Package Details: fsl 6.0.4-2

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: 11
Popularity: 0.048184
First Submitted: 2012-07-02 23:36
Last Updated: 2020-08-26 10:02

Latest Comments

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martin3141 commented on 2019-03-23 17:21

v6.0.1 is working for me now - thanks :)

My original problem with the check failure was also an issue with v6.0.1. Turned out the cause was that the python-deprecation package was missing from my system, maybe this should be added to the makedepends for fsl, or perhaps it should be a dependency (rather than a makedepends) for fslpy (there is a comment suggesting this from AKSoo).

tobac commented on 2019-03-23 10:18

Well, it's even simpler and somewhat embarrassing. I forgot to copy the adapted 001-use_distribution_environment.patch from my test environment to my "release environment". That's why it worked for me and didn't for you. You shouldn't do things in a hurry. Fixed.

martin3141 commented on 2019-03-23 07:00

Thanks for updating! I think you forgot to update a checksum : "001-use_distribution_environment.patch ... FAILED"

Skipping the check with --skipinteg reveals a further issue: " patching file fsl/etc/fslconf/fsl.sh patching file fsl/etc/fslconf/fsl.csh patching file fsl/etc/fslconf/fsl-devel.sh patching file fsl/extras/build patching file fsl/src/mist-clean/Makefile can't find file to patch at input line 110 Perhaps you used the wrong -p or --strip option? "

tobac commented on 2019-03-22 20:07

Updated to FSL version 6.0.1. I also decided to reduce the clunkiness of 001-use_distribution_environment.patch and ship {externallibs,systemvars}.mk as separate files. Seems less ugly this way.

martin3141 commented on 2019-03-22 14:27

Hi, this is for 6.0.0, but if you're working on 6.0.1 then no need to update as I don't mind waiting for the next version. Thanks for the effort!

tobac commented on 2019-03-22 14:24

Hi Martin, I'm in the process of packaging 6.0.1. Is this the 6.0.0 you're trying to build or did you modify the PKGBUILD etc. yourself for 6.0.1?

martin3141 commented on 2019-03-22 14:13

I'm getting the following error in check():

Starting SIENAX (including testing BET and FLIRT and FAST) at Fri 22 Mar 13:05:59 GMT 2019
child process exited abnormally
while executing
"fsl:exec "${FSLDIR}/bin/imcp $FEEDSDIR/data/structural $FEEDSDIR/results/structural"" invoked from within
"if { $feeds(sienax) } {

puts "\nStarting SIENAX (including testing BET and FLIRT and FAST) at [ exec date ]"

fsl:exec "${FSLDIR}/bin/imcp $FEEDSDIR/..."
(file "./RUN" line 233)
==> ERROR: A failure occurred in check().
Aborting...

fishburn commented on 2018-11-30 18:31

@tobac Great job with the package! Definitely much cleaner now. I just always hate trying to figure out what changed when the patch no longer applies after a version change (though still better than sed silently failing). Also curious to see if the phenomenon persists where a working package just changes hashes or stops building without any version change.

tobac commented on 2018-11-26 16:54

I adopted the package, rewrote the PKGBUILD to use less sed magic and adopted instead a patch-based modification technique (although having one huge patch file for environment modification doesn't strike me as particularly elegant either). Fishburn is absolutely right, it is an awful package to maintain. Anyway, it builds, tests run successfully and it seems to work.

fishburn commented on 2018-11-14 16:13

I'm abandoning this until they adopt a typical build system (e.g., automake, cmake). Best of luck