Hi, this might happen if your pip installation is somehow messed up. I had this happening recently, and turns out it was pip itself, so I deleted all my pip stuff, .local , .cache and so on
> On 18. Oct 2021, at 14:24, Joaquim Jornet Somoza <[email protected]> > wrote: > > Dear Alexandre, > > Thanks for your quick reply. > > Actually, I have tried to installed already with --robot option: > > eb Biopython-1.78-intel-2020a-Python-3.8.2.eb -r ./ > > I don't know why the santiy_check step tries to use a functionality not > listed on the > dependencies section, neither installed within Python-3.8.2-GCCcore-9.3.0.eb. > > I think the error comes from the sanity_check step. This is the error in the > log file: > > == 2021-10-18 12:21:38,634 build_log.py:169 ERROR EasyBuild crashed with an > error (at > easybuild/common/software/EasyBuild/4.4.1/lib/python2.7/site-packages/easybuild/base/exceptions.py:124 > in __init__): `pip check` failed: > yaff 1.4.2 requires h5py, which is not installed. > (at > easybuild/common/software/EasyBuild/4.4.1/lib/python2.7/site-packages/easybuild/easyblocks/generic/pythonpackage.py:886 > in sanity_check_step) > > > You suggested to install h5py by hand as an extension? > I.e including in the easyconfig file for Biopython something like: > > exts_list = [ > ('h5py', '3.0.0', { > 'checksums': > ['7d3803be1b530c68c2955faba726dc0f591079b68941a0c0269b5384a42ab519'], > ] > > Thank you ! > quim > > Missatge de Strube, Alexandre <[email protected] > <mailto:[email protected]>> del dia dl., 18 d’oct. 2021 a les 13:46: > Hola Joaquim, > > dependencies are dealt with --robot setting - which should bring the right > ones. > > In any case, you can always install h5py beforehand yourself. > >> On 18. Oct 2021, at 12:26, Joaquim Jornet Somoza <[email protected] >> <mailto:[email protected]>> wrote: >> >> Dear easybuilders, >> >> I am trying to install Biopython-1.78-intel-2020a-Python-3.8.2.eb, but after >> the installation and >> postprocessing, the sanity check step fails. >> >> I have found this error that I don't know how to avoid: >> >> == 2021-10-18 12:21:38,634 build_log.py:169 ERROR EasyBuild crashed with an >> error (at >> easybuild/common/software/EasyBuild/4.4.1/lib/python2.7/site-packages/easybuild/base/exceptions.py:124 >> in __init__): `pip check` failed: >> yaff 1.4.2 requires h5py, which is not installed. >> >> Could anyone help me? >> >> >> Best regards >> quim >> >> -- >> ---------------------------------------------------------------------------------------------------------------------------------------- >> Dr. Joaquim Jornet Somoza >> Técnico Superior de Cálculo Científico >> Servicios Generales a la Investigación (SGIker) >> Universidad del País Vasco (UPV/EHU) >> email: [email protected] <mailto:[email protected]> >> Edificio Joxe Maria Korta (Campus Gipuzkoa) >> Av. Tolosa 72, 4a planta >> 20018 Donostia-San Sebastián, >> Gipuzkoa, Spain >> >> External Collaborator. >> Nano-Bio Spectroscopy group >> Departamento de Física de Materiales >> Universidad del País Vasco (UPV/EHU) >> Donostia-San Sebastián, Gipuzkoa, Spain >> >> The Max Planck Institute for the Structure and Dynamics of Matter (MPSD) >> Bldg. 99 (CFEL) >> Luruper Chaussee 149 >> 22761 Hamburg, Germany > > > > -- > ---------------------------------------------------------------------------------------------------------------------------------------- > Dr. Joaquim Jornet Somoza > Técnico Superior de Cálculo Científico > Servicios Generales a la Investigación (SGIker) > Universidad del País Vasco (UPV/EHU) > email: [email protected] <mailto:[email protected]> > Edificio Joxe Maria Korta (Campus Gipuzkoa) > Av. Tolosa 72, 4a planta > 20018 Donostia-San Sebastián, > Gipuzkoa, Spain > w: http://www.ehu.es/sgi/ <http://www.ehu.es/sgi/> > tw: @izosgi > fb: izosgi >
signature.asc
Description: Message signed with OpenPGP
