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Library not loaded: @rpath/libarchive.13.dyli on M1 Mac
Any mamba command results in the following error for me. I use a M1 Macbook and a fresh miniconda installation. Mamba was installed using conda install mamba -n base -c conda-forge.
Traceback (most recent call last):
File "/Users/kdubovikov/miniconda3/bin/mamba", line 7, in <module>
from mamba.mamba import main
File "/Users/kdubovikov/miniconda3/lib/python3.9/site-packages/mamba/mamba.py", line 53, in <module>
import mamba.mamba_api as api
ImportError: dlopen(/Users/kdubovikov/miniconda3/lib/python3.9/site-packages/mamba/mamba_api.cpython-39-darwin.so, 0x0002): Library not loaded: @rpath/libarchive.13.dylib
Referenced from: /Users/kdubovikov/miniconda3/lib/python3.9/site-packages/mamba/mamba_api.cpython-39-darwin.so
Reason: tried: '/Users/kdubovikov/miniconda3/lib/libarchive.13.dylib' (no such file), '/Users/kdubovikov/miniconda3/lib/libarchive.13.dylib' (no such file), '/Users/kdubovikov/miniconda3/libarchive.13.dylib' (no such file), '/Users/kdubovikov/miniconda3/lib/python3.9/site-packages/mamba/../../../libarchive.13.dylib' (no such file), '/Users/kdubovikov/miniconda3/lib/libarchive.13.dylib' (no such file), '/Users/kdubovikov/miniconda3/lib/libarchive.13.dylib' (no such file), '/Users/kdubovikov/miniconda3/libarchive.13.dylib' (no such file), '/Users/kdubovikov/miniconda3/lib/python3.9/site-packages/mamba/../../../libarchive.13.dylib' (no such file), '/Users/kdubovikov/miniconda3/lib/libarchive.13.dylib' (no such file), '/Users/kdubovikov/miniconda3/bin/../lib/libarchive.13.dylib' (no such file), '/Users/kdubovikov/miniconda3/lib/libarchive.13.dylib' (no such file), '/Users/kdubovikov/miniconda3/bin/../lib/libarchive.13.dylib' (no such file), '/usr/local/lib/libarchive.13.dylib' (no such file), '/usr/lib/libarchive.13.dylib' (no such file)
can you send me your conda list? Is libarchive installed from the conda-forge channel?
I would advise you to start from mambaforge: https://github.com/conda-forge/miniforge#mambaforge
@wolfv , wow, that's a quick reply. Thank you.
# packages in environment at /Users/kdubovikov/miniconda3:
#
# Name Version Build Channel
boto3 1.24.28 py39hca03da5_0
botocore 1.27.28 py39hca03da5_0
brotlipy 0.7.0 py39h1a28f6b_1002
ca-certificates 2022.07.19 hca03da5_0
certifi 2022.6.15 py39hca03da5_0
cffi 1.15.0 py39h22df2f2_1
charset-normalizer 2.0.4 pyhd3eb1b0_0
conda 4.13.0 py39hca03da5_0
conda-package-handling 1.8.1 py39h1a28f6b_0
cryptography 37.0.1 py39h834c97f_0
idna 3.3 pyhd3eb1b0_0
jmespath 0.10.0 pyhd3eb1b0_0
libcxx 12.0.0 hf6beb65_1
libffi 3.4.2 hc377ac9_4
ncurses 6.3 h1a28f6b_3
openssl 1.1.1q h1a28f6b_0
pip 22.1.2 py39hca03da5_0
pycosat 0.6.3 py39h1a28f6b_0
pycparser 2.21 pyhd3eb1b0_0
pyopenssl 22.0.0 pyhd3eb1b0_0
pysocks 1.7.1 py39hca03da5_0
python 3.9.12 hbdb9e5c_0
python-dateutil 2.8.2 pyhd3eb1b0_0
python.app 3 py39h1a28f6b_0
readline 8.1.2 h1a28f6b_1
requests 2.28.1 py39hca03da5_0
ruamel_yaml 0.15.100 py39h1a28f6b_0
s3transfer 0.6.0 py39hca03da5_0
setuptools 61.2.0 py39hca03da5_0
six 1.16.0 pyhd3eb1b0_1
sqlite 3.38.5 h1058600_0
tk 8.6.12 hb8d0fd4_0
tqdm 4.64.0 py39hca03da5_0
tzdata 2022a hda174b7_0
urllib3 1.26.9 py39hca03da5_0
wheel 0.37.1 pyhd3eb1b0_0
xz 5.2.5 h1a28f6b_1
yaml 0.2.5 h1a28f6b_0
zlib 1.2.12 h5a0b063_2
I don't think that libarchive is installed, but I expected that to be installed as a dependency since the installation manual did not say to install it manually
I have installed libarchive with conda install libarchive -n base -c conda-forge and now everything works. Maybe mamba dependencies in conda-forge should be modified to include libarchive for Apple Silicon.
