missing shared libraries when installed from conda / mamba

[jsbyysheng]

Describe the problem

I got error about missing shared libraries when installed from conda / mamba.

antsRegistration: error while loading shared libraries: libITKIOBruker-5.3.so.1: cannot open shared object file: No such file or directory

There is no problem if I run binary downloaded from github.
To Reproduce

curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh
mamba create -n ants_reg python=3.9
mamba activate ants_reg
mamba install -c conda-forge itk ants
antsRegistration --help

Then I got:

antsRegistration: error while loading shared libraries: libITKIOBruker-5.3.so.1: cannot open shared object file: No such file or directory

System information (please complete the following information)

• OS: Linux version 5.15.0-97-generic (buildd@lcy02-amd64-102) (gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0, GNU ld

ANTs version information

• ANTs code version: [output of antsRegistration --version]
• ANTs installation type:

ants                      2.5.1                h00ab1b0_0    conda-forge

[gdevenyi]

Please provide the output of command -v antsRegistration to confirm the location of the binary you are trying to run

[gdevenyi]

Also, the places for bug reports for the ants conda package is at,
https://github.com/conda-forge/ants-feedstock

[jsbyysheng]

Please provide the output of command -v antsRegistration to confirm the location of the binary you are trying to run

(ants_registration) ➜  ~ command -v antsRegistration
/home/myusername/miniforge3/envs/ants_registration/bin/antsRegistration

Also, the places for bug reports for the ants conda package is at, https://github.com/conda-forge/ants-feedstock

Should I move this issue to this place?

[gdevenyi]

Should I move this issue to this place?

Yes. In the meantime, there are static binaries available from the Release page here which do work.

[cookpa]

If you're confident that the issue is unique to conda, then yeah, https://github.com/conda-forge/ants-feedstock would be the best place to get help. The developers there will open issues here if there's things that need fixing in ANTs itself.

[gdevenyi]

(I did a quick confirmation, the ants conda package is indeed broken as reported right now)

[jsbyysheng]

(I did a quick confirmation, the ants conda package is indeed broken as reported right now)

Alright, I will close this issue and move it to https://github.com/conda-forge/ants-feedstock.

[cookpa]

@gdevenyi where are you seeing the conda build being broken? The status badges on the https://github.com/conda-forge/ants-feedstock are all green

[gdevenyi]

@gdevenyi where are you seeing the conda build being broken? The status badges on the https://github.com/conda-forge/ants-feedstock are all green

"Broken as reported". I went through the same steps, and antsRegistration gives the same error and won't run.

[cookpa]

Ah OK, thanks