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#1 2022-01-14 14:53:13

nikinbaidarr
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Registered: 2021-05-06
Posts: 53

[SOLVED]Install libgsl.so.0 package

I am getting a missing library error when trying to run some programs.

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?

Last edited by nikinbaidarr (2022-01-16 09:48:38)

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#2 2022-01-14 14:58:30

Trilby
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Re: [SOLVED]Install libgsl.so.0 package

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.  If there are others among "some programs" all of them will need to be rebuilt.  If any of these are from repo packages, then it's likely due to a systemic problem like partial upgrades.


"UNIX is simple and coherent..." - Dennis Ritchie, "GNU's Not UNIX" -  Richard Stallman

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#3 2022-01-14 15:12:33

nikinbaidarr
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Registered: 2021-05-06
Posts: 53

Re: [SOLVED]Install libgsl.so.0 package

Trilby wrote:

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!

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#4 2022-01-14 16:18:35

Scimmia
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Re: [SOLVED]Install libgsl.so.0 package

Symlinking different libraries is NOT the answer. If you must have an old version because you're running old, proprietary binaries, you need to build and install the old version.

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#5 2022-01-15 01:02:49

Trilby
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Re: [SOLVED]Install libgsl.so.0 package

"Hey you were right, so I'm going to ignore the rest of your advice" *headdesk*

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.


"UNIX is simple and coherent..." - Dennis Ritchie, "GNU's Not UNIX" -  Richard Stallman

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#6 2022-01-15 05:35:42

nikinbaidarr
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Registered: 2021-05-06
Posts: 53

Re: [SOLVED]Install libgsl.so.0 package

Trilby wrote:

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.

Last edited by nikinbaidarr (2022-01-15 06:10:21)

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#7 2022-01-15 05:56:05

Trilby
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Re: [SOLVED]Install libgsl.so.0 package

Why would you downgrade the library - I said rebuild the failing programs against the current version of the library.

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.


"UNIX is simple and coherent..." - Dennis Ritchie, "GNU's Not UNIX" -  Richard Stallman

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#8 2022-01-15 06:22:58

nikinbaidarr
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Registered: 2021-05-06
Posts: 53

Re: [SOLVED]Install libgsl.so.0 package

Trilby wrote:

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.

Trilby wrote:

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.

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#9 2022-01-15 06:43:08

Trilby
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Re: [SOLVED]Install libgsl.so.0 package

Scimmia suggested getting an old version of the library to use for this binary if it was closed source.  This doesn't mean downgrading the current library (you can have multiple versions of a lib installed at once).  But this is beside the point as this is not closed source.

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.

Last edited by Trilby (2022-01-15 06:58:40)


"UNIX is simple and coherent..." - Dennis Ritchie, "GNU's Not UNIX" -  Richard Stallman

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#10 2022-01-15 07:38:45

nikinbaidarr
Member
Registered: 2021-05-06
Posts: 53

Re: [SOLVED]Install libgsl.so.0 package

Trilby wrote:

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.

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#11 2022-01-15 16:38:24

Trilby
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Re: [SOLVED]Install libgsl.so.0 package

I have no idea - just look at what's built and what you actually want installed, and add commands to the package function to cp/install those binaries.

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.


"UNIX is simple and coherent..." - Dennis Ritchie, "GNU's Not UNIX" -  Richard Stallman

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#12 2022-01-16 09:48:23

nikinbaidarr
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Registered: 2021-05-06
Posts: 53

Re: [SOLVED]Install libgsl.so.0 package

Trilby wrote:

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.

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