[Mrtrix-discussion] Unable to build on RedHat 6.x

Wed Jul 30 02:07:08 PDT 2014

Hi Stuart,

OK, it looks like you have the required packages installed. Can you provide
the listing of the files included in these packages, so we can see where
the library needed is actually located? Can you also check what the
/usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../libGLU.so file actually is?
Obviously it's actually in /usr/lib/libGLU.so, but I reckon it would be a
symbolic link to something else, it would be a good idea to check what that
would be. On my system, this is what I have:

$ ls -l /usr/lib/libGLU*
> lrwxrwxrwx 1 root root   15 Jun 30 05:58 /usr/lib/libGLU.so ->
> libGLU.so.1.3.1
> lrwxrwxrwx 1 root root   15 Jun 30 05:58 /usr/lib/libGLU.so.1 ->
> libGLU.so.1.3.1
> -rwxr-xr-x 1 root root 515K Jun 30 05:58 /usr/lib/libGLU.so.1.3.1

You might find you also need to have the libGLU.so.1 symlink in place for
this to work - sometimes the package maintainers do not include these.

As to the MRtrix3 issue with g++ not being found, I find that surprising.
Is /usr/bin in your PATH? What does 'g++ --version' report? Is there any
useful information in configure.log?

Cheers,
Donald.

On 29 July 2014 11:59, Luscombe, Stuart <s.luscombe at ucl.ac.uk> wrote:

