[mira_talk] Re: Install Mira on 10.7.5
- From: Shaun Jackman <sjackman@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 22 Oct 2012 23:24:27 -0700
Hi George,
You must link against boost_system:
make LIBS=-lboost_system-mt
Try Homebrew:
brew install mira
Cheers,
Shaun
On 2012-10-22, at 23:18, George Tsiamis <gtsiamis1@xxxxxxxxx> wrote:
> Dear all,
>
>
> I am trying to install Mira stable version 3.4.0.2 on my Mac running Lion
> 10.7.5. I have used macports to install gcc4.7, boost, expat, and flex.
>
> The commands that I give are:
>
> ./configure --with-tcmalloc=yes
>
> At the end of the configure I get
>
> --------------------------------------------------------------------------------
> Summary of MIRA configuration
> --------------------------------------------------------------------------------
>
> Linking against tcmalloc is disabled!
> Note that is the default for OS X, but you might want to try switching
> it on like this: --with-tcmalloc
>
> Building version .................................
> 3.4.0.2_prod_darwin11.4.2_x86_64_dynamic
> Production or development version?................ production
>
> We are building on ............................... Darwin
> CPU supports 64 bit? ......... ................... yes
> Compiler ......................................... gcc
> Compiler optimisation flags used ................. -O3 -funroll-loops
> Do we compile in 64 bit? ......................... yes
> Building completely static? ...................... no
> BOOST expected to compile and link?............... yes
> Linking with TCmalloc library?.................... no
>
> Can MIRA be built on this system? ................ yes
>
> Using CFLAGS : -mmacosx-version-min=10.5 -O3 -funroll-loops
> -I/usr/local/include
> Using CXXFLAGS : -DPUBLICQUIET -mmacosx-version-min=10.5 -O3 -funroll-loops
> -I/usr/local/include -pthread -I/opt/local/include
> Using LDFLAGS : -L/opt/local/lib -lboost_thread-mt -lboost_regex-mt
>
> Looks good, we do not expect compilation problems.
> --------------------------------------------------------------------------------
>
> Type 'make' to make the binaries
> and then 'make install' to install them.
>
> But then when I type "make" I get
>
> Undefined symbols for architecture x86_64:
> "boost::system::system_category()", referenced from:
> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein mira_101.o
> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein
> libmira.a(assembly.o)
> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein
> libmira.a(assembly_io.o)
> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein
> libmira.a(newpathfinder.o)
> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein libmira.a(skim.o)
> boost::mutex::lock() in libmira.a(skim.o)
> boost::unique_lock<boost::mutex>::lock() in libmira.a(skim.o)
> ...
> "boost::system::generic_category()", referenced from:
> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein mira_101.o
> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein
> libmira.a(assembly.o)
> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein
> libmira.a(assembly_io.o)
> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein
> libmira.a(newpathfinder.o)
> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein libmira.a(skim.o)
> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein
> libmira.a(assembly_swalign.o)
> global constructors keyed to _ZN12_GLOBAL__N_12_1Ein
> libmira.a(assembly_reduceskimhits.o)
> ...
> ld: symbol(s) not found for architecture x86_64
> collect2: ld returned 1 exit status
> make[2]: *** [mira_101] Error 1
> make[1]: *** [all-recursive] Error 1
> make: *** [all-recursive] Error 1
>
> and I am stuck here.
>
> I do not know what I can try next to overcome thisâ.
>
> Any suggestions?
>
> Thanks in advance
>
> George
>
>
>
>
>
> George Tsiamis, Ph.D.
> Lecturer in Environmental Microbiology
> Department of Environmental and Natural Resources Management
> University of Western Greece
> 2 Seferi str., Agrinio
> 30100, Greece
> e-mail: gtsiamis@xxxxxxxxx, gtsiamis1@xxxxxxxxx, gtsiamis@xxxxxx
> tel. +302641074149, fax. +302641074171
>
>
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