sourmash
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Published
20 hours ago •
sourmash-bio
sourmash-bio
conda install problem w/python3.10: `libffi.so.7: cannot open shared object file: No such file or directory`
Can't wait to try the new version!
$ mamba install sourmash # v4.5.0
$ sourmash -v
Traceback (most recent call last):
File "/home/shenwei/app/miniconda3/envs/kmcp/bin/sourmash", line 7, in <module>
from sourmash.__main__ import main
File "/home/shenwei/app/miniconda3/envs/kmcp/lib/python3.10/site-packages/sourmash/__init__.py", line 32, in <module>
from ._lowlevel import ffi, lib
File "/home/shenwei/app/miniconda3/envs/kmcp/lib/python3.10/site-packages/sourmash/_lowlevel.py", line 5, in <module>
from sourmash._lowlevel__ffi import ffi
File "/home/shenwei/app/miniconda3/envs/kmcp/lib/python3.10/site-packages/sourmash/_lowlevel__ffi.py", line 2, in <module>
import _cffi_backend
ImportError: libffi.so.7: cannot open shared object file: No such file or directory
# oops
Actually, libffi was installed, but the version seems too high. It needs to be specified.
$ fd libffi | grep kmcp | grep libffi
./envs/kmcp/lib/libffi.so.8
$ fd libffi | grep pkg | grep libffi.so.7
./pkgs/libffi-3.3-h58526e2_2/lib/libffi.so.7
$ fd libffi | grep pkg | grep libffi.so.8
./pkgs/libffi-3.4.2-h7f98852_5/lib/libffi.so.8
# centos 7
$ fd libffi /lib64/
/lib64/libffi.so.6
Then I tried:
$ mamba install libffi=3.3
Problem: package python-3.10.6-ha86cf86_0_cpython requires libffi >=3.4.2,<3.5.0a0, but none of the providers can be installed
OK, try Python 3.9:
$ mamba create -n kmcp2 python==3.9
The following NEW packages will be INSTALLED:
libffi conda-forge/linux-64::libffi-3.3-h58526e2_2
# looks promissing!
$ mamba install sourmash
$ sourmash -v
sourmash 4.5.0
It works!
Hope this helps!
Wei
thanks @shenwei356!
I checked and I can't replicate this on my Linux machine - when I do:
mamba create -n smash450 python=3.10 sourmash
it seems to work 🤔
Based on the message package python-3.10.6-ha86cf86_0_cpython requires libffi >=3.4.2,<3.5.0a0 I wonder if python3.10.6 is specifying a bad CFFI?
hmm.
mamba list gives:
...
cffi 1.15.1 py310h255011f_0 conda-forge
...
libffi 3.4.2 h7f98852_5 conda-forge
...
python 3.10.6 ha86cf86_0_cpython conda-forge
...
so it looks like I have the same versions of all the things.
Weird. Will keep digging!
I just created a fresh env, it still failed.
