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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: | |
Submitter: | fishburn |
Maintainer: | tobac |
Last Packager: | tobac |
Votes: | 12 |
Popularity: | 0.31 |
First Submitted: | 2012-07-02 23:36 |
Last Updated: | 2020-08-26 10:02 |
Dependencies (23)
- bc (bc-gh)
- boost-libs (boost171, boost-libs-git)
- fslpy
- gd
- glu (glu-git)
- gsl
- libpng (libpng-git, libpng-apng, libpng-minimal-git)
- libxml++2.6
- libxml2 (libxml2-linenum, libxml2-git)
- newmat (newmat-beta, newmat-shared)
- nlopt
- openblas (openblas-lapack-git, openblas-git, openblas-lapack-static, openblas-cblas-git, openblas-lapack, libopenblas)
- python (python-dbg)
- python3 (python)
- sqlite (sqlite-fossil, sqlite-replication, sqlite-fts3-parenthesis, sqlite-minimal-git)
- tcl (tcl85, tcl-nothreading)
- tk (tk85)
- vtk (vtk-visit, vtk-raytracing-git, vtk-git, vtk9)
- zlib (zlib-static, zlib-git, zlib-asm, minizip-asm, zlib-ng-git)
- boost (boost-git) (make)
- fftw (fftw-mpich, fftw-mpi, fftw-amd) (make)
- gcc9 (make)
- cuda (cuda65, cuda-11.0) (optional)
Required by (3)
- fsl-palm (optional)
- fsleyes (optional)
- python-nipype (optional)
Sources (12)
- 001-use_distribution_environment.patch
- 002-fix_meldata_usage_of_ifstream.patch
- 003-fix_fsl_exec_empty_errorCode.patch
- 004-fix_missing_LIB_PROB.patch
- 005-fix_cuda_thrust_include.patch
- 006-compile_ptx2_without_std-c++11.patch
- buildSettings.mk
- https://www.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.4-feeds.tar.gz
- https://www.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.4-sources.tar.gz
- imcp
- imglob
- immv
Latest Comments
1 2 3 4 5 6 ... Next › Last »
liamtimms commented on 2020-12-03 19:04
@quoctri thanks for investigating this, installing CUDA did the trick. Unfortunate to pull such a large dependency but it does work.
keiichiiownsu12 commented on 2020-11-21 02:05
@tobac would it help if some of us sent you information about the build environment we are using?
quoctri commented on 2020-11-20 14:07
Getting the same error as @liamtimms. Inspecting the builld logs for projects fdt and ptx2 while searching for
make:.*Error
yields the following linesfdt:
ptx2:
@tobac I'll send you the complete build.log file by email. I'll try to investigate further as well.
EDIT: I'm not there yet, but I feel like I'm getting somewhere. I'm logging my process here hoping it will be useful to someone.
The previous errors were mitigated by installing cuda
pacman -S cuda
Then I got an error in the check() of the PKGBUILD:
So the build completes succesfully, but something was wrong with the imcp. I manually ran
${FSLDIR}/bin/imcp
which gave:So fslpy wasn't found. I checked this by running
pip list
, which indeed did not containfslpy
. So I manually ran the dependencyyay -S fslpy
. Fired up the python console and ran:Now manually ran the dependency
yay -S python-dataclasses
and ran the above again.Voila! I reran the package build and it built correctly!
ASIDE: Whenever I assigned multiple cores to makepkg in order to speed up the build I received:
Building with 1 core eliminated this. I changed this using the
MAKEFLAGS="-j1"
flag in/etc/makepkg.conf
, but a different more package specific option would probably be better:keiichiiownsu12 commented on 2020-09-14 22:34
@liamtimms you should email either @tobac or @adkipnis for a binary package, if you need to update.
liamtimms commented on 2020-08-28 15:35
Getting this:
in the build log on the new update. Haven't had time to investigate further.
tobac commented on 2020-08-26 10:01
FSL 6.0.4. Good luck.
tobac commented on 2020-07-26 20:45
@adkipnis Sent you an email.
adkipnis commented on 2020-07-26 12:01
@tobac I'd like to compare the two binaries in practice. How may I access your version? :)
tobac commented on 2020-07-19 07:51
Or just write me an email and I'll provide you with a binary Arch package :)
adkipnis commented on 2020-07-18 19:36
If you NEED to use fsl on your Arch install but cannot build it from source: I have dual booted Ubuntu with Arch and installed fsl there instead, then copied the contents of
/opt/fsl
to Arch, edited.bashrc
to includeand source
.bashrc
(cf. the FSL wiki on the general setup procedure).Had to additionally edit
/opt/fsl/tcl/fslstart.tcl
to change the lineset HOSTNAME "the-hostname-of-my-arch-install"
.And now fsl seems to run properly. Will give updates if I encounter bugs.