Hi Henry,<div><br></div><div>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...</div>
<div><br></div><div>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:</div>
<div><ul><li>set up a CentOS6 system (either in a chroot or a VM)</li><li>compile MRtrix</li><li>find out what all the relevant runtime dependencies are (e.g. using the command "ldd bin/mrview")</li><li>locate those libaries that don't already exist on your RHEL6 system</li>
<li>copy these libraries into the MRtrix lib/ folder, alongside the MRtrix library itself</li><li>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)</li>
<li>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).</li>
</ul>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...</div>
<div><br></div><div>Hope that helps.</div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div><div><br></div><div><br><div class="gmail_quote">On 20 March 2013 10:24, Luis Concha <span dir="ltr"><<a href="mailto:lconcha@unam.mx" target="_blank">lconcha@unam.mx</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>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. <br>
<br></div>Sort of this:<br><a href="http://neuro.debian.net/blog/2011/2011-12-12_schroot_fslview.html" target="_blank">http://neuro.debian.net/blog/2011/2011-12-12_schroot_fslview.html</a><br><br></div>This way, you have your debian binaries running alongside the RHEL ones, and both of them are native. Consider this a tentative plan B.<span class="HOEnZb"><font color="#888888"><br>
<br></font></span></div><span class="HOEnZb"><font color="#888888">Luis<br></font></span></div><div class="gmail_extra"><div class="im"><br clear="all"><div>Dr. Luis Concha<br>Instituto de Neurobiología<br>Laboratorio C-12<br>
UNAM, Campus Juriquilla<br>Boulervard Juriquilla 3001<br>Juriquilla, Querétaro.<br>
C.P. 76230<br>México<br>Tel (442) 2 38 10 53<br>Fax (442) 2 38 10 46<br><a href="http://www.inb.unam.mx" target="_blank">www.inb.unam.mx</a><br></div>
<br><br></div><div><div class="h5"><div class="gmail_quote">On Tue, Mar 19, 2013 at 5:19 PM, Henry Mensch <span dir="ltr"><<a href="mailto:Henry.Mensch@va.gov" target="_blank">Henry.Mensch@va.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
That's what I expected, too, but RHEL doesn't come with the -devel bundles for this stuff:<br>
<br>
[root@musca dx-4.4.4]# yum -y install gtkmm24-devel<br>
Loaded plugins: refresh-packagekit, rhnplugin<br>
This system is receiving updates from RHN Classic or RHN Satellite.<br>
Setting up Install Process<br>
No package gtkmm24-devel available.<br>
Error: Nothing to do<br>
[root@musca dx-4.4.4]# yum -y install gtkmm24-devel-2.18.2-1<br>
Loaded plugins: refresh-packagekit, rhnplugin<br>
This system is receiving updates from RHN Classic or RHN Satellite.<br>
Setting up Install Process<br>
No package gtkmm24-devel-2.18.2-1 available.<br>
Error: Nothing to do<br>
[root@musca dx-4.4.4]# yum -y list gtkmm\*<br>
Loaded plugins: refresh-packagekit, rhnplugin<br>
This system is receiving updates from RHN Classic or RHN Satellite.<br>
Installed Packages<br>
gtkmm24.x86_64 2.18.2-1.el6 @anaconda-RedHatEnterpriseLinux-201009221801.x86_64/6.0<br>
<br>
so it's not clear to me where what you found actually comes from.<br>
<div><div><br>
On Mar 19, 2013, at 4:10 PM, Donald Tournier wrote:<br>
<br>
> 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: <a href="http://pkgs.org/centos-6-rhel-6/centos-rhel-i386/gtkmm24-devel-2.18.2-1.el6.i686.rpm.html" target="_blank">http://pkgs.org/centos-6-rhel-6/centos-rhel-i386/gtkmm24-devel-2.18.2-1.el6.i686.rpm.html</a> - looks like it might fit the bill...?<br>
><br>
> Cheers,<br>
><br>
> Donald.<br>
><br>
><br>
><br>
> On 20 March 2013 09:44, Henry Mensch <<a href="mailto:Henry.Mensch@va.gov" target="_blank">Henry.Mensch@va.gov</a>> wrote:<br>
> No, they don't. The files aren't there, and they're not in the packages.<br>
><br>
> On Mar 19, 2013, at 3:35 PM, Donald Tournier wrote:<br>
><br>
> > 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.<br>
> > On Tue, Mar 19, 2013 at 3:40 PM, Henry Mensch <<a href="mailto:Henry.Mensch@va.gov" target="_blank">Henry.Mensch@va.gov</a>> wrote:<br>