mamba is also not in your conda list output?
libarchive should definitely be installed. I also think it is needed for conda-package-handling. Very weird.
@wolfv I've actually removed mamba right before doing conda list so that's why it isn't there. I have re-installed it again after that.
Also, I don't see libarchive as a dependency for conda-package-handling:
conda-package-handling[1.8.1]
├─ python[3.9.13]
│ ├─ bzip2[1.0.8]
│ ├─ libffi[3.4.2]
│ │ └─ libcxx[14.0.6]
│ ├─ libzlib[1.2.12]
│ ├─ ncurses[6.3]
│ ├─ openssl[1.1.1q]
│ │ └─ ca-certificates[2022.6.15]
│ ├─ readline[8.1.2]
│ │ └─ ncurses already visited
│ ├─ sqlite[3.38.5]
│ │ ├─ readline already visited
│ │ └─ zlib[1.2.12]
│ ├─ tk[8.6.12]
│ │ └─ zlib already visited
│ ├─ tzdata[2022a]
│ ├─ xz[5.2.5]
│ └─ pip[22.1.2]
│ ├─ setuptools[61.2.0]
│ │ ├─ certifi[2022.6.15]
│ │ │ └─ python_abi[3.9]
│ ├─ wheel[0.37.1]
│ ├─ solvable:prereqmarker >>> NOT FOUND <<<
└─ tqdm[4.64.0]
└─ python already visited
interesting. It's definitely required for mamba, though. Do you have a new conda list? I think things would work if you also pass --strict-channel-priority.
Sure, here is a new one
# packages in environment at /Users/kdubovikov/miniconda3:
#
# Name Version Build Channel
boto3 1.24.28 py39hca03da5_0
botocore 1.27.28 py39hca03da5_0
brotlipy 0.7.0 py39h1a28f6b_1002
bzip2 1.0.8 h3422bc3_4 conda-forge
c-ares 1.18.1 h3422bc3_0 conda-forge
ca-certificates 2022.07.19 hca03da5_0
certifi 2022.6.15 py39h2804cbe_0 conda-forge
cffi 1.15.0 py39h22df2f2_1
charset-normalizer 2.0.4 pyhd3eb1b0_0
conda 4.13.0 py39h2804cbe_1 conda-forge
conda-package-handling 1.8.1 py39h1a28f6b_0
cryptography 37.0.1 py39h834c97f_0
icu 68.2 hbdafb3b_0 conda-forge
idna 3.3 pyhd3eb1b0_0
jmespath 0.10.0 pyhd3eb1b0_0
krb5 1.19.3 hf9b2bbe_0 conda-forge
libarchive 3.5.2 h69ec738_3 conda-forge
libcurl 7.83.1 h2fcd78c_0 conda-forge
libcxx 14.0.6 h04bba0f_0 conda-forge
libedit 3.1.20191231 hc8eb9b7_2 conda-forge
libev 4.33 h642e427_1 conda-forge
libffi 3.4.2 hc377ac9_4
libiconv 1.16 h642e427_0 conda-forge
libmamba 0.25.0 h1c735bf_1 conda-forge
