[Freesurfer] freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0-full.tar.gz, libexpat.so.0, Gentoo Linux x86_64
Dear all,
I've downloaded the latest freesurfer version (4.1.0) for x86_64 Linux. There seem to be some issues with libexpat.so.0, which is no longer available on my Gentoo linux systems.
The following files in freesurfer/bin depend on libexpat: freeview.bin libexpat.so.0 => not found libexpat.so.1 => /usr/lib/libexpat.so.1 (0x00002ac5281a8000) mris_volmask.bin libexpat.so.0 => not found orient_mri.bin libexpat.so.0 => not found qdec.bin libexpat.so.0 => not found scuba2.bin libexpat.so.0 => not found
I have scanned the freesurfer mailing list archives and got the impression that freesurfer 4.0.4 and above should not depend on depend on libexpat.so.0 anymore. I would be glad if someone could shed some light on this issue.
Yours,
Volkmar,
The libexpat you are seeing is a dependency via the VTK libs, so I will have to squash that in the next release. In the meantime, you will need to install libexpat on your system.
Nick
On Thu, 2008-11-20 at 16:42 +0100, Volkmar Glauche wrote:
Dear all,
I've downloaded the latest freesurfer version (4.1.0) for x86_64 Linux. There seem to be some issues with libexpat.so.0, which is no longer available on my Gentoo linux systems.
The following files in freesurfer/bin depend on libexpat: freeview.bin libexpat.so.0 => not found libexpat.so.1 => /usr/lib/libexpat.so.1 (0x00002ac5281a8000) mris_volmask.bin libexpat.so.0 => not found orient_mri.bin libexpat.so.0 => not found qdec.bin libexpat.so.0 => not found scuba2.bin libexpat.so.0 => not found
I have scanned the freesurfer mailing list archives and got the impression that freesurfer 4.0.4 and above should not depend on depend on libexpat.so.0 anymore. I would be glad if someone could shed some light on this issue.
Yours,
Nick,
I have got libexpat.so.1 installed, but it will be very difficult to install both libexpat.so.0 and libexpat.so.1 at the same time on Gentoo. Is there any special customisation for the VTK libs necessary? Otherwise, I would try to use the VTK libs shipped with Gentoo instead of the freesurfer ones.
All the best,
Volkmar
Quoting Nick Schmansky nicks@nmr.mgh.harvard.edu:
Volkmar,
The libexpat you are seeing is a dependency via the VTK libs, so I will have to squash that in the next release. In the meantime, you will need to install libexpat on your system.
Nick
On Thu, 2008-11-20 at 16:42 +0100, Volkmar Glauche wrote:
Dear all,
I've downloaded the latest freesurfer version (4.1.0) for x86_64 Linux. There seem to be some issues with libexpat.so.0, which is no longer available on my Gentoo linux systems.
The following files in freesurfer/bin depend on libexpat: freeview.bin libexpat.so.0 => not found libexpat.so.1 => /usr/lib/libexpat.so.1 (0x00002ac5281a8000) mris_volmask.bin libexpat.so.0 => not found orient_mri.bin libexpat.so.0 => not found qdec.bin libexpat.so.0 => not found scuba2.bin libexpat.so.0 => not found
I have scanned the freesurfer mailing list archives and got the impression that freesurfer 4.0.4 and above should not depend on depend on libexpat.so.0 anymore. I would be glad if someone could shed some light on this issue.
Yours,
To provide additional info: The vtk libs shipped with the freesurfer distribution don't seem to depend on libexpat.so.0, they link against libexpat.so.1, which is available. There must be something else that is linked against libexpat.so.0. Any idea?
Volkmar
Am Freitag, den 21.11.2008, 09:30 +0100 schrieb Volkmar Glauche:
Nick,
I have got libexpat.so.1 installed, but it will be very difficult to install both libexpat.so.0 and libexpat.so.1 at the same time on Gentoo. Is there any special customisation for the VTK libs necessary? Otherwise, I would try to use the VTK libs shipped with Gentoo instead of the freesurfer ones.
All the best,
Volkmar
Quoting Nick Schmansky nicks@nmr.mgh.harvard.edu:
Volkmar,
The libexpat you are seeing is a dependency via the VTK libs, so I will have to squash that in the next release. In the meantime, you will need to install libexpat on your system.
Nick
On Thu, 2008-11-20 at 16:42 +0100, Volkmar Glauche wrote:
Dear all,
I've downloaded the latest freesurfer version (4.1.0) for x86_64 Linux. There seem to be some issues with libexpat.so.0, which is no longer available on my Gentoo linux systems.