> > I'm on a CentOS 6 system:<br>
> ><br>
> > 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<br>
> ><br>
> > and I'm trying to build … the build fails early with these errors:<br>
> ><br>
> > [root@musca mrtrix-0.2.10]# ./build<br>
> > Package glibmm-2.4 was not found in the pkg-config search path.<br>
> > Perhaps you should add the directory containing `glibmm-2.4.pc'<br>
> > to the PKG_CONFIG_PATH environment variable<br>
> > No package 'glibmm-2.4' found<br>
> > WARNING: unable to find glibmm-2.4,gthread-2.0 configuration<br>
> > Package gtkmm-2.4 was not found in the pkg-config search path.<br>
> > Perhaps you should add the directory containing `gtkmm-2.4.pc'<br>
> > to the PKG_CONFIG_PATH environment variable<br>
> > No package 'gtkmm-2.4' found<br>
> > WARNING: unable to find gtkmm-2.4 configuration<br>
> > Package gtkmm-2.4 was not found in the pkg-config search path.<br>
> > Perhaps you should add the directory containing `gtkmm-2.4.pc'<br>
> > to the PKG_CONFIG_PATH environment variable<br>
> > No package 'gtkmm-2.4' found<br>
> > Package gtkglext-1.0 was not found in the pkg-config search path.<br>
> > Perhaps you should add the directory containing `gtkglext-1.0.pc'<br>
> > to the PKG_CONFIG_PATH environment variable<br>
> > No package 'gtkglext-1.0' found<br>
> > WARNING: unable to find gtkmm-2.4 configuration<br>
> > Package glibmm-2.4 was not found in the pkg-config search path.<br>
> > Perhaps you should add the directory containing `glibmm-2.4.pc'<br>
> > to the PKG_CONFIG_PATH environment variable<br>
> > No package 'glibmm-2.4' found<br>
> > WARNING: unable to find glibmm-2.4,gthread-2.0 configuration<br>
> > Package gtkmm-2.4 was not found in the pkg-config search path.<br>
> > Perhaps you should add the directory containing `gtkmm-2.4.pc'<br>
> > to the PKG_CONFIG_PATH environment variable<br>
> > No package 'gtkmm-2.4' found<br>
> > WARNING: unable to find gtkmm-2.4 configuration<br>
> > Package gtkmm-2.4 was not found in the pkg-config search path.<br>
> > Perhaps you should add the directory containing `gtkmm-2.4.pc'<br>
> > to the PKG_CONFIG_PATH environment variable<br>
> > No package 'gtkmm-2.4' found<br>
> > Package gtkglext-1.0 was not found in the pkg-config search path.<br>
> > Perhaps you should add the directory containing `gtkglext-1.0.pc'<br>
> > to the PKG_CONFIG_PATH environment variable<br>
> > No package 'gtkglext-1.0' found<br>
> > WARNING: unable to find gtkmm-2.4 configuration<br>
> > Traceback (most recent call last):<br>
> > File "./build", line 968, in <module><br>
> > [ Entry(item) for item in targets ]<br>
> > File "./build", line 245, in __init__<br>
> > if is_executable (<a href="http://self.name" target="_blank">self.name</a>): self.set_executable()<br>
> > File "./build", line 276, in set_executable<br>
> > '$bin$': [ <a href="http://self.name" target="_blank">self.name</a> ] })<br>
> > File "./build", line 375, in fillin<br>
> > if item in keyvalue: cmd += keyvalue[item]<br>
> > TypeError: 'NoneType' object is not iterable<br>
> > [root@musca mrtrix-0.2.10]# rpm -q -a | grep -i glibmm<br>
> > glibmm24-2.22.1-1.el6.x86_64<br>
> > ^P[root@musca mrtrix-0.2.10]# rpm -q -a | grep -i gtkmm<br>
> > gtkmm24-2.18.2-1.el6.x86_64<br>
> > [root@musca mrtrix-0.2.10]# rpm -q -a | grep glibmm<br>
> > glibmm24-2.22.1-1.el6.x86_64<br>
> ><br>
> > You can see that the libraries it seems to want have RPMs installed …<br>
> ><br>
> > and the libraries are actually present:<br>
> ><br>
> > [root@musca mrtrix-0.2.10]# find /usr -name libglibmm\* -print<br>
> > /usr/lib64/libglibmm-2.4.so.1<br>
> > /usr/lib64/libglibmm-2.4.so.1.2.0<br>
> > /usr/lib64/libglibmm_generate_extra_defs-2.4.so.1<br>
> > /usr/lib64/libglibmm_generate_extra_defs-2.4.so.1.2.0<br>
> ><br>
> > so it looks like the real problem is that there are no entries in /usr/lib64/pkgconfig for these libraries.<br>
> ><br>
> > SO: how do I get around this?<br>
> ><br>
> > --<br>
> > Henry Mensch / Systems and Storage Manager<br>
> > Center for Imaging of Neurodegenerative Diseases<br>
> > VA Medical Center, San Francisco CA USA<br>
> > a: +1.415.221.4810 x6466 / : +1.415.668.2864<br>
