Installation issue: biobb-* packages

Summary


Summary	Spack package build failure
Package info	biobb-common
System
Related

Steps to reproduce the issue

$ spack spec -I biobb-common

biobb-common@4.0.0%gcc@10.3.0 build_system=python_pip arch=linux-ubuntu22.04-x86_64
    ^py-biopython@1.79%gcc@10.3.0 build_system=python_pip arch=linux-ubuntu22.04-x86_64
        ^py-numpy@1.23.4%gcc@10.3.0+blas+lapack build_system=python_pip patches=873745d arch=linux-ubuntu22.04-x86_64
            ^openblas@0.3.21%gcc@10.3.0~bignuma~consistent_fpcsr+fortran~ilp64+locking+pic+shared build_system=makefile patches=d3d9b15 symbol_suffix=none threads=none arch=linux-ubuntu22.04-x86_64
                ^perl@5.36.0%gcc@10.3.0+cpanm+shared+threads build_system=generic arch=linux-ubuntu22.04-x86_64
                    ^berkeley-db@18.1.40%gcc@10.3.0+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=linux-ubuntu22.04-x86_64
                    ^bzip2@1.0.8%gcc@10.3.0~debug~pic+shared build_system=generic arch=linux-ubuntu22.04-x86_64
                        ^diffutils@3.8%gcc@10.3.0 build_system=autotools arch=linux-ubuntu22.04-x86_64
                            ^libiconv@1.16%gcc@10.3.0 build_system=autotools libs=shared,static arch=linux-ubuntu22.04-x86_64
                    ^gdbm@1.23%gcc@10.3.0 build_system=autotools arch=linux-ubuntu22.04-x86_64
                        ^readline@8.1.2%gcc@10.3.0 build_system=autotools arch=linux-ubuntu22.04-x86_64
                            ^ncurses@6.3%gcc@10.3.0~symlinks+termlib abi=none build_system=autotools arch=linux-ubuntu22.04-x86_64
                                ^pkgconf@1.8.0%gcc@10.3.0 build_system=autotools arch=linux-ubuntu22.04-x86_64
                    ^zlib@1.2.13%gcc@10.3.0+optimize+pic+shared build_system=makefile arch=linux-ubuntu22.04-x86_64
            ^py-cython@0.29.32%gcc@10.3.0 build_system=python_pip arch=linux-ubuntu22.04-x86_64
    ^py-pip@22.2.2%gcc@10.3.0 build_system=generic arch=linux-ubuntu22.04-x86_64
    ^py-pyyaml@6.0%gcc@10.3.0+libyaml build_system=python_pip arch=linux-ubuntu22.04-x86_64
        ^libyaml@0.2.5%gcc@10.3.0 build_system=autotools arch=linux-ubuntu22.04-x86_64
        ^py-cython@0.29.32%gcc@10.3.0 build_system=python_pip arch=linux-ubuntu22.04-x86_64
        ^py-setuptools@65.5.0%gcc@10.3.0 build_system=generic arch=linux-ubuntu22.04-x86_64
    ^py-requests@2.28.1%gcc@10.3.0~socks build_system=python_pip arch=linux-ubuntu22.04-x86_64
        ^py-certifi@2022.9.14%gcc@10.3.0 build_system=python_pip arch=linux-ubuntu22.04-x86_64
        ^py-charset-normalizer@2.0.12%gcc@10.3.0 build_system=python_pip arch=linux-ubuntu22.04-x86_64
        ^py-idna@3.4%gcc@10.3.0 build_system=python_pip arch=linux-ubuntu22.04-x86_64
            ^py-flit-core@3.7.1%gcc@10.3.0 build_system=python_pip arch=linux-ubuntu22.04-x86_64
        ^py-urllib3@1.26.12%gcc@10.3.0~brotli~secure~socks build_system=python_pip arch=linux-ubuntu22.04-x86_64
    ^py-setuptools@63.0.0%gcc@10.3.0 build_system=generic arch=linux-ubuntu22.04-x86_64
    ^py-wheel@0.37.1%gcc@10.3.0 build_system=generic arch=linux-ubuntu22.04-x86_64
    ^python@3.10.6%gcc@10.3.0+bz2+ctypes+dbm~debug+libxml2+lzma+nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib build_system=generic patches=0d98e93,7d40923,f2fd060 arch=linux-ubuntu22.04-x86_64

$ spack install biobb-common

==> biobb-common: Executing phase: 'install'
==> Error: ProcessError: Command exited with status 1:
    '/usr/bin/python3.10' '-m' 'pip' '-vvv' '--no-input' '--no-cache-dir' '--disable-pip-version-check' 'install' '--no-deps' '--ignore-installed' '--no-build-isolation' '--no-warn-script-location' '--no-index' '--prefix=/home/eleni/spack-instance-23-07/spack/opt/spack/linux-ubuntu22.04-x86_64/gcc-10.3.0/biobb-common-4.0.0-jky3nc7ls3ep6msuwfmt33njj4zsleho' '.'
See build log for details:
  /tmp/eleni/spack-stage/spack-stage-biobb-common-4.0.0-jky3nc7ls3ep6msuwfmt33njj4zsleho/spack-build-out.txt