details
$ mamba create -n smash450 python=3.10 sourmash
Getting conda-forge linux-64
Getting conda-forge noarch
Getting bioconda linux-64
Getting bioconda noarch
Getting pkgs/main linux-64
Getting pkgs/main noarch
Getting pkgs/r linux-64
Getting pkgs/r noarch
Looking for: ['python 3.10.*', 'sourmash']
290370 packages in https://conda.anaconda.org/conda-forge/linux-64
103732 packages in https://conda.anaconda.org/conda-forge/noarch
45824 packages in https://conda.anaconda.org/bioconda/linux-64
38095 packages in https://conda.anaconda.org/bioconda/noarch
26771 packages in https://repo.anaconda.com/pkgs/main/linux-64
4705 packages in https://repo.anaconda.com/pkgs/main/noarch
8442 packages in https://repo.anaconda.com/pkgs/r/linux-64
9492 packages in https://repo.anaconda.com/pkgs/r/noarch
## Package Plan ##
environment location: /home/shenwei/app/miniconda3/envs/smash450
added / updated specs:
- python=3.10
- sourmash
The following packages will be downloaded:
package | build
---------------------------|-----------------
bz2file-0.98 | py310h06a4308_1 14 KB
matplotlib-base-3.5.3 | py310h8d5ebf3_2 7.4 MB conda-forge
pyparsing-3.0.9 | py310h06a4308_0 153 KB
------------------------------------------------------------
Total: 7.5 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
bitstring conda-forge/noarch::bitstring-3.1.9-pyhd8ed1ab_0
brotli pkgs/main/linux-64::brotli-1.0.9-h5eee18b_7
brotli-bin pkgs/main/linux-64::brotli-bin-1.0.9-h5eee18b_7
bz2file pkgs/main/linux-64::bz2file-0.98-py310h06a4308_1
bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
ca-certificates pkgs/main/linux-64::ca-certificates-2022.07.19-h06a4308_0
cachetools conda-forge/noarch::cachetools-4.2.4-pyhd8ed1ab_0
certifi pkgs/main/linux-64::certifi-2022.6.15-py310h06a4308_0
cffi pkgs/main/linux-64::cffi-1.15.1-py310h74dc2b5_0
cycler pkgs/main/noarch::cycler-0.11.0-pyhd3eb1b0_0
deprecation pkgs/main/noarch::deprecation-2.1.0-pyhd3eb1b0_0
fonttools conda-forge/linux-64::fonttools-4.37.1-py310h5764c6d_0
freetype conda-forge/linux-64::freetype-2.12.1-hca18f0e_0
jpeg conda-forge/linux-64::jpeg-9e-h166bdaf_2
kiwisolver conda-forge/linux-64::kiwisolver-1.4.4-py310hbf28c38_0
lcms2 pkgs/main/linux-64::lcms2-2.12-h3be6417_0
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1
lerc conda-forge/linux-64::lerc-4.0.0-h27087fc_0
libblas conda-forge/linux-64::libblas-3.9.0-16_linux64_openblas
libbrotlicommon pkgs/main/linux-64::libbrotlicommon-1.0.9-h5eee18b_7
libbrotlidec pkgs/main/linux-64::libbrotlidec-1.0.9-h5eee18b_7
libbrotlienc pkgs/main/linux-64::libbrotlienc-1.0.9-h5eee18b_7
libcblas conda-forge/linux-64::libcblas-3.9.0-16_linux64_openblas
libdeflate conda-forge/linux-64::libdeflate-1.13-h166bdaf_0
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-12.1.0-h8d9b700_16
libgfortran-ng conda-forge/linux-64::libgfortran-ng-12.1.0-h69a702a_16
libgfortran5 conda-forge/linux-64::libgfortran5-12.1.0-hdcd56e2_16
libgomp conda-forge/linux-64::libgomp-12.1.0-h8d9b700_16
liblapack conda-forge/linux-64::liblapack-3.9.0-16_linux64_openblas
libnsl conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
libopenblas conda-forge/linux-64::libopenblas-0.3.21-pthreads_h78a6416_3
libpng conda-forge/linux-64::libpng-1.6.37-h753d276_4
libsqlite conda-forge/linux-64::libsqlite-3.39.3-h753d276_0
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-12.1.0-ha89aaad_16
libtiff conda-forge/linux-64::libtiff-4.4.0-h0e0dad5_3
libuuid conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
libwebp-base conda-forge/linux-64::libwebp-base-1.2.4-h166bdaf_0
libxcb conda-forge/linux-64::libxcb-1.13-h7f98852_1004
libzlib conda-forge/linux-64::libzlib-1.2.12-h166bdaf_2
matplotlib-base conda-forge/linux-64::matplotlib-base-3.5.3-py310h8d5ebf3_2
