[mira_talk] Re: Install Mira on 10.7.5
- From: Shaun Jackman <sjackman@xxxxxxxxx>
- To: George Tsiamis <gtsiamis1@xxxxxxxxx>
- Date: Sun, 28 Oct 2012 13:36:02 -0700
Hi George,
Sorry for the bad link. That should have been
brew install
https://raw.github.com/sjackman/homebrew/mira/Library/Formula/mira.rb
Cheers,
Shaun
On 23 October 2012 09:21, George Tsiamis <gtsiamis1@xxxxxxxxx> wrote:
> Hi Shaun,
>
> I tried the command that you mention and now I am getting
>
> pc-5:GT_Files gtsiamis$ brew install
> http://github.com/sjackman/homebrew/blob/mira/Library/Formula/mira.rb
> ########################################################################
> 100.0%
> Error: /Library/Caches/Homebrew/Formula/mira.rb:4: syntax error, unexpected
> '<'
> <!DOCTYPE html>
> ^
> /Library/Caches/Homebrew/Formula/mira.rb:5: syntax error, unexpected '<'
> <html>
> ^
> /Library/Caches/Homebrew/Formula/mira.rb:7: syntax error, unexpected '<'
> <meta charset='utf-8'>
> ^
> /Library/Caches/Homebrew/Formula/mira.rb:8: syntax error, unexpected '<'
> <meta http-equiv="X-UA-Compatible" content="IE=edge">
> ^
> /Library/Caches/Homebrew/Formula/mira.rb:8: syntax error, unexpected
> tIDENTIFIER, expecting $end
> <meta http-equiv="X-UA-Compatible" content="IE=edge">
> ^
> Please report this bug:
> https://github.com/mxcl/homebrew/wiki/troubleshooting
> /usr/local/Library/Homebrew/formula.rb:396:in `require'
> /usr/local/Library/Homebrew/formula.rb:396:in `factory'
> /usr/local/Library/Homebrew/extend/ARGV.rb:20:in `formulae'
> /usr/local/Library/Homebrew/extend/ARGV.rb:20:in `map'
> /usr/local/Library/Homebrew/extend/ARGV.rb:20:in `formulae'
> /usr/local/Library/Homebrew/cmd/install.rb:21:in `install'
> /usr/local/bin/brew:94:in `send'
> /usr/local/bin/brew:94
>
>
> Any suggestions
>
> 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 7:13 PM, Shaun Jackman wrote:
>
>> 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
>>>>>
>>>>>
>>>>> --
>>>>> You have received this mail because you are subscribed to the mira_talk
>>>>> mailing list. For information on how to subscribe or unsubscribe, please
>>>>> visit http://www.chevreux.org/mira_mailinglists.html
>>>
>
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