Package Details: minc-toolkit-v2 1.9.17-2

Git Clone URL: https://aur.archlinux.org/minc-toolkit-v2.git (read-only)
Package Base: minc-toolkit-v2
Description: Medical Imaging NetCDF Toolkit
Upstream URL: https://www.mcgill.ca/bic/software/minc
Licenses: GPL3
Provides: minc-toolkit
Submitter: m-pilia
Maintainer: m-pilia
Last Packager: m-pilia
Votes: 0
Popularity: 0.000000
First Submitted: 2017-10-29 11:36
Last Updated: 2019-04-07 17:54

Required by (0)

Sources (2)

Latest Comments

bobschi commented on 2018-05-03 14:12

After some research I think the problem is related to hdf5 packages. There are three of them hdf5, hdf5-openmpi, hdf5-openmpi-java (from AUR). I had hdf5-openmpi-java installed (dependency of hdfview-beta), which seems to break the build process of this package (maybe because of the different compilers?). So I installed hdf5 and libhdf5 and now it works. But this is not really a solution... Any thoughts?

m-pilia commented on 2018-04-26 06:53

Hi! Ok, I am not really sure what the root cause is. I guess there is something wrong with how the shared library is built, either something unusual in your toolchain or some wrong/missing flag somewhere. I just tried a clean build of libhdf5 and minc-toolkit-v2 on another machine, and I could not reproduce this. I am really sorry this does not ring any obvious bell to me, but you may try asking in the forum, where you can find users definitely more experienced than me.

bobschi commented on 2018-04-25 20:21

Hi. I have tried reinstalling libhdf5, but still the same error occurs.

m-pilia commented on 2018-04-25 17:56

Hello bobschi!

From that error, it seems there is something wrong with the libhdf5.a library (the static version of hdf5). Have you already tried rebuilding and reinstalling the libhdf5 package, just to be sure?

To double check, I just tried to rebuild the MINC toolkit package on my machine, and it went fine (I have libhdf5-1.10.1-1 built from AUR).

As a side note, right now I am also updating this PKGBUILD to use the AUR package for ANTs, but this should be unrelated to this problem.

bobschi commented on 2018-04-25 11:07

Hi. I get the following error, when I try to install it.

/usr/bin/ld: /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.1/../../../../lib/libhdf5.a(H5Dint.o)(.text+0xe7b): unresolvable R_X86_64_PC32 relocation against symbol `H5D_def_dxpl_cache' /usr/bin/ld: final link failed: Nonrepresentable section on output collect2: error: ld returned 1 exit status make[2]: [ray_trace/CMakeFiles/ray_trace.dir/build.make:190: ray_trace/ray_trace] Error 1 make[1]: [CMakeFiles/Makefile2:16096: ray_trace/CMakeFiles/ray_trace.dir/all] Error 2 make: *** [Makefile:163: all] Error 2

Do you have any ideas how to fix this?