[mira_talk] Re: Install Mira on 10.7.5
- From: Shaun Jackman <sjackman@xxxxxxxxx>
- To: George Tsiamis <gtsiamis1@xxxxxxxxx>
- Date: Tue, 23 Oct 2012 09:13:54 -0700
Hi George,
I'm working on updating MIRA in homebrew. Try
brew install
http://github.com/sjackman/homebrew/blob/mira/Library/Formula/mira.rb
Cheers,
Shaun
On 22 October 2012 23:50, George Tsiamis <gtsiamis1@xxxxxxxxx> wrote:
> Hi Shaun,
>
> Thanks for the Homebrew tip and above all your quick reply.
>
> I just installed Homebrew and run
>
> brew install mira
>
> What I get now is
>
> ==> Downloading
> http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-3.4.0.1.ta
>
> curl: (22) The requested URL returned error: 404
> Error: Download failed:
> http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-3.4.0.1.tar.bz2
>
>
> I think the problem is that at the source forge they have the 3.4.0.2version
> and not the 3.4.0.1
>
> How we can sort this out?
>
> 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
>
> On Oct 23, 2012, at 9:24 AM, Shaun Jackman wrote:
>
>> 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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