Fedora 37 Install

Renku (CLI)
1

Hello together, having some problems with the dependencies on Fedora 37 (with default repositories). Any Idea on this point ?

[renkuuser@fedora ~]$ pipx install --verbose renku
pipx >(setup:757): pipx version is 1.1.0
pipx >(setup:758): Default python interpreter is ‘/usr/bin/python3’
pipx >(package_name_from_spec:323): Determined package name: renku
pipx >(package_name_from_spec:324): Package name determined in 0.0s
creating virtual environment…
pipx >(run_subprocess:173): running /usr/bin/python3 -m venv --without-pip /home/renkuuser/.local/pipx/venvs/renku
pipx >(run_subprocess:173): running /home/renkuuser/.local/pipx/venvs/renku/bin/python -c import sysconfig; print(sysconfig.get_path(‘purelib’))
pipx >(run_subprocess:173): running /home/renkuuser/.local/pipx/shared/bin/python -c import sysconfig; print(sysconfig.get_path(‘purelib’))
pipx >(run_subprocess:173): running /home/renkuuser/.local/pipx/venvs/renku/bin/python --version
pipx >(_parsed_package_to_package_or_url:128): cleaned package spec: renku
installing renku…
pipx >(run_subprocess:173): running /home/renkuuser/.local/pipx/venvs/renku/bin/python -m pip install renku
pipx >(subprocess_post_check_handle_pip_error:335): ‘/home/renkuuser/.local/pipx/venvs/renku/bin/python -m pip install renku’ failed
pipx >(subprocess_post_check_handle_pip_error:352): Fatal error from pip prevented installation. Full pip output in file:
/home/renkuuser/.local/pipx/logs/cmd_2023-02-01_17.38.14_pip_errors.log

pipx >(analyze_pip_output:298): pip failed to build packages:
numpy
psutil
zstandard
BTrees
zodbpickle

