Bona tarda! Usually you have to cleanup everything related to pip on your local install, and depending on the system, on the global install. That messes up things
Also, give it a try with “pip check” > On 20. Oct 2021, at 15:02, Joaquim Jornet Somoza <j.jornet.som...@gmail.com> > wrote: > > Hi Alexandre, > > Thank you for your reply. > I tried deleting the ~/.local and ~/.cache pip related staff...but the > problem still appears. > > Should I delete anything else? > > Thank you again ! > quim > > Missatge de Strube, Alexandre <a.str...@fz-juelich.de > <mailto:a.str...@fz-juelich.de>> del dia dl., 18 d’oct. 2021 a les 23:20: > 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 <joaquim.jor...@ehu.eus >> <mailto:joaquim.jor...@ehu.eus>> 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 <a.str...@fz-juelich.de >> <mailto:a.str...@fz-juelich.de>> 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 <j.jornet.som...@gmail.com >>> <mailto:j.jornet.som...@gmail.com>> 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: j.jornet.som...@gmail.com <mailto:j.jornet.som...@gmail.com> >>> 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: joaquim.jor...@ehu.eus <mailto:joaquim.jor...@ehu.eus> >> 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 >> > > > > -- > ---------------------------------------------------------------------------------------------------------------------------------------- > Dr. Joaquim Jornet Somoza > Técnico Superior de Cálculo Científico > Servicios Generales a la Investigación (SGIker) > Universidad del País Vasco (UPV/EHU) > email: j.jornet.som...@gmail.com <mailto:j.jornet.som...@gmail.com> > 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
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