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ImportError: libffi.so.7: cannot open shared object file: No such file or directory
Troubleshooting docs
- [X] My problem is not solved in the Troubleshooting docs
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Mambaforge
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ImportError: libffi.so.7
Latest version of Mamba
- [X] My problem is not solved with the latest version
Tried in Conda?
I have this problem with Conda as well, without using Mamba
Describe your issue
After mamba update mamba, I get
mamba create -n spades3.15.5 spades
ImportError: libffi.so.7: cannot open shared object file: No such file or directory
mamba update mamba
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mamba (0.23.0) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
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Looking for: ['mamba']
pkgs/main/linux-64 No change
conda-forge/linux-64 No change
conda-forge/noarch No change
bioconda/linux-64 No change
bioconda/noarch No change
pkgs/r/noarch No change
pkgs/main/noarch No change
pkgs/r/linux-64 No change
Pinned packages:
- python 3.9.*
Transaction
Prefix: /home/lorencm/miniconda3
Updating specs:
- mamba
- ca-certificates
- certifi
- openssl
Package Version Build Channel Size
──────────────────────────────────────────────────────────────────────────────────────────────
Install:
──────────────────────────────────────────────────────────────────────────────────────────────
+ archspec 0.2.2 pyhd8ed1ab_0 conda-forge/noarch Cached
+ boltons 23.0.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ conda-libmamba-solver 23.11.1 pyhd8ed1ab_0 conda-forge/noarch Cached
+ conda-package-streaming 0.9.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ fmt 10.1.1 h00ab1b0_0 conda-forge/linux-64 Cached
+ jsonpatch 1.33 pyhd8ed1ab_0 conda-forge/noarch Cached
+ jsonpointer 2.4 py39hf3d152e_3 conda-forge/linux-64 Cached
+ libnsl 2.0.1 hd590300_0 conda-forge/linux-64 Cached
+ libsqlite 3.44.0 h2797004_0 conda-forge/linux-64 Cached
+ libuuid 2.38.1 h0b41bf4_0 conda-forge/linux-64 Cached
+ packaging 23.2 pyhd8ed1ab_0 conda-forge/noarch Cached
+ pluggy 1.3.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ ruamel.yaml 0.18.5 py39hd1e30aa_0 conda-forge/linux-64 Cached
+ ruamel.yaml.clib 0.2.7 py39hd1e30aa_2 conda-forge/linux-64 Cached
+ zstandard 0.22.0 py39h6e5214e_0 conda-forge/linux-64 Cached
Upgrade:
──────────────────────────────────────────────────────────────────────────────────────────────
- c-ares 1.18.1 h7f98852_0 conda-forge
+ c-ares 1.21.0 hd590300_0 conda-forge/linux-64 Cached
- ca-certificates 2021.10.8 ha878542_0 conda-forge
+ ca-certificates 2023.11.17 hbcca054_0 conda-forge/linux-64 Cached
- certifi 2021.10.8 py39hf3d152e_2 conda-forge
+ certifi 2023.11.17 pyhd8ed1ab_0 conda-forge/noarch Cached
- conda 4.12.0 py39hf3d152e_0 conda-forge
+ conda 23.10.0 py39hf3d152e_1 conda-forge/linux-64 Cached
- conda-package-handling 1.7.3 py39h27cfd23_1 pkgs/main
+ conda-package-handling 2.2.0 pyh38be061_0 conda-forge/noarch Cached
- cryptography 36.0.0 py39h9ce1e76_0 pkgs/main
+ cryptography 41.0.5 py39hd4f0224_0 conda-forge/linux-64 Cached
- icu 70.1 h27087fc_0 conda-forge
+ icu 73.2 h59595ed_0 conda-forge/linux-64 Cached
- krb5 1.19.3 h3790be6_0 conda-forge
+ krb5 1.21.2 h659d440_0 conda-forge/linux-64 Cached
- ld_impl_linux-64 2.35.1 h7274673_9 pkgs/main
+ ld_impl_linux-64 2.40 h41732ed_0 conda-forge/linux-64 Cached