Some possibly relevant errors from pip install:
libraries mkl_rt not found in [‘/home/renkuuser/.local/pipx/venvs/renku/lib’, ‘/usr/local/lib64’, ‘/usr/local/lib’, ‘/usr/lib64’, ‘/usr/lib’, ‘/usr/lib/’]
libraries blis not found in [‘/home/renkuuser/.local/pipx/venvs/renku/lib’, ‘/usr/local/lib64’, ‘/usr/local/lib’, ‘/usr/lib64’, ‘/usr/lib’, ‘/usr/lib/’]
libraries openblas not found in [‘/home/renkuuser/.local/pipx/venvs/renku/lib’, ‘/usr/local/lib64’, ‘/usr/local/lib’, ‘/usr/lib64’, ‘/usr/lib’, ‘/usr/lib/’]
libraries tatlas not found in [‘/home/renkuuser/.local/pipx/venvs/renku/lib’, ‘/usr/local/lib64’, ‘/usr/local/lib’, ‘/usr/lib64’, ‘/usr/lib’, ‘/usr/lib/’]
libraries satlas not found in [‘/home/renkuuser/.local/pipx/venvs/renku/lib’, ‘/usr/local/lib64’, ‘/usr/local/lib’, ‘/usr/lib64’, ‘/usr/lib’, ‘/usr/lib/’]
libraries ptf77blas,ptcblas,atlas not found in [‘/home/renkuuser/.local/pipx/venvs/renku/lib’, ‘/usr/local/lib64’, ‘/usr/local/lib’, ‘/usr/lib64’, ‘/usr/lib’, ‘/usr/lib/’]
libraries f77blas,cblas,atlas not found in [‘/home/renkuuser/.local/pipx/venvs/renku/lib’, ‘/usr/local/lib64’, ‘/usr/local/lib’, ‘/usr/lib64’, ‘/usr/lib’, ‘/usr/lib/’]
Optimized (vendor) Blas libraries are not found.
libraries blas not found in [‘/home/renkuuser/.local/pipx/venvs/renku/lib’, ‘/usr/local/lib64’, ‘/usr/local/lib’, ‘/usr/lib64’, ‘/usr/lib’, ‘/usr/lib/’]
Blas (BLAS (Basic Linear Algebra Subprograms)) libraries not found.
Blas (BLAS (Basic Linear Algebra Subprograms)) sources not found.
libraries openblas,lapack not found in [‘/home/renkuuser/.local/pipx/venvs/renku/lib’, ‘/usr/local/lib64’, ‘/usr/local/lib’, ‘/usr/lib64’, ‘/usr/lib’, ‘/usr/lib/’]
libraries flame not found in [‘/home/renkuuser/.local/pipx/venvs/renku/lib’, ‘/usr/local/lib64’, ‘/usr/local/lib’, ‘/usr/lib64’, ‘/usr/lib’, ‘/usr/lib/’]
libraries lapack_atlas not found in /home/renkuuser/.local/pipx/venvs/renku/lib
libraries tatlas,tatlas not found in /home/renkuuser/.local/pipx/venvs/renku/lib
libraries lapack_atlas not found in /usr/local/lib64
libraries tatlas,tatlas not found in /usr/local/lib64
libraries lapack_atlas not found in /usr/local/lib
libraries tatlas,tatlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib64
libraries tatlas,tatlas not found in /usr/lib64
libraries lapack_atlas not found in /usr/lib
libraries tatlas,tatlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib/
libraries tatlas,tatlas not found in /usr/lib/
libraries satlas,satlas not found in /home/renkuuser/.local/pipx/venvs/renku/lib
libraries satlas,satlas not found in /usr/local/lib64
libraries satlas,satlas not found in /usr/local/lib
libraries satlas,satlas not found in /usr/lib64
libraries satlas,satlas not found in /usr/lib
libraries satlas,satlas not found in /usr/lib/
libraries ptf77blas,ptcblas,atlas not found in /home/renkuuser/.local/pipx/venvs/renku/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/lib64
libraries ptf77blas,ptcblas,atlas not found in /usr/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/lib/
libraries f77blas,cblas,atlas not found in /home/renkuuser/.local/pipx/venvs/renku/lib
libraries f77blas,cblas,atlas not found in /usr/local/lib64
libraries f77blas,cblas,atlas not found in /usr/local/lib
libraries f77blas,cblas,atlas not found in /usr/lib64
libraries f77blas,cblas,atlas not found in /usr/lib
libraries f77blas,cblas,atlas not found in /usr/lib/
libraries lapack not found in [‘/home/renkuuser/.local/pipx/venvs/renku/lib’, ‘/usr/local/lib64’, ‘/usr/local/lib’, ‘/usr/lib64’, ‘/usr/lib’, ‘/usr/lib/’]
Lapack (LAPACK — Linear Algebra PACKage) libraries not found.
Lapack (LAPACK — Linear Algebra PACKage) sources not found.

pipx >(rmdir:55): removing directory /home/renkuuser/.local/pipx/venvs/renku
Error installing renku.

After dowloading the current package from pypi and changing the requirement for numpy to 1.22.0, the install worked. So my question to the developers: Are these tight build restrictions like numpy = “>=1.20.0,<1.22.0” really neccessary ? What is in 1.21.1 that much different compared to 1.22.0 ?

2

Hello @dbozic-at-hslu,

We don’t have a hard dependency on numpy < 1.22.0; it’s just our dependency auto-upgrade tool that didn’t update it. So, it’s fine to use this or a higher version. We had some issues we newer versions of packages before, but AFAIK at the moment it’s safe to update dependencies if some older versions don’t work for you.

Please also note that we are moving away from using pipx to install Renku CLI. It’s better if you use pip or pipenv.

Laura told me that you would like to have a phone call with us regarding Renku installation. I’m available anytime this week, so, please let me know when would be suitable for you to have a call.

Kind regards,
Mohammad

3

I had a similar issue on fedora and used pyenv GitHub - pyenv/pyenv: Simple Python version management to install a python version slightly older than the one fedora ships with and pip installed renku in there which worked well. I’ve found it useful for other stuff that doesn’t quite keep pace with fedoras rolling nature.