MIRA on Mac OS X

[ondovb]

Has anyone gotten MIRA to work on OS X?

I found this post that implies that it should work.

However, I'm having trouble with the Boost library. I tried staging the latest version (1.4.2) and setting $BOOST_ROOT, but MIRA's configure script couldn't find it. I would have installed it, as recommended, but I can't figure out how to. Boost 1.4.2 has no makefile or configure script, and the docs just say "often, there's nothing to build". They list some libraries (such as thread, which MIRA needs) that have to be built, but they don't say how to build them. I tried going back to Boost 1.35 (the minimum required for MIRA). This version at least has a configure script, but it throws a bunch of errors when making, and then MIRA's configure script says "BOOST thread lib must be available".

Anyone have better luck?

[maubp]

Which Mac OS X are you using? Snow Leopard?

A while back under Leopard (Mac OS X 10.5) I installed BOOST 1.4.0 (the latest at the time) and managed to compile and run the then latest pre-release MIRA v3rc4. But only in 32bit mode

I'm now on Snow Leopard (which is more 64bit than Leopard was) and plan to try the latest MIRA shortly...

[ondovb]

Yeah, it's Snow Leopard. I finally figured out how to build Boost 1.4.2 (you have to use their tool, BJam), but that failed on a bunch of libraries, including thread. The errors were all "ld: unknown option: -R".

[maubp]

Yeah, it's Snow Leopard. I finally figured out how to build Boost 1.4.2 (you have to use their tool, BJam), but that failed on a bunch of libraries, including thread. The errors were all "ld: unknown option: -R".

They do document the fact you have to use bjam (even if it could be much clearer). What I used was just:

cd boost_1_42_0
./bootstrap.sh
./bjam
./bjam install --prefix=/Users/myusername/

However, I had a problem with the Python bindings (which I think is a 64bit issue as the error message was about the Apple provided Python 2.5 not their 64-bit capable Python 2.6):

...failed updating 56 targets...
...skipped 5 targets...
...updated 7743 targets...

I don't think we need to worry about the Boost Python stuff for MIRA.

[maubp]

See also:

http://www.freelists.org/post/mira_talk/Compiling-MIRA-303-on-Mac-OS-X-106-Snow-Leopard

[maubp]

I ran into some issues with multiple copies of libexpat (apparently from Apple, BOOST and EMBOSS). I tried to get rid of my out of date EMBOSS, and removed the full BOOST install. I was able to simplify the BOOST installation to just this:

cd boost_1_42_0
./bootstrap.sh --with-libraries=thread
./bjam
./bjam install --prefix=/Users/myusername

I am now able to install a working MIRA 3.0.0 on Snow Leopard, but not 3.0.1, 3.0.2 or 3.0.3 (which all fail immediately with an abort trap). I'm still investigating (with Bastein etc).

An error is occurring during static initialisation, before even the main()
starts. The code for this is new in 3.0.1 and works flawlessly on Linux and
other MacOS ... "This is not supposed to happen." [tm]

I'm not entirely sure, but I wouldn't search the cause for this in libraries.
looks like a weird compiler or linker bug.

I'll send you some files this evening to try out a few things, but let's take
this discussion offline now (and post a summary later), it's probably not
interesting for most of the subscribers.

Other uses on the MIRA talk mailing list report MIRA 3.0.0 though 3.0.3 all building and working fine on Snow Leopard - so this isn't a general issue.

[maubp]

Other uses on the MIRA talk mailing list report MIRA 3.0.0 though 3.0.3 all building and working fine on Snow Leopard - so this isn't a general issue.

That turned out to be a miss-communication. To summarise:

• MIRA 3.0.0 works on Mac OS 10.6 Snow Leopard (but has some known issues fixed in the later point releases).
  
• MIRA 3.0.1, 3.0.2 and 3.0.3 all fail on the Mac (they compile but when run immediately abort).
  
• Bastien has tracked down the cause of the problem, and seems to have fixed it on the development branch.

In order to compile MIRA on Mac OS 10.6 Snow Leopard you can use the Apple provided libexpat (which will be detected automatically if there are no other versions present). You don't need all of BOOST, install just the threading library. I choose to install this under my home directory rather than at the system level:

cd boost_1_42_0
./bootstrap.sh --with-libraries=thread
./bjam
./bjam install --prefix=/Users/myusername

Then to compile MIRA,

cd mira-3.0.0
./configure --with-boost=/Users/myusername
make
make check

Peter

[ondovb]

Thanks for the help. I now have 3.0.0 running an assembly.