libmambapy 0.25.0 py39h5b36d7b_1 conda-forge
libnghttp2 1.47.0 he723fca_0 conda-forge
libpq 12.9 h65cfe13_3
libsolv 0.7.22 h1280f1d_0 conda-forge
libssh2 1.10.0 hb80f160_2 conda-forge
libxml2 2.9.14 h8c5e841_0
libzlib 1.2.12 ha287fd2_2 conda-forge
lz4-c 1.9.3 hbdafb3b_1 conda-forge
lzo 2.10 h642e427_1000 conda-forge
mamba 0.25.0 py39hde45b87_1 conda-forge
ncurses 6.3 h1a28f6b_3
openssl 1.1.1q ha287fd2_0 conda-forge
pip 22.1.2 py39hca03da5_0
psycopg2 2.8.6 py39hf27765b_1
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.3 py39h1a28f6b_0
pycparser 2.21 pyhd3eb1b0_0
pyopenssl 22.0.0 pyhd3eb1b0_0
pysocks 1.7.1 py39hca03da5_0
python 3.9.13 hc596b02_0_cpython conda-forge
python-dateutil 2.8.2 pyhd3eb1b0_0
python.app 3 py39h1a28f6b_0
python_abi 3.9 2_cp39 conda-forge
readline 8.1.2 h1a28f6b_1
reproc 14.2.3 h3422bc3_0 conda-forge
reproc-cpp 14.2.3 hbdafb3b_0 conda-forge
requests 2.28.1 py39hca03da5_0
ruamel_yaml 0.15.100 py39h1a28f6b_0
s3transfer 0.6.0 py39hca03da5_0
setuptools 61.2.0 py39hca03da5_0
six 1.16.0 pyhd3eb1b0_1
sqlite 3.38.5 h1058600_0
tk 8.6.12 hb8d0fd4_0
tqdm 4.64.0 py39hca03da5_0
tzdata 2022a hda174b7_0
urllib3 1.26.9 py39hca03da5_0
wheel 0.37.1 pyhd3eb1b0_0
xz 5.2.5 h1a28f6b_1
yaml 0.2.5 h1a28f6b_0
yaml-cpp 0.7.0 h9a09cb3_1 conda-forge
zlib 1.2.12 h5a0b063_2
zstd 1.5.2 h861e0a7_0 conda-forge
i've experienced the same problem, and the hack proposed above works. conda install libarchive -n base -c conda-forge
Experienced the same problem, with the same solution. With the pkgs/main version of libarchive 3.5.2, there's a libarchive.18.dylib in ~/miniconda3/lib, but no libarchive.13.dylib. With the conda-forge version, there's a libarchive.13.dylib, which mamba expects.
I was installing some specific packages for my environment install libllvm15 lit llvm llvm-tools llvmdev that really messed up some of my paths!
Still reproducing this error and didn't find a way to go around it.
My solution was uninstalling everything and starting over with a clean installation.
Hi,
I am getting a similar problem after upgrading mamba in the base env from 1.0.0 to 1.2.0.
