Package Details: fsl 6.0.7.7-1

Git Clone URL: https://aur.archlinux.org/fsl.git (read-only, click to copy)
Package Base: fsl
Description: A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data
Upstream URL: http://www.fmrib.ox.ac.uk/fsl/
Licenses: custom
Submitter: fishburn
Maintainer: tobac
Last Packager: tobac
Votes: 12
Popularity: 0.000000
First Submitted: 2012-07-02 23:36 (UTC)
Last Updated: 2024-03-03 11:32 (UTC)

Dependencies (1)

Required by (4)

Sources (1)

Latest Comments

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liamtimms commented on 2022-02-04 15:14 (UTC) (edited on 2022-02-04 15:14 (UTC) by liamtimms)

out of curiosity, has anyone been able to get this build to complete at all recently? my last successful build was in October

tobac commented on 2021-11-29 17:41 (UTC)

You certainly can, but it's probably the same error that's been popping up and we don't have solution for.

liamtimms commented on 2021-11-29 13:26 (UTC)

getting a failed build in fslsurface, do you want me to email log file?

tobac commented on 2021-10-07 23:33 (UTC)

It should and will be.

liamtimms commented on 2021-10-07 21:45 (UTC)

@tobac thanks, maybe it should be a make dependency? (if it is not needed after building+checking)

tobac commented on 2021-10-07 16:33 (UTC)

@liamtimms: "inetutils" has to be installed, I might add this to the dependencies.

liamtimms commented on 2021-10-07 16:32 (UTC)

hitting an error in the check function: 


Build completed successfully.
==> Starting check()...
couldn't execute "hostname": no such file or directory
    while executing
"exec hostname "
    (file "/home/ripley/.cache/paru/clone/fsl/src/fsl/tcl/fslstart.tcl" line 10)
    invoked from within
"source ${FSLDIR}/tcl/fslstart.tcl"
    (file "./RUN" line 179)
==> ERROR: A failure occurred in check().
    Aborting...

javierbg commented on 2021-09-12 19:11 (UTC) (edited on 2021-09-12 19:12 (UTC) by javierbg)

I really don't think this is a CPU issue, this has to be a linker configuration error, albeit a weird one.

I have let makepkg prepare the sources and canceled right before building and tried from scratch. It built successfully.

I have investigated the specific link errors given on the log (fslsurface_name::getFSLtoNIFTIxfm, fslsurface_name::meshRegLeastSq, fslsurface_name::vertexMVglm, fslsurface_name::FtoP, fslsurface_name::reconAllSurfacesAndSave, and fslsurface_name::reconSurface_from_bvars) and they are all defined in the same header, fslsurface/fslsurface_first.h, which is both in src and include, although my knowledge of how the linker works is too limited to know if that means anything.

tobac commented on 2021-09-10 17:04 (UTC) (edited on 2021-09-11 05:46 (UTC) by tobac)

That's strange. Did you delete the sources before manually building it? My thinking is, maybe a dependency of fslsurface gets created later, i.e. too late, during the build process and by keeping the sources (and resulting files) in place you can make it build because that dependency still exists.

EDIT: I'm going to get my hands on an AMD machine, this weirdness has to stop (not that the CPU is necessarily the culprit, but it's a clue at least)

EDIT 2: It builds just fine on a recent Ryzen machine

javierbg commented on 2021-09-10 16:57 (UTC)

Reinstalling CUDA did not solve this. I tried running './build fslsurface' in the "src/fsl" directory and, surprisingly, it completed successfully. I have actually been able to build everything by copying the commands from the PKGBUILD file (NJOBS=6), but running makepkg is unsuccessful.

It is running on a laptop with an AMD Ryzen 5 4500U laptop (HP Probook x360 435 G7).

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