[maubp]

To summarise:

• MIRA 3.0.0 works on Mac OS 10.6 Snow Leopard (but has some known issues fixed in the later point releases).
  
• MIRA 3.0.1, 3.0.2 and 3.0.3 all fail on the Mac (they compile but when run immediately abort).
  
• Bastien has tracked down the cause of the problem, and seems to have fixed it on the development branch.

I've just compiled the just released MIRA 3.0.5 (using the method described earlier on this thread), and it seems to work

[carcalas]

Need help, please!!!!!!

Hi friends,
I have a problem with MIRA-3.2.0rc2, and I would be very grateful to you if you can help me. I am a novel user of Unix, and so my knowledge is very very limited. I have a Mac with system 10.5.8. First of all, I had to install the Xcode tools because gcc was not available by default. But one solved this problem, I had the following error when executing ./configure:

checking whether the Boost::Thread library is available... no

+++++++++++++++++++++++++++++++++++++
BOOST_CPPFLAGS: -I/include/boost-0
BOOST LDFLAGS: -L/lib
ac_boost_path: /opt/local
ac_boost_lib_path:
BOOST_THREAD_LIB:
CFLAGS now: -O2
CXXFLAGS now: -O2
LDFLAGS now: -L/usr/lib
+++++++++++++++++++++++++++++++++++++
Automatic recognition of Boost thread lib failed? I have
////// BOOST_CPPFLAGS: -I/include/boost-0
////// BOOST LDFLAGS: -L/lib
////// ac_boost_path: /opt/local
////// ac_boost_lib_path:
////// BOOST_THREAD_LIB:
////// BOOST_ROOT:
Please give the configure script the location of your BOOST
libraries. Or, if needed, the name of your thread library (without
'lib' in front):
--with-boost=DIR
or --with-boost-libdir=LIB_DIR
or --with-boost-thread=special-lib

configure: error: Stopping here as BOOST thread lib must be available at this stage. Sorry.

I previouslly installed boost 1.44 thinking that with this application all was OK. Do you know the reason why I cannot configure MIRA? Can you help me?.
Please, try to explain with as much details as possible, as I have commented before, I have no experience with Unix.
Thanks a lot in advance.

[maubp]

Hi friends,
I have a problem with MIRA-3.2.0rc2, ... the following error when executing ./configure:

checking whether the Boost::Thread library is available... no
...

I previouslly installed boost 1.44 thinking that with this application all was OK.

Where did you install BOOST? Since MIRA can't find it, you will have to tell MIRA where to look using the --with-boost argument to configure.

[carcalas]

I located the folder in the desktop. May be this is the problem?. Where do I have to put the folder, inside the mira folder?.
Thanks a lot again

[maubp]

You don't just unzip the BOOST files into a folder - it has to be compiled. Have you tried the method I gave earlier in this thread? See post 7:

http://seqanswers.com/forums/showpost.php?p=16181&postcount=7

[carcalas]

Thanks a lot for your fast reponse. I compiled Boost following the instructions I found in a forum:

1. The first thing to do is to download the Boost distribution from the Boost downloads page.
2. Unpack the archive somewhere sensible, I’d suggest the desktop. Don’t do it where the absolute folder path will have any spaces in the name e.g. “/users/matt/code/bad folder/”, this will prevent the install script from working later. I found this out the hard way.
3. Next open a terminal window and navigate to the Boost root folder you just unpacked, it will be called “boost_1_39_0″ if you are using the current version. If it’s on your desktop you will need to use “cd /users/username/desktop/boost_1_39_0“. We refer to this path in future as the $BOOST_ROOT
4. Next run the bootstrap script by typing “./bootstrap.sh“. This configures the install tools for your environment. Check it for error messages, this is where I found out my path was bad.
5. If you run the “ls” command you should now have an executable called bjam.
6. To compile Boost, type “./bjam architecture=combined” and press enter, this will build Universal (x86 and PowerPC compatible) libraries.
7. Make a cup of coffee and wait while the libraries build.

Is this OK?. I did it exactly as indicated in these instructions, including point 7.

[maubp]

OK. Were there any errors? Where did it put the files?

e.g. Can you find libboost_thread.dylib (and note that Spotlight may not check the system folders - try looking in /local/usr/lib as a guess).