Traceback (most recent call last):
File "/Users/jovan/miniconda3/bin/mamba", line 7, in <module>
from mamba.mamba import main
File "/Users/jovan/miniconda3/lib/python3.8/site-packages/mamba/mamba.py", line 49, in <module>
import libmambapy as api
File "/Users/jovan/miniconda3/lib/python3.8/site-packages/libmambapy/__init__.py", line 7, in <module>
raise e
File "/Users/jovan/miniconda3/lib/python3.8/site-packages/libmambapy/__init__.py", line 4, in <module>
from libmambapy.bindings import * # noqa: F401,F403
ImportError: dlopen(/Users/jovan/miniconda3/lib/python3.8/site-packages/libmambapy/bindings.cpython-38-darwin.so, 0x0002): Library not loaded: @rpath/libarchive.13.dylib
Referenced from: <DC674B59-AD78-3A3E-9D76-D190B3490F4D> /Users/jovan/miniconda3/lib/libmamba.2.0.0.dylib
Reason: tried: '/Users/jovan/miniconda3/lib/libarchive.13.dylib' (no such file), '/Users/jovan/miniconda3/lib/python3.8/site-packages/libmambapy/../../../libarchive.13.dylib' (no such file), '/Users/jovan/miniconda3/lib/python3.8/site-packages/libmambapy/../../../libarchive.13.dylib' (no such file), '/Users/jovan/miniconda3/bin/../lib/libarchive.13.dylib' (no such file), '/Users/jovan/miniconda3/bin/../lib/libarchive.13.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS@rpath/libarchive.13.dylib' (no such file), '/Users/jovan/miniconda3/lib/libarchive.13.dylib' (no such file), '/Users/jovan/miniconda3/lib/python3.8/site-packages/libmambapy/../../../libarchive.13.dylib' (no such file), '/Users/jovan/miniconda3/lib/python3.8/site-packages/libmambapy/../../../libarchive.13.dylib' (no such file), '/Users/jovan/miniconda3/bin/../lib/libarchive.13.dylib' (no such file), '/Users/jovan/miniconda3/bin/../lib/libarchive.13.dylib' (no such file), '/usr/local/lib/libarchive.13.dylib' (no such file), '/usr/lib/libarchive.13.dylib' (no such file, not in dyld cache)
The hack of re-installing mamba and/or libarchive did not work..
Here is a my conda list if that helps
# Name Version Build Channel
appnope 0.1.2 py38h10201cd_2 conda-forge
asttokens 2.2.1 pyhd8ed1ab_0 conda-forge
awscli 1.22.74 py38h10201cd_0 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
botocore 1.24.19 pyhd8ed1ab_0 conda-forge
brotlipy 0.7.0 py38hea4295b_1003 conda-forge
bzip2 1.0.8 h3422bc3_4 conda-forge
c-ares 1.18.1 h3422bc3_0 conda-forge
ca-certificates 2022.12.7 h4653dfc_0 conda-forge
certifi 2022.12.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.0 py38hc67bbb8_0 conda-forge
chardet 4.0.0 py38hca03da5_1003
charset-normalizer 2.0.12 pyhd8ed1ab_0 conda-forge
colorama 0.4.3 py_0 conda-forge
commonmark 0.9.1 py_0 conda-forge
conda 22.11.1 py38h10201cd_1 conda-forge
conda-package-handling 1.8.0 py38h33210d7_0 conda-forge
cryptography 38.0.2 py38h23f6d3d_2 conda-forge
curl 7.87.0 h9049daf_0 conda-forge
dataclasses 0.8 pyhc8e2a94_3 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
distro 1.6.0 pyhd8ed1ab_0 conda-forge
docutils 0.15.2 py38h10201cd_3 conda-forge
executing 1.2.0 pyhd8ed1ab_0 conda-forge
expat 2.4.7 h6b3803e_0 conda-forge
fmt 9.1.0 hffc8910_0 conda-forge
future 0.18.2 py38h10201cd_4 conda-forge
gettext 0.21.1 h0186832_0 conda-forge
git 2.35.1 pl5321hdb569e8_0 conda-forge
icu 69.1 hbdafb3b_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
ipython 8.1.1 py38h10201cd_0 conda-forge
jedi 0.18.1 py38h10201cd_0 conda-forge
jmespath 0.10.0 pyh9f0ad1d_0 conda-forge
krb5 1.20.1 h69eda48_0 conda-forge
libarchive 3.6.2 h3d4dd14_0