>  Hi Donald,
>
>
>
> Thanks for your response.
>
>
>
> These are the libGLU packages installed:
>
>
>
> mesa-libGLU.i686
> 9.2-0.5.el6_5.2
> @rhel-x86_64-workstation-6
>
> mesa-libGLU.x86_64
> 9.2-0.5.el6_5.2
>                                       @rhel-x86_64-workstation-6
>
> mesa-libGLU-devel.i686
> 9.2-0.5.el6_5.2
> @rhel-x86_64-workstation-6
>
> mesa-libGLU-devel.x86_64
>                                9.2-0.5.el6_5.2
> @rhel-x86_64-workstation-6
>
>
>
> I believe both architectures are required for compatibility reasons.
>
>
>
> I was pointed to try and build mrtrix3 by the person who’s machine this
> is, but when trying to build that I get the message that g++ cannot be
> found, even though it is installed and located in /usr/bin.
>
>
>
> Many Thanks,
>
>
>
> --
> Stuart Luscombe
> Systems Administrator
> Dementia Research Centre / NIHR Queen Square Dementia Biomedical Research
> Unit
> 8-11 Queen Square
> London, WC1N 3BG
>
> E-mail: s.luscombe at ucl.ac.uk
> Phone: 0203 448 3875
>
>
>
> *From:* J-Donald Tournier [mailto:jdtournier at gmail.com]
> *Sent:* Tuesday, July 29, 2014 11:10 AM
> *To:* Luscombe, Stuart
> *Cc:* mrtrix mailinglist
> *Subject:* Re: [Mrtrix-discussion] Unable to build on RedHat 6.x
>
>
>
> Hi Stuart,
>
> Looks like the version of the GLU (GL utilities) library you have
> installed on that system isn't the right one for your architecture - maybe
> you're trying to build a 64-bit version of MRtrix, but you only have the
> 32-bit version of libGLU installed? Can you have a look through your list
> of installed packages and make sure you have the necessary version of
> libglu installed?
>
> Cheers,
> Donald
>
> --
> Dr J-Donald Tournier (PhD)
>
> Senior Lecturer, Biomedical Engineering
> Division of Imaging Sciences & Biomedical Engineering
> King's College London
>
> A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
> Thomas' Hospital, London. SE1 7EH
> T: +44 (0)20 7188 7118 ext 53613
> W:
> http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
>
>
> On 28 Jul 2014 11:42, "Luscombe, Stuart" <s.luscombe at ucl.ac.uk> wrote:
>
> Hi,
>
>
>
> I am trying to build mrtrix for one of my users who is running Red Hat
> Enterprise 6.5. It keeps failing with the following error:
>
>
>
> [LB] bin/disp_profile
>
> [LB] bin/mrview
>
>
>
> ERROR: [LB] bin/disp_profile
>
>
>
> g++ -Wl,-rpath,$ORIGIN/../lib -Llib src/icon.o cmd/disp_profile.o
> src/dwi/renderer.o src/dwi/SH.o src/dwi/render_frame.o -lmrtrix-0_2_12
> -lgsl -lgslcblas -Wl,--export-dynamic -lgtkmm-2.4 -latkmm-1.6 -lgdkmm-2.4
> -lgiomm-2.4 -lpangomm-1.4 -lglibmm-2.4 -lcairomm-1.0 -lsigc-2.0
> -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXmu -lXt -lSM -lICE
> -lgtk-x11-2.0 -lpangox-1.0 -lX11 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0
> -lpangoft2-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpango-1.0
> -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 -lz -o
> bin/disp_profile
>
>
>
> failed with output:
>
>
>
> /usr/bin/ld: skipping incompatible
> /usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../libGLU.so when searching
> for -lGLU
>
> /usr/bin/ld: skipping incompatible /usr/lib/libGLU.so when searching for
> -lGLU
>
> /usr/bin/ld: cannot find -lGLU
>
> collect2: ld returned 1 exit status
>
>
>
> STOP
>
>
>
> ERROR: [LB] bin/mrview
>
>
>
> g++ -Wl,-rpath,$ORIGIN/../lib -Llib src/mrview/display_area.o
> src/mrview/mode/normal.o src/mrview/window.o src/mrview/dialog/progress.o
> src/mrview/sidebar/roi_analysis.o
> src/mrview/sidebar/roi_analysis/roi_list.o src/mrview/texture.o
> src/dialog/file.o src/mrview/mode/base.o
> src/mrview/sidebar/tractography/roi_list.o src/icon.o
> src/dwi/tractography/mds.o src/mrview/dialog/opengl.o src/mrview/pane.o
> cmd/mrview.o src/mrview/sidebar/tractography/track_list_item.o
> src/mrview/sidebar/overlay.o src/mrview/sidebar/orientation_plot.o
> src/mrview/slice.o src/dwi/renderer.o
> src/mrview/sidebar/tractography/track_list.o
> src/mrview/sidebar/screen_capture.o src/dwi/tractography/file.o
> src/mrview/dialog/error.o src/mrview/sidebar/tractography.o
> src/mrview/dialog/properties.o src/dwi/render_frame.o src/dwi/SH.o
> src/mrview/sidebar/main.o src/mrview/image.o -lmrtrix-0_2_12 -lgsl
> -lgslcblas -Wl,--export-dynamic -lgtkmm-2.4 -latkmm-1.6 -lgdkmm-2.4
> -lgiomm-2.4 -lpangomm-1.4 -lglibmm-2.4 -lcairomm-1.0 -lsigc-2.0
> -lgtkglext-x11-1.0 -lgdkglext-x11-1.0 -lGLU -lGL -lXmu -lXt -lSM -lICE
> -lgtk-x11-2.0 -lpangox-1.0 -lX11 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0
> -lpangoft2-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpango-1.0
> -lfreetype -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 -lz -o
> bin/mrview
>
>
>
> failed with output:
>
>
>
> /usr/bin/ld: skipping incompatible
> /usr/lib/gcc/x86_64-redhat-linux/4.4.6/../../../libGLU.so when searching
> for -lGLU
>
> /usr/bin/ld: skipping incompatible /usr/lib/libGLU.so when searching for
> -lGLU
>
> /usr/bin/ld: cannot find -lGLU
>
> collect2: ld returned 1 exit status
>
>
>
> STOP
>
>
>
>
>
> All of the mesa-libGL* packages are up to date.
>
>
>
> I have also tried building on a machine running an older version of Red
> Hat, which did get a bit further initially but ultimately came back with
> the same error. Both machines are running proprietary AMD/Nvidia drivers.
>
>
>
> Many Thanks,
>
>
>
> --
> Stuart Luscombe
> Systems Administrator
> Dementia Research Centre / NIHR Queen Square Dementia Biomedical Research
> Unit
> 8-11 Queen Square
> London, WC1N 3BG
>
> E-mail: s.luscombe at ucl.ac.uk
> Phone: 0203 448 3875
>
>
>
>
> _______________________________________________
> Mrtrix-discussion mailing list
> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>

-- 
*Dr J-Donald Tournier (PhD)*

*Senior Lecturer, **Biomedical Engineering*

*Division of Imaging Sciences & Biomedical EngineeringKing's College London*

*A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH*
*T: +44 (0)20 7188 7118 ext 53613*
*W: http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering
<http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering>*
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