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)

Most upvoted comments

I have noticed libarchive was not installed from conda-forge

conda install libarchive==3.5.2 -c 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.2 build with dependency on

 ldd /users/blissadm/conda/miniconda/envs/foo/lib/python3.7/site-packages/libmambapy/../../../libmamba.so.2
...
	libarchive.so.13 => /usr/lib/x86_64-linux-gnu/libarchive.so.13 (0x00007f5c3398f000)

but libarchive shipped with conda/mamba contains only libarchive.so.18 or libarchive.so.19

Dont know how to solve it correctly, but what I did:

find /you_conda_folder/ -name 'libarchive.so'
cd /to_the_lib_folders/
ln -s libarchive.so libarchive.so.13

thanks @wolfv I forced reinstall libarchive from conda-forge using $ conda install libarchive --force-reinstall -yc conda-forge and now things look good.

this is the only thing that worked for me . Thanks! $ conda install libarchive --force-reinstall -yc conda-forge