libblas 3.9.0 16_osxarm64_openblas conda-forge
libcblas 3.9.0 16_osxarm64_openblas conda-forge
libcurl 7.87.0 h9049daf_0 conda-forge
libcxx 14.0.6 h2692d47_0 conda-forge
libedit 3.1.20191231 hc8eb9b7_2 conda-forge
libev 4.33 h642e427_1 conda-forge
libffi 3.4.2 h3422bc3_5 conda-forge
libgfortran 5.0.0 11_3_0_hd922786_27 conda-forge
libgfortran5 11.3.0 hdaf2cc0_27 conda-forge
libiconv 1.17 he4db4b2_0 conda-forge
liblapack 3.9.0 16_osxarm64_openblas conda-forge
libmamba 1.2.0 h7d1d596_0 conda-forge
libmambapy 1.2.0 py38hee20f4a_0 conda-forge
libnghttp2 1.47.0 h519802c_1 conda-forge
libopenblas 0.3.21 openmp_hc731615_3 conda-forge
libsolv 0.7.23 hb5ab8b9_0 conda-forge
libssh2 1.10.0 h7a5bd25_3 conda-forge
libxml2 2.9.14 h815018a_4 conda-forge
libzlib 1.2.13 h03a7124_4 conda-forge
llvm-openmp 15.0.7 h7cfbb63_0 conda-forge
lz4-c 1.9.4 hb7217d7_0 conda-forge
lzo 2.10 h642e427_1000 conda-forge
mamba 1.2.0 py38hb2d7053_0 conda-forge
matplotlib-inline 0.1.3 pyhd8ed1ab_0 conda-forge
ncurses 6.3 hc470f4d_0 conda-forge
numpy 1.24.1 py38hac8ee1c_0 conda-forge
openssl 3.0.7 h03a7124_2 conda-forge
pandas 1.5.2 py38h61dac83_0 conda-forge
parso 0.8.3 pyhd8ed1ab_0 conda-forge
pcre2 10.37 hc5de063_0 conda-forge
perl 5.32.1 2_h9b22ae9_perl5 conda-forge
pexpect 4.8.0 pyh9f0ad1d_2 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pip 22.0.4 pyhd8ed1ab_0 conda-forge
pluggy 1.0.0 pyhd8ed1ab_5 conda-forge
prompt-toolkit 3.0.27 pyha770c72_0 conda-forge
psutil 5.9.0 py38hea4295b_0 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
py-cpuinfo 8.0.0 pyhd8ed1ab_0 conda-forge
pyasn1 0.4.8 py_0 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.3 py38hea4295b_1009 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.11.2 pyhd8ed1ab_0 conda-forge
pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 py38h10201cd_4 conda-forge
python 3.8.13 hd3575e6_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python.app 3 py38h1230e6a_0
python_abi 3.8 2_cp38 conda-forge
pytz 2022.7.1 pyhd8ed1ab_0 conda-forge
pyyaml 5.4.1 py38hea4295b_1 conda-forge
readline 8.1 h1230e6a_0
reproc 14.2.3 h3422bc3_0 conda-forge
reproc-cpp 14.2.3 hbdafb3b_0 conda-forge
requests 2.27.1 pyhd8ed1ab_0 conda-forge
rich 11.2.0 pyhd8ed1ab_0 conda-forge
rsa 4.7.2 pyh44b312d_0 conda-forge
ruamel.yaml 0.17.21 py38hb991d35_2 conda-forge
ruamel.yaml.clib 0.2.7 py38hb991d35_1 conda-forge
ruamel_yaml 0.15.100 py38h1230e6a_0
s3transfer 0.5.2 pyhd8ed1ab_0 conda-forge
setuptools 60.9.3 py38h10201cd_0 conda-forge
six 1.16.0 pyhd3eb1b0_0
sqlite 3.37.1 h7e3ccbd_0 conda-forge
sshuttle 1.1.0 pyhd8ed1ab_0 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
textual 0.1.17 pyhd8ed1ab_0 conda-forge
tiptop 0.2.5 pyhd8ed1ab_0 conda-forge
tk 8.6.12 he1e0b03_0 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
tqdm 4.63.0 pyhd8ed1ab_0 conda-forge
traitlets 5.1.1 pyhd8ed1ab_0 conda-forge
typing-extensions 3.10.0.2 hd8ed1ab_0 conda-forge
typing_extensions 3.10.0.2 pyha770c72_0 conda-forge
urllib3 1.26.8 pyhd8ed1ab_1 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xz 5.2.10 h80987f9_1
yaml 0.2.5 h3422bc3_2 conda-forge
yaml-cpp 0.7.0 hb7217d7_2 conda-forge
zlib 1.2.13 h03a7124_4 conda-forge
zstd 1.5.2 hf913c23_6 conda-forge
Any advice short of re-installing everything? (I would not want to use my other environments.. )
Edit: downgrading mamba to 1.0.0 makes things work again. I might keep it like this until I am in a position to do a re-install..
