AUR (en) - fsl

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)

@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 (UTC)

@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 (UTC) (edited on 2020-11-20 19:20 (UTC) by quoctri)

Getting the same error as @liamtimms. Inspecting the builld logs for projects fdt and ptx2 while searching for make:.*Error yields the following lines

fdt:

make: /opt/cuda/bin/nvcc: No such file or directory                                                                               
make: *** [Makefile:174: libbedpostx_cuda.so] Error 127    
...
/usr/bin/ld: cannot find -lcudart                                                                                                   
/usr/bin/ld: cannot find -lcurand                                                                                                   
/usr/bin/ld: cannot find -lbedpostx_cuda                                                                                            
collect2: error: ld returned 1 exit status                                                                                        
make: *** [Makefile:185: xfibres_gpu] Error 1

ptx2:

make: /opt/cuda/bin/nvcc: No such file or directory                                                                               
make: *** [Makefile:116: tractography_gpu.o] Error 127

@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:

==> Starting build()...
Building projects - see build.log file for progress...
Build completed successfully.
==> Starting check()...

FSL Evaluation and Example Data Suite v6.0.4

start time = Fri Nov 20 04:36:17 PM CET 2020
hostname = beast-pc
os = Linux beast-pc 5.9.9-arch1-1 #1 SMP PREEMPT Wed, 18 Nov 2020 19:52:04 +0000 x86_64 GNU/Linux


/bin/rm -rf /home/an/builds/fsl/src/feeds/results ; mkdir /home/an/builds/fsl/src/feeds/results


Starting PRELUDE & FUGUE at Fri Nov 20 04:36:17 PM CET 2020
% error = 0.0
% error = 0.0

Starting SUSAN at Fri Nov 20 04:36:18 PM CET 2020
% error = 0.03

Starting SIENAX (including testing BET and FLIRT and FAST) at Fri Nov 20 04:36:32 PM CET 2020
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 235)
==> ERROR: A failure occurred in check().
    Aborting...

real    0m15.055s
user    0m14.832s
sys 0m0.204s

So the build completes succesfully, but something was wrong with the imcp. I manually ran ${FSLDIR}/bin/imcp which gave:

Traceback (most recent call last):
  File "./imcp", line 33, in <module>
    sys.exit(load_entry_point('fslpy==3.2.2', 'console_scripts', 'imcp')())
  File "./imcp", line 22, in importlib_load_entry_point
    for entry_point in distribution(dist_name).entry_points
  File "/usr/lib/python3.8/importlib/metadata.py", line 504, in distribution
    return Distribution.from_name(distribution_name)
  File "/usr/lib/python3.8/importlib/metadata.py", line 177, in from_name
    raise PackageNotFoundError(name)
importlib.metadata.PackageNotFoundError: fslpy

So fslpy wasn't found. I checked this by running pip list, which indeed did not contain fslpy. So I manually ran the dependency yay -S fslpy. Fired up the python console and ran:

$ python      
Python 3.8.6 (default, Sep 30 2020, 04:00:38) 
[GCC 10.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from pkg_resources import load_entry_point
>>> load_entry_point('fslpy==3.2.2.', 'console_scripts', 'imcp')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python3.8/site-packages/pkg_resources/__init__.py", line 473, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/usr/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2843, in load_entry_point
    return ep.load()
  File "/usr/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2446, in load
    self.require(*args, **kwargs)
  File "/usr/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2469, in require
    items = working_set.resolve(reqs, env, installer, extras=self.extras)
  File "/usr/lib/python3.8/site-packages/pkg_resources/__init__.py", line 770, in resolve
    raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'dataclasses' distribution was not found and is required by the application

Now manually ran the dependency yay -S python-dataclasses and ran the above again.

$ python                   
Python 3.8.6 (default, Sep 30 2020, 04:00:38) 
[GCC 10.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from pkg_resources import load_entry_point
>>> load_entry_point('fslpy==3.2.2.', 'console_scripts', 'imcp')
<function main at 0x7f79202dff70>

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:

