Regards,
Craig
From: Bastien Chevreux <bach@xxxxxxxxxxxx<mailto:bach@xxxxxxxxxxxx>>
Subject: [mira_talk] Re: Compiling MIRA 3.0.3 on Mac OS X 10.6 Snow Leopard
Date: Wed, 17 Mar 2010 20:51:17 +0100
On Dienstag 16 März 2010 Peter wrote:
I've recently updated my Mac to Snow Leopard, and installed Boost
1.42.0 under my home directory (most of it - there was a problem with
the python bindings), and attempted to install MIRA 3.0.3 from source
as follows:
[...]
-L/Users/pjxxx//lib -lmira -lmiraEdIt -lmiraExamine -lmirasupport
-lmiraestass -lmiraerrorhandling -lmirautil -lmiradptools -lmirafio
-lmiracaf -lmiraKNN_abi373 -lm -lexpat -lz -lboost_thread -pthread
Undefined symbols:
"_eXML_Parse", referenced from:
NCBIInfoXML::readXMLFile(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&,
std::list<NCBIInfoXML::ncbitraceelements_t,
std::allocator<NCBIInfoXML::ncbitraceelements_t> >&)in
libmirafio.a(ncbiinfoxml.o)
[...]
Oh dear, my old nemesis: Apple ... and the Apple linker.
To be honest: no idea. Please try compiling 3.0.0 on that machine: if it
succeeds, then it's my fault and I'll need to ponder what I could've changed
in the build process between .0 and .3 that could break it (I'd say 'nothing',
but one never knows).
If 3.0.0 also fails ... then we have a problem. The linker apparently does not
find the 'z' and 'expat' libraries ... or perhaps a wrong version?
Try searching for different version of "libz*" and "libexpat*" on your system.
I hope there are multiple versions, because then one could think of
deactivating them one by one.
Regards,
Bastien
--
Craig Marshall craig.marshall@xxxxxxxxxxx<mailto:craig.marshall@xxxxxxxxxxx>
Biochemistry http://biochem.otago.ac.nz/staff/marshall/cmarshall.html
University of Otago Phone +64 3 479 7570 Fax +64 3 479 7866
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