If you're open to trying Micromamba: it doesn't have those kinds of problems.
@jonashaag I am very open :). In fact I use micromamba docker for productionizing some projects. I would happily switch to either that or mambaforge as suggested by @wolfv when the current batch of projects wraps up..
Hi, I had the same issue on my M1 Mac when installing the latest mamba (1.3.1). As with @JovanVeljanoski, downgrading to 1.0.0 fixed the issue (did not try any of the versions in-between).
I had the same problem and tried method of @kdubovikov but the problem still exists. Then tried the answer from here and successed:
brew install libarchive
ln -s /usr/local/opt/libarchive/lib/libarchive.13.dylib /usr/local/lib/
Neither the libarchive install hacks work for me on my M1. I basically have just given up on using mamba for the last six months rather than spend many more hours experimenting with how to fix this. ;-(
I finally had some time in between projects, just reinstalled conda, reinstalled mamba, and had my environments all up and running with no problems in 10 mins (multiple environments). No problems. Probably reinstalling your conda/mamba env every 1-2 years is not that bad of an idea..
I have a relatively new Mac M1 machine and set it up 6 months ago. There is a limit to how many experimental installs I am willing to do to work around bugs. The fact is that the mamba distribution is currently broken on the M1. It really should not be depending on files from outside the conda environment that might not exist or may not be compatible.
The M1 is a relatively new architecture, so it probably will still take a while before it gets supported routinely. :-(
I had the same problem and tried method of @kdubovikov but the problem still exists. Then tried the answer from here and successed:
brew install libarchive ln -s /usr/local/opt/libarchive/lib/libarchive.13.dylib /usr/local/lib/
Worked for me. thanks!
If you're open to trying Micromamba: it doesn't have those kinds of problems.
I couldn't get any of the suggested fixes in these threads to work, so I switched to micromamba. My errors are all resolved, and env creation is shockingly fast now! Thanks for the tip :)
I experienced the same error on an x86 Mac, but my libarchive was actually installed so conda install libarchive -n base -c conda-forge didn't work. I managed to figure out that somehow I ended up with the wrong version of the library, 19 instead of 13 and I managed to work around it by copying the 19 to the place of the 13 (I ran cp ./libarchive.19.dylib ./libarchive.13.dylib in the miniconda3 folder)
I had a very similar issue on my new M2 MacBook Pro. I found that a number of conda packages were not appearing for me in conda search even though I know they are distributed on bioconda. I found another thread that helped me fix that, using this command:
conda config --add subdirs osx-64
However, upon installing one of the desired tools, I had the same sort of "Library not loaded" as described by OP. After some frustration, I realized that there is a very simple solution. First, I noticed that my /usr/local directory doesn't contain a lib subdirectory. So I just did the following, linking my Homebrew lib to /usr/local and that seems to be working:
sudo ln -s /opt/homebrew/lib/ /usr/local/lib
Just so it doesn't get lost somewhere in the thread: Micromamba shouldn't have those problems, try that!
