mamba: Undefined symbol: archive_write_add_filter_zstd
Hi,
Since few days i have problems to install properly mamba.
I though it was local issues, but in case:
> conda create -n foo python=3.7.* git mamba
> conda activate foo
> mamba
Traceback (most recent call last):
File "/users/blissadm/conda/miniconda/envs/foo/bin/mamba", line 7, in <module>
from mamba.mamba import main
File "/users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/mamba/mamba.py", line 49, in <module>
import libmambapy as api
File "/users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/__init__.py", line 7, in <module>
raise e
File "/users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/__init__.py", line 4, in <module>
from libmambapy.bindings import * # noqa: F401,F403
ImportError: /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../../libmamba.so.2: undefined symbol: archive_write_add_filter_zstd
Sounds like the libarchive from the system is used
> ldd /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../../libmamba.so.2
linux-vdso.so.1 (0x00007ffdd2916000)
libsolv.so.1 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././libsolv.so.1 (0x00007f5c340e0000)
libsolvext.so.1 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././libsolvext.so.1 (0x00007f5c340c7000)
libarchive.so.13 => /usr/lib/x86_64-linux-gnu/libarchive.so.13 (0x00007f5c3398f000)
libcurl.so.4 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././libcurl.so.4 (0x00007f5c33fff000)
libcrypto.so.1.1 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././libcrypto.so.1.1 (0x00007f5c336bb000)
libyaml-cpp.so.0.7 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././libyaml-cpp.so.0.7 (0x00007f5c33634000)
libreproc++.so.14 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././libreproc++.so.14 (0x00007f5c33ff7000)
libreproc.so.14 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././libreproc.so.14 (0x00007f5c33fee000)
libstdc++.so.6 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././libstdc++.so.6 (0x00007f5c33480000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f5c3317c000)
libgcc_s.so.1 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././libgcc_s.so.1 (0x00007f5c33fd3000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f5c32ddd000)
/lib64/ld-linux-x86-64.so.2 (0x00007f5c33f5c000)
libz.so.1 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../../././libz.so.1 (0x00007f5c33fb9000)
libnettle.so.6 => /usr/lib/x86_64-linux-gnu/libnettle.so.6 (0x00007f5c32ba6000)
libacl.so.1 => /lib/x86_64-linux-gnu/libacl.so.1 (0x00007f5c3299d000)
liblzo2.so.2 => /lib/x86_64-linux-gnu/liblzo2.so.2 (0x00007f5c3277b000)
liblzma.so.5 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././liblzma.so.5 (0x00007f5c33f8e000)
liblz4.so.1 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././liblz4.so.1 (0x00007f5c32740000)
libbz2.so.1.0 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././libbz2.so.1.0 (0x00007f5c3272c000)
libxml2.so.2 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././libxml2.so.2 (0x00007f5c325c4000)
libnghttp2.so.14 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../../././libnghttp2.so.14 (0x00007f5c3259b000)
libssh2.so.1 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../../././libssh2.so.1 (0x00007f5c32557000)
libssl.so.1.1 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../../././libssl.so.1.1 (0x00007f5c324c6000)
libgssapi_krb5.so.2 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../../././libgssapi_krb5.so.2 (0x00007f5c32473000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f5c3226b000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f5c3204e000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f5c31e4a000)
libattr.so.1 => /lib/x86_64-linux-gnu/libattr.so.1 (0x00007f5c31c45000)
libicuuc.so.58 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../../././libicuuc.so.58 (0x00007f5c31a92000)
libkrb5.so.3 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././././libkrb5.so.3 (0x00007f5c319bb000)
libk5crypto.so.3 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././././libk5crypto.so.3 (0x00007f5c319a1000)
libcom_err.so.3 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././././libcom_err.so.3 (0x00007f5c33f82000)
libkrb5support.so.0 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././././libkrb5support.so.0 (0x00007f5c31992000)
libkeyutils.so.1 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././././libkeyutils.so.1 (0x00007f5c3198b000)
libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007f5c31774000)
libicudata.so.58 => /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../.././././libicudata.so.58 (0x00007f5c2fe72000)
libarchive is installed in the env
> conda list archive
# packages in environment at /users/blissadm/conda/miniconda/envs/foo:
#
# Name Version Build Channel
libarchive 3.5.2 h5de8990_0
Here is the installed mamba
> conda list mamba
# packages in environment at /users/blissadm/conda/miniconda/envs/foo:
#
# Name Version Build Channel
libmamba 0.24.0 hd8a31e3_1 conda-forge
libmambapy 0.24.0 py37h1ee4b26_1 conda-forge
mamba 0.24.0 py37h6dacc13_1 conda-forge
Do you have any idea if all this things are normal?
About this issue
- Original URL
- State: closed
- Created 2 years ago
- Comments: 17 (5 by maintainers)
I have noticed libarchive was not installed from conda-forge
With that extra update, everything looks to work fine
Feel free to close the issue. I am not sure there a problem or not.
Dont know how its possibly to close the issue when its not resolved…
Problem is that
libmamba.so.2build with dependency onbut
libarchiveshipped with conda/mamba contains onlylibarchive.so.18orlibarchive.so.19Dont know how to solve it correctly, but what I did:
thanks @wolfv I forced reinstall libarchive from
conda-forgeusing$ conda install libarchive --force-reinstall -yc conda-forgeand now things look good.this is the only thing that worked for me . Thanks!
$ conda install libarchive --force-reinstall -yc conda-forge