Can't start latest stable on ubuntu 20.04

[RafaelPalomar]

@pieper qt5dxcb-plugin seems to be a component of QtGui that can be built with the -qt-xcb flag (Qt XCB). I guess to include this in the slicer packaging QT should be included as a whole? I’m with you on avoiding the user installing packages to use the packaged binaries, but we need to be careful not ending up packaging all the way to the Linux kernel

[manjula (Manjula Herath)]

@RafaelPalomar

• [Error 2] Slicer crashes with a segmentation fault on application launch. It seems the crash produces on the interaction of python (ctypes extension) with libffi ( /usr/lib/x86_64-linux-gnu/libffi.so.8 ). In Ubuntu 20.10 libffi is packaged in its 3.4 version, while in other distributions not having this problem the version is 3.3. This would suggest incompatibility between the python deployed in Slicer and libffi installed in Ubuntu 20.10; @manjula, could you check the version of libffi in PoP OS 20.10 just to discard this end?

3.4~20200819gead65ca871-0ubuntu3

[RafaelPalomar]

thanks @manjula. It is exactly the same version as in Ubuntu 20.10. We may not be hitting the right diagnostic here with the compatibility. Would you mind to paste a list of your installed packages in dpaste?

to do this you can install xclip:

sudo apt install xclip

and then copy the list of packages in the clipboard

sudo apt list --installed | xclip -selection c

thenk you can go to dpaste, paste (Ctrl+V) the results and post here the link. If PoP is almost Ubuntu, maybe we find the difference.

Thanks in advance.

[manjula (Manjula Herath)]

Please note that most of my packages i have is in flatpak but here is the link.

dpaste/sNOh (Python)

[manjula (Manjula Herath)]

I mentioned about flatpak because when I was figuring out what was going wrong with linkSlicerBlender the deb version of the Blender was giving error in importing numpy, Apparently it was a know issue with blender but when i switch to flatpak it went away.

[RafaelPalomar]

I have installed PopOS 20.10 (also the packages from @manjula) and got the same results as with Ubuntu 20.10:

• Error due to missing libxcb-xinerama0 on Slicer stable (4.11.20200930). When libxcb-xinerama0 is installed, segmentation fault is produced on startup.
• Segmentation fault is removed by compiling python with BUILTIN_CTYPES=ON.

I still think the problem is leaning towards a compatibility problem between python and libffi 3.4.

[kotloski]

I think I am experiencing the same issue with Ubuntu 20.10. Can you tell me how to use the BUILTIN_CTYPES=ON work-around? I have not been able to figure it out from the online documentation. Thanks!

[jcfr (Jean Christophe Fillion Robin (Kitware))]

@kotloski

Can you tell me how to use the BUILTIN_CTYPES=ON work-around?

This is a build option for the cpython-cmake-buildsystem project, you can enable this option adding

-DBUILTIN_CTYPES=ON

under CMAKE_CACHE_ARGS in this file:

Slicer/Slicer/blob/de2e43a7271b2f72d5537ea0a9af1288beb44055/SuperBuild/External_python.cmake#L138

Then, you would have to re-build Slicer from the top-level.

[kotloski]

Thanks! Adding -DBUILTIN_CTYPES:BOOL=ON worked. Though the extension I need doesn’t won’t run in the latest build. Oh well, it’s been that kind of year.

[jcfr (Jean Christophe Fillion Robin (Kitware))]

@kotloski

Though the extension I need doesn’t won’t run in the latest build.

Which extension it is ?

[kotloski]

Segmentation Wizard. It last worked for me in 4.10.2. The extension seems to install OK and I can see it in the Extensions manager window, but I can not find it under modules in the main program and it is listed as “not loaded” when I search using Module finder. Thanks for any help; I just need to finish up a little bit of old data.

Documentation/Nightly/Extensions/SegmentationWizard - Slicer Wiki

[lassoan (Andras Lasso)]

Yes. Your system is not compatible with the precompiled binaries that we provide.

[manjula (Manjula Herath)]

I today tried building Slicer in Manjaro Linux on a fresh install. it failed, with the following errors.

This is the output from the finals parts

https://pastebin.com/0gAANfae

As @RafaelPalomar said i checked the version of libffi

core/libffi 3.3-4 [installed]
Portable foreign function interface library
community/haskell-libffi 0.1-20
A binding to libffi
multilib/lib32-libffi 3.3-2 [installed]
A portable, high level programming interface to various calling conventions (32-bit)

[RafaelPalomar]

@manjula, I think your problem is not related to the issue discussed in this thread. This thread is starting to be a mix of different issues and is becoming difficult to follow. I suggest that you open a new thread for discussing it.

Regards,
Rafael

[lassoan (Andras Lasso)]

It may be better to keep this thread as general discussion topic here and create separate issues in the issue tracker to discuss technical details there.

[fuentesdt (David Fuentes)]

apt-get install libxcb-xinerama0-dev

seemed to work for me on ubuntu 16.04

[Karam_AbuGhalieh]

I found this solution here and worked fine for me:

sudo apt-get install --reinstall libxcb-xinerama0

[lassoan (Andras Lasso)]

Thank you. This is also described in the Slicer install instructions.

@Karam_AbuGhalieh Do you have a suggestion how to make the instructions easier to find?

[Karam_AbuGhalieh]

I was there before facing the problem, now I am surprised the solution is there!

I think what I did is just reading the Linux section and ignoring the next Debian/Ubuntu one!!

[pieper (Steve Pieper (Isomics, Inc.))]

Note that for another machine where I started from a fresh unbuntu 20.04 that wasn’t configured as a desktop workstation I also needed to add this package to get past the xcb startup issue: sudo apt-get install libxcb-shape0

I also installed these packages to get xvfb-run to work with Slicer:

sudo apt-get install libxcb-icccm4-dev libxcb-image0-dev libxcb-keysyms1-dev libxcb-randr0 libxcb-render-util0 libxcb-xkb-dev libxkbcommon-x11-dev