same problem while building a Docker container:
RUN conda install mamba=0.15.3 -n base -c conda-forge
#19 [15/55] RUN mamba --version
#19 0.731 Traceback (most recent call last):
#19 0.731 File "/root/miniconda/bin/mamba", line 7, in <module>
#19 0.731 from mamba.mamba import main
#19 0.731 File "/root/miniconda/lib/python3.9/site-packages/mamba/mamba.py", line 53, in <module>
#19 0.731 import mamba.mamba_api as api
#19 0.731 ImportError: libarchive.so.13: cannot open shared object file: No such file or directory
#19 ERROR: process "/bin/bash -c mamba --version" did not complete successfully: exit code: 1
I added this after installing mamba before running mamba --version
RUN conda install libarchive -n base -c conda-forge
# strangely, this does nothing and just reports > # All requested packages already installed.
and I also added apt-get update & upgrade to the top of the Dockerfile, now everything seems to work...
I ran into an error that might be related to this.
I made a complete fresh install of the latest miniconda (23.5.2) and installed mamba from conda-forge. I am unable to install anything using mamba, since it always throws this error:
ImportError: dlopen(~/miniconda3/lib/python3.11/site-packages/libmambapy/bindings.cpython-311-darwin.so, 2): Library not loaded: @rpath/libarchive.13.dylib Referenced from: ~/miniconda3/lib/libmamba.2.0.0.dylib Reason: image not found
On another machine I am running miniconda 23.1.0 in combination with mamba and it works perfect (and also did for a long time). So, I did the same on this machine and clean uninstalled miniconda 23.5.2 and replaced it with miniconda 23.1.0 and reinstalled mamba and now it works. There seems to be an incompatibility of mamba with the newest version of miniconda. Can anyone confirm this?
I have
2023-08-30T16:42:44Z #11 0.733 Traceback (most recent call last):
2023-08-30T16:42:44Z #11 0.733 File "/opt/conda/bin/mamba", line 7, in <module>
2023-08-30T16:42:44Z #11 0.733 from mamba.mamba import main
2023-08-30T16:42:44Z #11 0.733 File "/opt/conda/lib/python3.11/site-packages/mamba/mamba.py", line 49, in <module>
2023-08-30T16:42:44Z #11 0.733 import libmambapy as api
2023-08-30T16:42:44Z #11 0.733 File "/opt/conda/lib/python3.11/site-packages/libmambapy/__init__.py", line 7, in <module>
2023-08-30T16:42:44Z #11 0.734 raise e
2023-08-30T16:42:44Z #11 0.734 File "/opt/conda/lib/python3.11/site-packages/libmambapy/__init__.py", line 4, in <module>
2023-08-30T16:42:44Z #11 0.734 from libmambapy.bindings import * # noqa: F401,F403
2023-08-30T16:42:44Z #11 0.735 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2023-08-30T16:42:44Z #11 0.735 ImportError: libarchive.so.13: cannot open shared object file: No such file or directory
From building this Dockerfile https://github.com/Ouranosinc/PAVICS-e2e-workflow-tests/blob/cb53fec969539440269b313d8424dd436451269d/docker/Dockerfile#L1-L9
FROM continuumio/miniconda3
# Use mamba for much improved performance over conda.
# The 'channel_priority strict' did help conda but it was not enough.
RUN conda update conda -n base && \
conda install mamba -n base -c conda-forge -c defaults
mamba breaks right away on first use with the error above.
I am on Linux, not Mac but this is the only issue about libarchive.13 currently open so I thought I would centralize all the info here.
Don't mix conda-forge and defaults
With the ordering I used, conda-forge should have precedence over defaults.