- libarchive 3.5.2 hccf745f_1 conda-forge
+ libarchive 3.7.2 h039dbb9_0 conda-forge/linux-64 Cached
- libcurl 7.83.0 h7bff187_0 conda-forge
+ libcurl 8.4.0 hca28451_0 conda-forge/linux-64 Cached
- libffi 3.3 he6710b0_2 pkgs/main
+ libffi 3.4.2 h7f98852_5 conda-forge/linux-64 Cached
- libgcc-ng 11.2.0 h1d223b6_16 conda-forge
+ libgcc-ng 13.2.0 h807b86a_3 conda-forge/linux-64 Cached
- libiconv 1.16 h516909a_0 conda-forge
+ libiconv 1.17 h166bdaf_0 conda-forge/linux-64 Cached
- libmamba 0.23.0 hd8a31e3_1 conda-forge
+ libmamba 1.5.3 had39da4_2 conda-forge/linux-64 Cached
- libmambapy 0.23.0 py39hd55135b_1 conda-forge
+ libmambapy 1.5.3 py39h10defb6_2 conda-forge/linux-64 Cached
- libnghttp2 1.47.0 h727a467_0 conda-forge
+ libnghttp2 1.58.0 h47da74e_0 conda-forge/linux-64 Cached
- libsolv 0.7.22 h6239696_0 conda-forge
+ libsolv 0.7.26 hfc55251_0 conda-forge/linux-64 Cached
- libssh2 1.10.0 ha56f1ee_2 conda-forge
+ libssh2 1.11.0 h0841786_0 conda-forge/linux-64 Cached
- libstdcxx-ng 11.2.0 he4da1e4_16 conda-forge
+ libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge/linux-64 Cached
- libxml2 2.9.14 h22db469_0 conda-forge
+ libxml2 2.11.6 h232c23b_0 conda-forge/linux-64 Cached
- libzlib 1.2.11 h166bdaf_1014 conda-forge
+ libzlib 1.2.13 hd590300_5 conda-forge/linux-64 Cached
- mamba 0.23.0 py39hfa8f2c8_1 conda-forge
+ mamba 1.5.3 py39hc5d2bb1_2 conda-forge/linux-64 Cached
- openssl 1.1.1n h166bdaf_0 conda-forge
+ openssl 3.1.4 hd590300_0 conda-forge/linux-64 Cached
- pyopenssl 21.0.0 pyhd3eb1b0_1 pkgs/main
+ pyopenssl 23.3.0 pyhd8ed1ab_0 conda-forge/noarch Cached
- python 3.9.7 h12debd9_1 pkgs/main
+ python 3.9.16 h2782a2a_0_cpython conda-forge/linux-64 Cached
- setuptools 58.0.4 py39h06a4308_0 pkgs/main
+ setuptools 68.2.2 pyhd8ed1ab_0 conda-forge/noarch Cached
- tk 8.6.11 h1ccaba5_0 pkgs/main
+ tk 8.6.13 noxft_h4845f30_101 conda-forge/linux-64 Cached
- xz 5.2.5 h7b6447c_0 pkgs/main
+ xz 5.2.6 h166bdaf_0 conda-forge/linux-64 Cached
- yaml-cpp 0.6.3 he1b5a44_4 conda-forge
+ yaml-cpp 0.8.0 h59595ed_0 conda-forge/linux-64 Cached
- zlib 1.2.11 h166bdaf_1014 conda-forge
+ zlib 1.2.13 hd590300_5 conda-forge/linux-64 Cached
- zstd 1.5.2 ha95c52a_0 conda-forge
+ zstd 1.5.5 hfc55251_0 conda-forge/linux-64 Cached
Summary:
Install: 15 packages
Upgrade: 32 packages
Total download: 0 B
──────────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done```
### mamba info / micromamba info
```shell
mamba info
ImportError: libffi.so.7: cannot open shared object file: No such file or directory
thread '<unnamed>' panicked at /home/conda/feedstock_root/build_artifacts/cryptography-split_1698192008573/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/pyo3-0.18.3/src/err/mod.rs:790:5:
Python API call failed
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
Traceback (most recent call last):
File "/home/lorencm/miniconda3/bin/mamba", line 7, in <module>
from mamba.mamba import main
File "/home/lorencm/miniconda3/lib/python3.9/site-packages/mamba/mamba.py", line 17, in <module>
from conda.cli.install import check_prefix, clone, get_revision
File "/home/lorencm/miniconda3/lib/python3.9/site-packages/conda/cli/install.py", line 20, in <module>
from ..core.index import calculate_channel_urls, get_index
File "/home/lorencm/miniconda3/lib/python3.9/site-packages/conda/core/index.py", line 24, in <module>
from .subdir_data import SubdirData, make_feature_record