The following files in freesurfer/bin depend on libexpat: freeview.bin libexpat.so.0 => not found libexpat.so.1 => /usr/lib/libexpat.so.1 (0x00002ac5281a8000) mris_volmask.bin libexpat.so.0 => not found orient_mri.bin libexpat.so.0 => not found qdec.bin libexpat.so.0 => not found scuba2.bin libexpat.so.0 => not found
I have scanned the freesurfer mailing list archives and got the impression that freesurfer 4.0.4 and above should not depend on depend on libexpat.so.0 anymore. I would be glad if someone could shed some light on this issue.
Yours,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Volkmar, we also had an exception thrown relating to libexpat (what does it do, anyway?), but we solved it by creating a soft link between so.1 and so.0 in the same directory (can be dome with ln -s command on unix/linux, link what you already have, with what the software wants.. ) Seemed to work for us, up till now, i.e :-) Hope this helps sid.
On Fri, Nov 21, 2008 at 12:30 AM, Volkmar Glauche < volkmar.glauche@uniklinik-freiburg.de> wrote:
Nick,
I have got libexpat.so.1 installed, but it will be very difficult to install both libexpat.so.0 and libexpat.so.1 at the same time on Gentoo. Is there any special customisation for the VTK libs necessary? Otherwise, I would try to use the VTK libs shipped with Gentoo instead of the freesurfer ones.
All the best,
Volkmar
Quoting Nick Schmansky nicks@nmr.mgh.harvard.edu:
Volkmar,
The libexpat you are seeing is a dependency via the VTK libs, so I will have to squash that in the next release. In the meantime, you will need to install libexpat on your system.
Nick
On Thu, 2008-11-20 at 16:42 +0100, Volkmar Glauche wrote:
Dear all,
I've downloaded the latest freesurfer version (4.1.0) for x86_64 Linux. There seem to be some issues with libexpat.so.0, which is no longer available on my Gentoo linux systems.
The following files in freesurfer/bin depend on libexpat: freeview.bin libexpat.so.0 => not found libexpat.so.1 => /usr/lib/libexpat.so.1 (0x00002ac5281a8000) mris_volmask.bin libexpat.so.0 => not found orient_mri.bin libexpat.so.0 => not found qdec.bin libexpat.so.0 => not found scuba2.bin libexpat.so.0 => not found
I have scanned the freesurfer mailing list archives and got the impression that freesurfer 4.0.4 and above should not depend on depend on libexpat.so.0 anymore. I would be glad if someone could shed some light on this issue.
Yours,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Volkmar,
If creating the softlink doesnt solve the problem for you (and I think that it should, as it did for Sid), then you can get a new v4.1.0 for x86_64 that i posted here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/centos4_x86_64
It has the libexpat dependency removed from the vtk-lib dependent apps. It was an oversight on my part when building vtk 5.2 failing to disable using the system expat libs (when it should use the vtk-expat libs instead, ie, in cmake, VTK_USE_SYSTEM_EXPAT should be OFF).
libexpat is a XML toolkit used by vtkIO (run 'ldd libvtkIO.so').
Nick
On Fri, 2008-11-21 at 10:53 -0800, Siddharth Srivastava wrote:
Hi Volkmar, we also had an exception thrown relating to libexpat (what does it do, anyway?), but we solved it by creating a soft link between so.1 and so.0 in the same directory (can be dome with ln -s command on unix/linux, link what you already have, with what the software wants.. ) Seemed to work for us, up till now, i.e :-) Hope this helps sid.
On Fri, Nov 21, 2008 at 12:30 AM, Volkmar Glauche volkmar.glauche@uniklinik-freiburg.de wrote: Nick,
I have got libexpat.so.1 installed, but it will be very difficult to install both libexpat.so.0 and libexpat.so.1 at the same time on Gentoo. Is there any special customisation for the VTK libs necessary? Otherwise, I would try to use the VTK libs shipped with Gentoo instead of the freesurfer ones. All the best, Volkmar Quoting Nick Schmansky <nicks@nmr.mgh.harvard.edu>: Volkmar, The libexpat you are seeing is a dependency via the VTK libs, so I will have to squash that in the next release. In the meantime, you will need to install libexpat on your system. Nick On Thu, 2008-11-20 at 16:42 +0100, Volkmar Glauche wrote: Dear all, I've downloaded the latest freesurfer version (4.1.0) for x86_64 Linux. There seem to be some issues with libexpat.so.0, which is no longer available on my Gentoo linux systems. The following files in freesurfer/bin depend on libexpat: freeview.bin libexpat.so.0 => not found libexpat.so.1 => /usr/lib/libexpat.so.1 (0x00002ac5281a8000) mris_volmask.bin libexpat.so.0 => not found orient_mri.bin libexpat.so.0 => not found qdec.bin libexpat.so.0 => not found scuba2.bin libexpat.so.0 => not found I have scanned the freesurfer mailing list archives and got the impression that freesurfer 4.0.4 and above should not depend on depend on libexpat.so.0 anymore. I would be glad if someone could shed some light on this issue. Yours, _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Nick Schmansky -
Siddharth Srivastava -
Volkmar Glauche