missing shared libraries when installed from conda / mamba
jsbyysheng opened this issue · comments
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 --helpThen 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
Please provide the output of command -v antsRegistration to confirm the location of the binary you are trying to run
Also, the places for bug reports for the ants conda package is at,
https://github.com/conda-forge/ants-feedstock
Please provide the output of
command -v antsRegistrationto confirm the location of the binary you are trying to run
(ants_registration) ➜ ~ command -v antsRegistration
/home/myusername/miniforge3/envs/ants_registration/bin/antsRegistrationAlso, 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?
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.
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.
(I did a quick confirmation, the ants conda package is indeed broken as reported right now)
(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.
@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 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.
Ah OK, thanks