[mira_talk] Re: Install Mira on 10.7.5
- From: George Tsiamis <gtsiamis1@xxxxxxxxx>
- To: Shaun Jackman <sjackman@xxxxxxxxx>
- Date: Tue, 23 Oct 2012 19:21:26 +0300
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 this….
>>>>
>>>> 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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>>
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