[Mrtrix-discussion] having trouble building on CentOS 6

Donald Tournier d.tournier at brain.org.au
Tue Mar 19 16:51:27 PDT 2013 

Hi Henry,

Yes, that package was for CentOS6, not RHEL6 as such. I'd expect it to work
just as well though, given that (as far as I know) CentOS6 is based on
RHEL6 - it certainly looks that way from that link I posted. I guess to
install that package you'd have to add the CentOS6 repository to your RPM
manager's list (not sure how to do this), or download all of the CentOS6
-devel packages manually...

Another option similar to Luis' is to grab a compiled version from a
similar system where the dependencies are available, and bring over all of
the missing runtime stuff with it. For example, you could:

   - set up a CentOS6 system (either in a chroot or a VM)
   - compile MRtrix
   - find out what all the relevant runtime dependencies are (e.g. using
   the command "ldd bin/mrview")
   - locate those libaries that don't already exist on your RHEL6 system
   - copy these libraries into the MRtrix lib/ folder, alongside the MRtrix
   library itself
   - copy the bin/ and lib/ folder over to your RHEL6 installation (for the
   lib/ folder, you only need to copy over the actual libraries, not the code)
   - on your RHEL6 system, set up LD_LIBRARY_PATH to point to the MRtrix
   lib/ folder, or set up ldconfig, as you normally would for a standard
   install (the MRtrix library needs to be in the linker search path anyway).

I managed to get FSLView working on more recent non-Qt3 distros that way
(Ubuntu 12.04 & Arch). It is a bit of work, but actually not all that much
once you've figured out what needs to be done. Certainly no more work than
the full schroot option typically suggested to get around this issue, and
also in my opinion a cleaner solution...

Hope that helps.
Cheers,

Donald.



On 20 March 2013 10:24, Luis Concha <lconcha at unam.mx> wrote:

> I really hope you do get it compiled natively, but I thought I'd clarify
> my previous post. I am not suggesting that you install ubuntu, but rather
> that you have a schroot debian environment _inside_ your CentOS.
>
> Sort of this:
> http://neuro.debian.net/blog/2011/2011-12-12_schroot_fslview.html
>
> This way, you have your debian binaries running alongside the RHEL ones,
> and both of them are native. Consider this a tentative plan B.
>
> Luis
>
> Dr. Luis Concha
> Instituto de Neurobiología
> Laboratorio C-12
> UNAM, Campus Juriquilla
> Boulervard Juriquilla 3001
> Juriquilla, Querétaro.
> C.P. 76230
> México
> Tel (442) 2 38 10 53
> Fax (442) 2 38 10 46
> www.inb.unam.mx
>
>
> On Tue, Mar 19, 2013 at 5:19 PM, Henry Mensch <Henry.Mensch at va.gov> wrote:
>
>> That's what I expected, too, but RHEL doesn't come with the -devel
>> bundles for this stuff:
>>
>> [root at musca dx-4.4.4]# yum -y install gtkmm24-devel
>> Loaded plugins: refresh-packagekit, rhnplugin
>> This system is receiving updates from RHN Classic or RHN Satellite.
>> Setting up Install Process
>> No package gtkmm24-devel available.
>> Error: Nothing to do
>> [root at musca dx-4.4.4]# yum -y install gtkmm24-devel-2.18.2-1
>> Loaded plugins: refresh-packagekit, rhnplugin
>> This system is receiving updates from RHN Classic or RHN Satellite.
>> Setting up Install Process
>> No package gtkmm24-devel-2.18.2-1 available.
>> Error: Nothing to do
>> [root at musca dx-4.4.4]# yum -y list gtkmm\*
>> Loaded plugins: refresh-packagekit, rhnplugin
>> This system is receiving updates from RHN Classic or RHN Satellite.
>> Installed Packages
>> gtkmm24.x86_64     2.18.2-1.el6
>> @anaconda-RedHatEnterpriseLinux-201009221801.x86_64/6.0
>>
>> so it's not clear to me where what you found actually comes from.
>>
>> On Mar 19, 2013, at 4:10 PM, Donald Tournier wrote:
>>
>> > OK, I just did a very quick search and I think I know where the problem
>> is. These packages typically come in pairs: runtime and development. The
>> runtime would only contain the libraries, and the development package
>> should contain everything needed to compile against it, including headers
>> and hopefully the relevant pkg-config file. I came across this on my
>> search:
>> http://pkgs.org/centos-6-rhel-6/centos-rhel-i386/gtkmm24-devel-2.18.2-1.el6.i686.rpm.html- looks like it might fit the bill...?
>> >
>> > Cheers,
>> >
>> > Donald.
>> >
>> >
>> >
>> > On 20 March 2013 09:44, Henry Mensch <Henry.Mensch at va.gov> wrote:
>> > No, they don't. The files aren't there, and they're not in the packages.
>> >
>> > On Mar 19, 2013, at 3:35 PM, Donald Tournier wrote:
>> >
>> > > Assuming these files do exist, then it should be a simple matter of
>> making sure pkg-config knows where to look for them - you should be able to
>> set the PKG_CONFIG_PATH to achieve that, at least according the pkg-config
>> man page.
>> > > On Tue, Mar 19, 2013 at 3:40 PM, Henry Mensch <Henry.Mensch at va.gov>
>> wrote:
>> > > I'm on a CentOS 6 system:
>> > >
>> > > Linux musca 2.6.32-358.0.1.el6.x86_64 #1 SMP Wed Feb 20 11:05:23 EST
>> 2013 x86_64 x86_64 x86_64 GNU/Linux
>> > >
>> > > and I'm trying to build … the build fails early with these errors:
>> > >
>> > > [root at musca mrtrix-0.2.10]# ./build
>> > > Package glibmm-2.4 was not found in the pkg-config search path.
>> > > Perhaps you should add the directory containing `glibmm-2.4.pc'
>> > > to the PKG_CONFIG_PATH environment variable
>> > > No package 'glibmm-2.4' found
>> > > WARNING: unable to find glibmm-2.4,gthread-2.0 configuration
>> > > Package gtkmm-2.4 was not found in the pkg-config search path.
>> > > Perhaps you should add the directory containing `gtkmm-2.4.pc'
>> > > to the PKG_CONFIG_PATH environment variable
>> > > No package 'gtkmm-2.4' found
>> > > WARNING: unable to find gtkmm-2.4 configuration
>> > > Package gtkmm-2.4 was not found in the pkg-config search path.
>> > > Perhaps you should add the directory containing `gtkmm-2.4.pc'
>> > > to the PKG_CONFIG_PATH environment variable
>> > > No package 'gtkmm-2.4' found
>> > > Package gtkglext-1.0 was not found in the pkg-config search path.
>> > > Perhaps you should add the directory containing `gtkglext-1.0.pc'
>> > > to the PKG_CONFIG_PATH environment variable
>> > > No package 'gtkglext-1.0' found
>> > > WARNING: unable to find gtkmm-2.4 configuration
>> > > Package glibmm-2.4 was not found in the pkg-config search path.
>> > > Perhaps you should add the directory containing `glibmm-2.4.pc'
>> > > to the PKG_CONFIG_PATH environment variable
>> > > No package 'glibmm-2.4' found
>> > > WARNING: unable to find glibmm-2.4,gthread-2.0 configuration
>> > > Package gtkmm-2.4 was not found in the pkg-config search path.