/usr/bin/ld: /usr/bin/ld: DWARF error: could not find variable specification at offset 4de0d
/usr/bin/ld: DWARF error: could not find variable specification at offset 4dc00
/usr/bin/ld: DWARF error: could not find variable specification at offset 3338
/usr/bin/ld: DWARF error: could not find variable specification at offset 3395
/usr/bin/ld: DWARF error: could not find variable specification at offset 33fe
/usr/bin/ld: DWARF error: could not find variable specification at offset 2d3a4
/usr/bin/ld: DWARF error: could not find variable specification at offset 2d3b0
/usr/bin/ld: DWARF error: could not find variable specification at offset 2d9bf
/usr/bin/ld: DWARF error: could not find variable specification at offset 2da06
/usr/bin/ld: DWARF error: could not find variable specification at offset 2da4d
/usr/bin/ld: DWARF error: could not find variable specification at offset 2da94
/usr/bin/ld: DWARF error: could not find variable specification at offset 2dac3
/usr/bin/ld: DWARF error: could not find variable specification at offset 2dafe
/usr/bin/ld: DWARF error: could not find variable specification at offset 2db0a
/usr/bin/ld: DWARF error: could not find variable specification at offset 2db45
/usr/bin/ld: DWARF error: could not find variable specification at offset 2db51
/usr/bin/ld: DWARF error: could not find variable specification at offset 600d
/usr/bin/ld: DWARF error: could not find variable specification at offset 8c4a
/usr/bin/ld: DWARF error: could not find variable specification at offset 8c59
/usr/bin/ld: DWARF error: could not find variable specification at offset 8b8b
/usr/bin/ld: DWARF error: could not find variable specification at offset 8be8
/usr/bin/ld: DWARF error: could not find variable specification at offset 8c92
/usr/bin/ld: DWARF error: could not find variable specification at offset 8ca4
/usr/bin/ld: DWARF error: could not find variable specification at offset 8cda
/usr/bin/ld: DWARF error: could not find variable specification at offset 8ce9
/usr/bin/ld: DWARF error: could not find variable specification at offset 9a77
/usr/bin/ld: DWARF error: could not find variable specification at offset 9b22
/usr/bin/ld: DWARF error: could not find variable specification at offset 55ccb
/usr/bin/ld: DWARF error: could not find variable specification at offset 4d981
/usr/bin/ld: DWARF error: could not find variable specification at offset 4db8e
fslsurfacemaths.o: in function `main':
/home/an/builds/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:330: undefined reference to `fslsurface_name::getFSLtoNIFTIxfm(NEWIMAGE::volume<float> const&)'
/usr/bin/ld: /home/an/builds/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:355: undefined reference to `fslsurface_name::meshRegLeastSq(fslsurface_name::fslSurface<float, unsigned int> const&, fslsurface_name::fslSurface<float, unsigned int> const&, unsigned int const&)'
/usr/bin/ld: /home/an/builds/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:609: undefined reference to `fslsurface_name::reconSurface_from_bvars(fslsurface_name::fslSurface<float, unsigned int>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/usr/bin/ld: /home/an/builds/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:638: undefined reference to `fslsurface_name::FtoP(std::vector<float, std::allocator<float> > const&, int const&, int const&)'
/usr/bin/ld: /home/an/builds/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:647: undefined reference to `fslsurface_name::vertexMVglm(fslsurface_name::fslSurface<float, unsigned int>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
/usr/bin/ld: /home/an/builds/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:625: undefined reference to `fslsurface_name::reconAllSurfacesAndSave(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/usr/bin/ld: /home/an/builds/fsl/src/fsl/src/fslsurface/fslsurfacemaths.cpp:695: undefined reference to `NEWIMAGE::volume<short> fslsurface_name::fillMesh<float, unsigned int>(fslsurface_name::fslSurface<float, unsigned int> const&, NEWIMAGE::volume<short> const&, int const&)'
collect2: error: ld returned 1 exit status
make: *** [Makefile:61: fslsurfacemaths] Error 1
ar -r libfslsurface_backcompat.a fslsurface_first.o fslsurface_dataconv.o
ar: creating libfslsurface_backcompat.a
make: Target 'all' not remade because of errors.

 ========================= 
ERROR::Could not make fslsurface successfully

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 (UTC)

@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 (UTC)

Getting this:

!!ERROR in BUILD!!
  Could not make the following projects successfully:
    fdt ptx2

in the build log on the new update. Haven't had time to investigate further.

tobac commented on 2020-08-26 10:01 (UTC)

FSL 6.0.4. Good luck.

tobac commented on 2020-07-26 20:45 (UTC)

@adkipnis Sent you an email.

adkipnis commented on 2020-07-26 12:01 (UTC)

@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 (UTC)

Or just write me an email and I'll provide you with a binary Arch package :)

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liamtimms commented on 2020-12-03 19:04 (UTC)