File "/home/lorencm/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 52, in <module>
from ..trust.signature_verification import signature_verification
File "/home/lorencm/miniconda3/lib/python3.9/site-packages/conda/trust/signature_verification.py", line 13, in <module>
from conda_content_trust.authentication import verify_delegation, verify_root
File "/home/lorencm/miniconda3/lib/python3.9/site-packages/conda_content_trust/authentication.py", line 27, in <module>
import cryptography.exceptions
File "/home/lorencm/miniconda3/lib/python3.9/site-packages/cryptography/exceptions.py", line 9, in <module>
from cryptography.hazmat.bindings._rust import exceptions as rust_exceptions
pyo3_runtime.PanicException: Python API call failed
Logs
mamba install -v
ImportError: libffi.so.7: cannot open shared object file: No such file or directory
thread '<unnamed>' panicked at /home/conda/feedstock_root/build_artifacts/cryptography-split_1698192008573/_build_env/.cargo/registry/src/index.crates.io-6f17d22bba15001f/pyo3-0.18.3/src/err/mod.rs:790:5:
Python API call failed
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
Traceback (most recent call last):
File "/home/lorencm/miniconda3/bin/mamba", line 7, in <module>
from mamba.mamba import main
File "/home/lorencm/miniconda3/lib/python3.9/site-packages/mamba/mamba.py", line 17, in <module>
from conda.cli.install import check_prefix, clone, get_revision
File "/home/lorencm/miniconda3/lib/python3.9/site-packages/conda/cli/install.py", line 20, in <module>
from ..core.index import calculate_channel_urls, get_index
File "/home/lorencm/miniconda3/lib/python3.9/site-packages/conda/core/index.py", line 24, in <module>
from .subdir_data import SubdirData, make_feature_record
File "/home/lorencm/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 52, in <module>
from ..trust.signature_verification import signature_verification
File "/home/lorencm/miniconda3/lib/python3.9/site-packages/conda/trust/signature_verification.py", line 13, in <module>
from conda_content_trust.authentication import verify_delegation, verify_root
File "/home/lorencm/miniconda3/lib/python3.9/site-packages/conda_content_trust/authentication.py", line 27, in <module>
import cryptography.exceptions
File "/home/lorencm/miniconda3/lib/python3.9/site-packages/cryptography/exceptions.py", line 9, in <module>
from cryptography.hazmat.bindings._rust import exceptions as rust_exceptions
pyo3_runtime.PanicException: Python API call failed
environment.yml
No response
~/.condarc
> cat ~/.condarc
channels:
- conda-forge
- bioconda
- defaults
envs_dirs:
- /work/x/miniconda2/envs/
Same issue when build with dockerfile.
FROM pytorch/pytorch:1.12.1-cuda11.3-cudnn8-runtime
# Download from https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
COPY Miniforge3-Linux-x86_64.sh /tmp/Miniforge3-Linux-x86_64.sh
SHELL ["/bin/bash", "-c"]
RUN conda init bash
RUN source "/opt/conda/bin/activate"
RUN conda install python=3.10
RUN bash /tmp/Miniforge3-Linux-x86_64.sh -b
RUN conda install -n base --override-channels -c conda-forge mamba 'python_abi=*=*cp*'
RUN mamba -V
Hmm I don't know if this is supposed to work. You're installing Miniforge over an existing installation of Conda
My issue is resolved with:
FROM pytorch/pytorch:1.12.1-cuda11.3-cudnn8-runtime
SHELL ["/bin/bash", "-c"]
RUN conda init bash
RUN source "/opt/conda/bin/activate"
RUN conda install -n base --override-channels -c conda-forge libarchive mamba 'python_abi=*=*cp*'
RUN mamba -V