munkres pkgs/main/noarch::munkres-1.1.4-py_0
ncurses pkgs/main/linux-64::ncurses-6.3-h5eee18b_3
numpy conda-forge/linux-64::numpy-1.23.2-py310h53a5b5f_0
openjpeg conda-forge/linux-64::openjpeg-2.5.0-h7d73246_1
openssl conda-forge/linux-64::openssl-3.0.5-h166bdaf_2
packaging pkgs/main/noarch::packaging-21.3-pyhd3eb1b0_0
pillow conda-forge/linux-64::pillow-9.2.0-py310hbd86126_2
pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001
pycparser pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0
pyparsing pkgs/main/linux-64::pyparsing-3.0.9-py310h06a4308_0
python conda-forge/linux-64::python-3.10.6-ha86cf86_0_cpython
python-dateutil pkgs/main/noarch::python-dateutil-2.8.2-pyhd3eb1b0_0
python_abi conda-forge/linux-64::python_abi-3.10-2_cp310
readline pkgs/main/linux-64::readline-8.1.2-h7f8727e_1
scipy conda-forge/linux-64::scipy-1.9.1-py310hdfbd76f_0
screed conda-forge/noarch::screed-1.0.5-pyhd8ed1ab_1
setuptools conda-forge/linux-64::setuptools-65.3.0-py310hff52083_0
six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
sourmash bioconda/noarch::sourmash-4.5.0-hdfd78af_0
sourmash-minimal conda-forge/linux-64::sourmash-minimal-4.5.0-py310h3392aa1_0
tk pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0
tzdata conda-forge/noarch::tzdata-2022c-h191b570_0
unicodedata2 conda-forge/linux-64::unicodedata2-14.0.0-py310h5764c6d_1
xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h7f98852_0
xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h7f98852_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
zlib conda-forge/linux-64::zlib-1.2.12-h166bdaf_2
zstd conda-forge/linux-64::zstd-1.5.2-h6239696_4
Proceed ([y]/n)? y
Downloading and Extracting Packages
pyparsing-3.0.9 | 153 KB | ################################################################################################################################################# | 100%
matplotlib-base-3.5. | 7.4 MB | ################################################################################################################################################# | 100%
bz2file-0.98 | 14 KB | ################################################################################################################################################# | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate smash450
#
# To deactivate an active environment, use
#
# $ conda deactivate
$ conda activate smash450
(smash450) [shenwei@gys-svr ~]$ sourmash -v
Traceback (most recent call last):
File "/home/shenwei/app/miniconda3/envs/smash450/bin/sourmash", line 7, in <module>
from sourmash.__main__ import main
File "/home/shenwei/app/miniconda3/envs/smash450/lib/python3.10/site-packages/sourmash/__init__.py", line 32, in <module>
from ._lowlevel import ffi, lib
File "/home/shenwei/app/miniconda3/envs/smash450/lib/python3.10/site-packages/sourmash/_lowlevel.py", line 5, in <module>
from sourmash._lowlevel__ffi import ffi
File "/home/shenwei/app/miniconda3/envs/smash450/lib/python3.10/site-packages/sourmash/_lowlevel__ffi.py", line 2, in <module>
import _cffi_backend
ImportError: libffi.so.7: cannot open shared object file: No such file or directory
BTW, The cffi is slightly different in my env; it's installed from pypi.
$ mamba list | grep ffi
cffi 1.15.1 pypi_0 pypi
libffi 3.4.2 h7f98852_5 conda-forge
(kmcp) [shenwei@gys-svr gtdb202]$ mamba list | grep python
ipython 8.4.0 pypi_0 pypi
ipython_genutils 0.2.0 py_1 conda-forge
msgpack-python 1.0.4 py310hbf28c38_0 conda-forge
python 3.10.6 ha86cf86_0_cpython conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python_abi 3.10 2_cp310 conda-forge
thank you! my current guess is this is a linux-64-specific issue, will continue to work on it!!