Error message


ERROR: Package 'biobb-common' requires a different Python: 3.10.6 not in '<=3.10,>=3.7'
Exception information:
Traceback (most recent call last):
  File "/home/eleni/spack-instance-23-07/spack/opt/spack/linux-ubuntu22.04-x86_64/gcc-10.3.0/py-pip-22.2.2-6tj7qrme2dcjugyfzcvojribqy4muiic/local/lib/python3.10/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 92, in resolve
    result = self._result = resolver.resolve(
  File "/home/eleni/spack-instance-23-07/spack/opt/spack/linux-ubuntu22.04-x86_64/gcc-10.3.0/py-pip-22.2.2-6tj7qrme2dcjugyfzcvojribqy4muiic/local/lib/python3.10/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 481, in resolve
    state = resolution.resolve(requirements, max_rounds=max_rounds)
  File "/home/eleni/spack-instance-23-07/spack/opt/spack/linux-ubuntu22.04-x86_64/gcc-10.3.0/py-pip-22.2.2-6tj7qrme2dcjugyfzcvojribqy4muiic/local/lib/python3.10/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 385, in resolve
    raise ResolutionImpossible(self.state.backtrack_causes)
pip._vendor.resolvelib.resolvers.ResolutionImpossible: [RequirementInformation(requirement=RequiresPythonRequirement('<=3.10,>=3.7'), parent=LinkCandidate('file:///tmp/eleni/spack-stage/spack-stage-biobb-common-4.0.0-jky3nc7ls3ep6msuwfmt33njj4zsleho/spack-src'))]
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/eleni/spack-instance-23-07/spack/opt/spack/linux-ubuntu22.04-x86_64/gcc-10.3.0/py-pip-22.2.2-6tj7qrme2dcjugyfzcvojribqy4muiic/local/lib/python3.10/dist-packages/pip/_internal/cli/base_command.py", line 167, in exc_logging_wrapper
status = run_func(*args)
File "/home/eleni/spack-instance-23-07/spack/opt/spack/linux-ubuntu22.04-x86_64/gcc-10.3.0/py-pip-22.2.2-6tj7qrme2dcjugyfzcvojribqy4muiic/local/lib/python3.10/dist-packages/pip/_internal/cli/req_command.py", line 247, in wrapper
return func(self, options, args)
File "/home/eleni/spack-instance-23-07/spack/opt/spack/linux-ubuntu22.04-x86_64/gcc-10.3.0/py-pip-22.2.2-6tj7qrme2dcjugyfzcvojribqy4muiic/local/lib/python3.10/dist-packages/pip/_internal/commands/install.py", line 369, in run
requirement_set = resolver.resolve(
File "/home/eleni/spack-instance-23-07/spack/opt/spack/linux-ubuntu22.04-x86_64/gcc-10.3.0/py-pip-22.2.2-6tj7qrme2dcjugyfzcvojribqy4muiic/local/lib/python3.10/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 101, in resolve
raise error from e
pip._internal.exceptions.UnsupportedPythonVersion: Package 'biobb-common' requires a different Python: 3.10.6 not in '<=3.10,>=3.7'
Removed build tracker: '/tmp/pip-build-tracker-mak1w7uz'

Information on your system

Additional information

spack-build-out.txt

Designs

Child items ...

Activity

Eleni Mathioulaki added build-error label 1 year ago

added build-error label
Eleni Mathioulaki @elmath · 1 year ago

Author Owner

Hi @dbeltran, we had this issue when trying to install the biobb-* packages with python 3.10 (python 3.10.6, 3.10.8 etc). In order to include all 3.10.* versions, python_requires='<=3.10' needs to be python_requires='<3.11' (in setup.py)

Is the version limitation intentional?

Edited 1 year ago by Eleni Mathioulaki
Dani Beltrán @dbeltran · 1 year ago

Contributor

Hi @elmath,

Thank you for reaching out. The limitation is not intentional, BioBBs should work with all versions of python 3.10. We will correct the setup.py with python_requires='<3.11' in the next release, which should be drop in 1 month.

By the way, why are you trying to install BioBBs in python 3.10? Is python 3.8.11 not a strict requirement anymore?
Eleni Mathioulaki @elmath · 1 year ago

Author Owner

OK, perfect, thanks! :)

We still use python 3.8.11 in the Lab, but the EBRAINS releases are now being installed in the Fenix HPC systems as well - that's where we had this issue. Temporarily, until your next release, we'll add a patch (see !375 (merged)) to be able to also install with python 3.10.
Eleni Mathioulaki mentioned in merge request !425 (closed) 1 year ago

mentioned in merge request !425 (closed)
sofia karvounari assigned to @elmath 9 months ago

assigned to @elmath

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