> > :: <a href="mailto:henry.mensch@va.gov" target="_blank">henry.mensch@va.gov</a><br>
> > w: <a href="http://www.cind.research.va.gov/" target="_blank">http://www.cind.research.va.gov/</a><br>
> ><br>
> ><br>
> ><br>
> ><br>
> > _______________________________________________<br>
> > Mrtrix-discussion mailing list<br>
> > <a href="mailto:Mrtrix-discussion@www.nitrc.org" target="_blank">Mrtrix-discussion@www.nitrc.org</a><br>
> > <a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
> ><br>
> ><br>
> > _______________________________________________<br>
> > Mrtrix-discussion mailing list<br>
> > <a href="mailto:Mrtrix-discussion@www.nitrc.org" target="_blank">Mrtrix-discussion@www.nitrc.org</a><br>
> > <a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
> ><br>
> ><br>
> ><br>
> ><br>
> > --<br>
> > Dr Jacques-Donald Tournier<br>
> > Research Fellow<br>
> ><br>
> > The Florey Institute of Neuroscience and Mental Health<br>
> > Melbourne Brain Centre - Austin Campus<br>
> > 245 Burgundy Street<br>
> > Heidelberg Vic 3084<br>
> > Ph: <a href="tel:%2B61%203%209035%207033" value="+61390357033" target="_blank">+61 3 9035 7033</a><br>
> > Fax: <a href="tel:%2B61%203%209035%207307" value="+61390357307" target="_blank">+61 3 9035 7307</a><br>
> > <a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a><br>
> ><br>
> > _______________________________________________<br>
> > Mrtrix-discussion mailing list<br>
> > <a href="mailto:Mrtrix-discussion@www.nitrc.org" target="_blank">Mrtrix-discussion@www.nitrc.org</a><br>
> > <a href="http://www.nitrc.org/mailman/listinfo/mrtrix-discussion" target="_blank">http://www.nitrc.org/mailman/listinfo/mrtrix-discussion</a><br>
><br>
> --<br>
> Henry Mensch / Systems and Storage Manager<br>
> Center for Imaging of Neurodegenerative Diseases<br>
> VA Medical Center, San Francisco CA USA<br>
> a: <a href="tel:%2B1.415.221.4810%20x6466" value="+14152214810" target="_blank">+1.415.221.4810 x6466</a> / : <a href="tel:%2B1.415.668.2864" value="+14156682864" target="_blank">+1.415.668.2864</a><br>
> :: <a href="mailto:henry.mensch@va.gov" target="_blank">henry.mensch@va.gov</a><br>
> w: <a href="http://www.cind.research.va.gov/" target="_blank">http://www.cind.research.va.gov/</a><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
><br>
> --<br>
> Dr Jacques-Donald Tournier<br>
> Research Fellow<br>
><br>
> The Florey Institute of Neuroscience and Mental Health<br>
> Melbourne Brain Centre - Austin Campus<br>
> 245 Burgundy Street<br>
> Heidelberg Vic 3084<br>
> Ph: <a href="tel:%2B61%203%209035%207033" value="+61390357033" target="_blank">+61 3 9035 7033</a><br>
> Fax: <a href="tel:%2B61%203%209035%207307" value="+61390357307" target="_blank">+61 3 9035 7307</a><br>
> <a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a><br>
><br>
<br>
--<br>
Henry Mensch / Systems and Storage Manager<br>
Center for Imaging of Neurodegenerative Diseases<br>
VA Medical Center, San Francisco CA USA<br>
a: <a href="tel:%2B1.415.221.4810%20x6466" value="+14152214810" target="_blank">+1.415.221.4810 x6466</a> / : <a href="tel:%2B1.415.668.2864" value="+14156682864" target="_blank">+1.415.668.2864</a><br>
:: <a href="mailto:henry.mensch@va.gov" target="_blank">henry.mensch@va.gov</a><br>
w: <a href="http://www.cind.research.va.gov/" target="_blank">http://www.cind.research.va.gov/</a><br>
<br>
<br>
<br>
<br>
<br>
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</div></div></blockquote></div><br></div></div></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><font color="#ff6600" size="1"><b>Dr Jacques-Donald Tournier<br></b></font><div><font color="#ff6600" size="1">Research Fellow</font></div><div><font size="1"><br>
</font></div><div><font size="1">The Florey Institute of Neuroscience and Mental Health</font></div><div><font size="1">Melbourne Brain Centre - Austin Campus</font></div><div><font size="1">245 Burgundy Street</font></div>
<div><font size="1">Heidelberg Vic 3084</font></div><div><font size="1">Ph: +61 3 9035 7033</font></div><div><font size="1">Fax: +61 3 9035 7307</font></div><div><font size="1"><a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a></font></div>
<br>
</div>