>> > > Perhaps you should add the directory containing `gtkmm-2.4.pc'
>> > > to the PKG_CONFIG_PATH environment variable
>> > > No package 'gtkmm-2.4' found
>> > > WARNING: unable to find gtkmm-2.4 configuration
>> > > Package gtkmm-2.4 was not found in the pkg-config search path.
>> > > Perhaps you should add the directory containing `gtkmm-2.4.pc'
>> > > to the PKG_CONFIG_PATH environment variable
>> > > No package 'gtkmm-2.4' found
>> > > Package gtkglext-1.0 was not found in the pkg-config search path.
>> > > Perhaps you should add the directory containing `gtkglext-1.0.pc'
>> > > to the PKG_CONFIG_PATH environment variable
>> > > No package 'gtkglext-1.0' found
>> > > WARNING: unable to find gtkmm-2.4 configuration
>> > > Traceback (most recent call last):
>> > >   File "./build", line 968, in <module>
>> > >     [ Entry(item) for item in targets ]
>> > >   File "./build", line 245, in __init__
>> > >     if is_executable (self.name): self.set_executable()
>> > >   File "./build", line 276, in set_executable
>> > >     '$bin$': [ self.name ] })
>> > >   File "./build", line 375, in fillin
>> > >     if item in keyvalue: cmd += keyvalue[item]
>> > > TypeError: 'NoneType' object is not iterable
>> > > [root at musca mrtrix-0.2.10]# rpm -q -a | grep -i glibmm
>> > > glibmm24-2.22.1-1.el6.x86_64
>> > > ^P[root at musca mrtrix-0.2.10]# rpm -q -a | grep -i gtkmm
>> > > gtkmm24-2.18.2-1.el6.x86_64
>> > > [root at musca mrtrix-0.2.10]# rpm -q -a | grep glibmm
>> > > glibmm24-2.22.1-1.el6.x86_64
>> > >
>> > > You can see that the libraries it seems to want have RPMs installed …
>> > >
>> > > and the libraries are actually present:
>> > >
>> > > [root at musca mrtrix-0.2.10]# find /usr -name libglibmm\* -print
>> > > /usr/lib64/libglibmm-2.4.so.1
>> > > /usr/lib64/libglibmm-2.4.so.1.2.0
>> > > /usr/lib64/libglibmm_generate_extra_defs-2.4.so.1
>> > > /usr/lib64/libglibmm_generate_extra_defs-2.4.so.1.2.0
>> > >
>> > > so it looks like the real problem is that there are no entries in
>> /usr/lib64/pkgconfig for these libraries.
>> > >
>> > > SO: how do I get around this?
>> > >
>> > > --
>> > > Henry Mensch / Systems and Storage Manager
>> > > Center for Imaging of Neurodegenerative Diseases
>> > > VA Medical Center, San Francisco CA  USA
>> > > a: +1.415.221.4810 x6466 / : +1.415.668.2864
>> > > :: henry.mensch at va.gov
>> > > w: http://www.cind.research.va.gov/
>> > >
>> > >
>> > >
>> > >
>> > > _______________________________________________
>> > > Mrtrix-discussion mailing list
>> > > Mrtrix-discussion at www.nitrc.org
>> > > http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>> > >
>> > >
>> > > _______________________________________________
>> > > Mrtrix-discussion mailing list
>> > > Mrtrix-discussion at www.nitrc.org
>> > > http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>> > >
>> > >
>> > >
>> > >
>> > > --
>> > > Dr Jacques-Donald Tournier
>> > > Research Fellow
>> > >
>> > > The Florey Institute of Neuroscience and Mental Health
>> > > Melbourne Brain Centre - Austin Campus
>> > > 245 Burgundy Street
>> > > Heidelberg  Vic  3084
>> > > Ph:  +61 3 9035 7033
>> > > Fax:  +61 3 9035 7307
>> > > www.florey.edu.au
>> > >
>> > > _______________________________________________
>> > > Mrtrix-discussion mailing list
>> > > Mrtrix-discussion at www.nitrc.org
>> > > http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>> >
>> > --
>> > Henry Mensch / Systems and Storage Manager
>> > Center for Imaging of Neurodegenerative Diseases
>> > VA Medical Center, San Francisco CA  USA
>> > a: +1.415.221.4810 x6466 / : +1.415.668.2864
>> > :: henry.mensch at va.gov
>> > w: http://www.cind.research.va.gov/
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > --
>> > Dr Jacques-Donald Tournier
>> > Research Fellow
>> >
>> > The Florey Institute of Neuroscience and Mental Health
>> > Melbourne Brain Centre - Austin Campus
>> > 245 Burgundy Street
>> > Heidelberg  Vic  3084
>> > Ph:  +61 3 9035 7033
>> > Fax:  +61 3 9035 7307
>> > www.florey.edu.au
>> >
>>
>> --
>> Henry Mensch / Systems and Storage Manager
>> Center for Imaging of Neurodegenerative Diseases
>> VA Medical Center, San Francisco CA  USA
>> a: +1.415.221.4810 x6466 / : +1.415.668.2864
>> :: henry.mensch at va.gov
>> w: http://www.cind.research.va.gov/
>>
>>
>>
>>
>>
>> _______________________________________________
>> Mrtrix-discussion mailing list
>> Mrtrix-discussion at www.nitrc.org
>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>
>
>
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>
>


-- 
*Dr Jacques-Donald Tournier
*
Research Fellow

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg  Vic  3084
Ph:  +61 3 9035 7033
Fax:  +61 3 9035 7307
www.florey.edu.au
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