You could probably get help from the AUR maintainer as they almost certainly know more about this software - I'd never even heard of it before this thread.
Thanks. I've written an email to them. Thank you for you help. I'll mark this thread as solved now.
]]>You could probably get help from the AUR maintainer as they almost certainly know more about this software - I'd never even heard of it before this thread.
]]>If the "extras" are just the SUMA programs, then I suspect modifying the PKGBUILD by adding a `make -j1 suma` after the `make -j1 vastness` would suffice for the build. The package function might also need an adjustment to install the SUMA binaries.
Okay adding `make -j1 suma` after the `make -j1 vastness` does seem to work. But what sort of adjustment do I need to need to make to the package function? Because the I get an error at the end of the build
/bin/cp: cannot stat 'SUMA/suma': No such file or directory
For all the SUMA programs.
]]>As for that command the AFNI devs suggested, did you bother to look at what that script does? It downloads a bunch of precompiled binaries and likely overwrites what you installed from the AUR. So you don't have an AUR build of these binaries any more which is why you have the error in your first post. So once again, the solution is to build it from source properly. And you should know how to do it as you already did it once before: with makepkg.
If there are missing binaries from the AUR build, lets fix that, not overwrite everything with binaries compiled for another system.
If the "extras" are just the SUMA programs, then I suspect modifying the PKGBUILD by adding a `make -j1 suma` after the `make -j1 vastness` would suffice for the build. The package function might also need an adjustment to install the SUMA binaries.
]]>Why would you downgrade the library - I said rebuild the failing programs against the current version of the library.
No you didn't @Scimmia suggested it.
You built this from the link I provided, really? You didn't just download their precompiled binaries using one of their shell scripts? If you had built it yourself, you wouldn't get the error you reported in your first post.
I actually installed it from the AUR. Which used this build. But it had some missing binaries so one of the AFNI devs suggested I use
@update.afni.binaries -package linux_openmp_64 -do_extras
You advised me to rebuild those binaries and as much I appreciate your advice, I don't exactly know how to do that. The source source code does have a "Makefile.linux_openmp_64" file but I have no idea where to go from there.
]]>You built this from the link I provided, really? You didn't just download their precompiled binaries using one of their shell scripts? If you had built it yourself, you wouldn't get the error you reported in your first post.
]]>This is open source GPL software with source code availlable. If all of the "some programs" that are giving this sort of error are all AFNI components, then you can get the source tarball here and build it properly.
Yeah those were AFNI components and I built them from the AUR which uses this build. However, it had some missing packages so I ran
@update.afni.binaries -package linux_openmp_64 -do_extras
as suggested by the developers of AFNI. So I don't exactly know how to rebuild those AFNI packages.
I if I downgrade the library isn't there a chance other programs may fail because they look for the new one? What problems could I possibly face with the symlink that I created? Nonetheless, if it's not the correct way to the solve the problem I am willing to fix it the right way.
]]>This is open source GPL software with source code availlable. If all of the "some programs" that are giving this sort of error are all AFNI components, then you can get the source tarball here and build it properly.
]]>libsgl.so is provided by [extra]/gsl. But there is no .so.0, so the 3dSkullStrip will just need to be rebuilt against the current library.
Hey you were right. So did some scrapping on the local host and creating a symlink with libgsl.so.27 fixed the issue. Should have spent a little time figuring it out before creating an issue here. Thank you mate!
]]>3dSkullStrip: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
Apparently the library is called "libgsl.so.0". I cannot find a package name for this library anywhere. I tried running an AUR search for libgsl. I couldn't find anything. Can someone please point to the correct package?
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