[Mrtrix-discussion] having trouble building on CentOS 6

Tue Mar 19 15:35:30 PDT 2013

Hi Henry,

This does seem a bit odd if you can see the libraries are in fact
installed. The error messages actually relate to problems with pkg-config
trying to find the right configuration files for these libraries, so it can
figure out the correct compiler & linker flags. This is similar to a recent
issue on MacOSX<http://www.nitrc.org/pipermail/mrtrix-discussion/2013-March/000651.html>,
which was also related to pkg-config.

I suggest you try to figure out whether the *glibmm24-2.22.1-1.el6.x86_64*and
*gtkmm24-2.18.2-1.el6.x86_64* RPMs do in fact contain the *glibmm-2.4.pc*and
*gtkmm-2.4.pc* files respectively that pkg-config is looking for. It's been
a while since I handled RPMs, but a quick Google search would suggest that
the commands

$ rpm -ql glibmm24-2.22.1-1.el6.x86_64 | grep glibmm-2.4.pc
$ rpm -ql gtkmm24-2.18.2-1.el6.x86_64 | grep gtkmm-2.4.pc

should give you that information pretty quickly.

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 <http://linux.die.net/man/1/pkg-config>.

Good luck! Let us know how you go, I'm sure others would appreciate the
feedback, as Luis pointed out.

Cheers,
Donald.

On 20 March 2013 08:58, Luis Concha <lconcha at unam.mx> wrote:

> The computer cluster I used had CentOS 5 installed. I gave up trying to
> compile on CentOS and looked into a debian chroot environment. I never had
> the time to finish it, but it looked promising. I ended up building my own
> beowulf cluster with ubuntu. I wish you luck in your compilation attempts.
> If you succeed, please let us know, as I suspect there are more CentOS
> users around here.
>
> 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 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/
>>
>>
>>
>>
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>> Mrtrix-discussion at www.nitrc.org
>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>
>
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-- 
*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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