Re: [easybuild] Biopython-1.78-intel-2020a-Python-3.8.2.eb failed : yaff 1.4.2 requires h5py, which is not installed.

2021-10-26 Thread Joaquim Jornet Somoza 
Moltes gràcies Alexandre,

I will check it !

Best regards
quim

Missatge de Strube, Alexandre  del dia dl., 25
d’oct. 2021 a les 17:51:

> 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  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 
>> 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  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> 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
>>> 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
>> Edificio Joxe Maria Korta (Campus Gipuzkoa)
>> Av. Tolosa 72, 4a planta
>> 20018 Donostia-San Sebastián,
>> Gipuzkoa, Spain
>> w:  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
> Edificio Joxe

Re: [easybuild] Biopython-1.78-intel-2020a-Python-3.8.2.eb failed : yaff 1.4.2 requires h5py, which is not installed.

2021-10-25 Thread Strube, Alexandre 
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  
> 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  > 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 > > 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 > > 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 >> > 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 
>>> 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 
>> Edificio Joxe Maria Korta (Campus Gipuzkoa)
>> Av. Tolosa 72, 4a planta
>> 20018 Donostia-San Sebastián,
>> Gipuzkoa, Spain
>> w:  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 
>

Re: [easybuild] Biopython-1.78-intel-2020a-Python-3.8.2.eb failed : yaff 1.4.2 requires h5py, which is not installed.

2021-10-20 Thread Joaquim Jornet Somoza 
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  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 
> 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  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> 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
>> 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
> Edificio Joxe Maria Korta (Campus Gipuzkoa)
> Av. Tolosa 72, 4a planta
> 20018 Donostia-San Sebastián,
> Gipuzkoa, Spain
> w:  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
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

Re: [easybuild] Biopython-1.78-intel-2020a-Python-3.8.2.eb failed : yaff 1.4.2 requires h5py, which is not installed.

2021-10-18 Thread Strube, Alexandre 
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  
> 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  > 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 > > 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 
>> 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 
> Edificio Joxe Maria Korta (Campus Gipuzkoa)
> Av. Tolosa 72, 4a planta
> 20018 Donostia-San Sebastián,
> Gipuzkoa, Spain
> w:  http://www.ehu.es/sgi/ 
> tw: @izosgi
> fb:  izosgi
> 



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Re: [easybuild] Biopython-1.78-intel-2020a-Python-3.8.2.eb failed : yaff 1.4.2 requires h5py, which is not installed.

2021-10-18 Thread Joaquim Jornet Somoza 
Thank you for your reply.

I succeeded to install the module by setting:
sanity_pip_check = False

But I don't know if this can cause misbehaviour to the package ...

Bests
quim

Missatge de Yann Sagon  del dia dl., 18 d’oct. 2021 a
les 14:32:

> Hi,
>
> I had the same issue for another Python bundle (and I was using --robot)
>
> == restore after iterating...
> == postprocessing...
> == sanity checking...
> == ... (took 11 secs)
> == FAILED: Installation ended unsuccessfully (build directory: 
> /dev/shm/ebbuild/Spyder/4.1.5/foss-2020a-Python-3.8.2): build failed (first 
> 300 chars): `pip check` failed:
> spyder 4.1.5 requires intervaltree, which is not installed.
>
> The reason is probably that some python packages updated their
> dependencies and the eb should be update as well.
>
> Best
>
> Yann
>
>
> Le 18.10.2021 à 13:46, Strube, Alexandre a écrit :
>
> 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> 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
> 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
>
>
> --
>
>   [image: Logo UNIGE] Yann Sagon
> Référent HPC
>
> Division du système et des technologies de l'information et de la
> communication
> Université de Genève | 24 rue Général-Dufour
> Tél 022 379 77 37 | Bureau 151
>
> www.unige.ch/stic
>


-- 

*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
Edificio Joxe Maria Korta (Campus Gipuzkoa)
Av. Tolosa 72, 4a planta
20018 Donostia-San Sebastián,
Gipuzkoa, Spain
w:  http://www.ehu.es/sgi/
tw: @izosgi
fb:  izosgi

Re: [easybuild] Biopython-1.78-intel-2020a-Python-3.8.2.eb failed : yaff 1.4.2 requires h5py, which is not installed.

2021-10-18 Thread Joaquim Jornet Somoza 
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  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> 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
> 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
Edificio Joxe Maria Korta (Campus Gipuzkoa)
Av. Tolosa 72, 4a planta
20018 Donostia-San Sebastián,
Gipuzkoa, Spain
w:  http://www.ehu.es/sgi/
tw: @izosgi
fb:  izosgi

Re: [easybuild] Biopython-1.78-intel-2020a-Python-3.8.2.eb failed : yaff 1.4.2 requires h5py, which is not installed.

2021-10-18 Thread Yann Sagon 

Hi,

I had the same issue for another Python bundle (and I was using --robot)

== restore after iterating...
== postprocessing...
== sanity checking...
== ... (took 11 secs)
== FAILED: Installation ended unsuccessfully (build directory: 
/dev/shm/ebbuild/Spyder/4.1.5/foss-2020a-Python-3.8.2): build failed (first 300 
chars): `pip check` failed:
spyder 4.1.5 requires intervaltree, which is not installed.

The reason is probably that some python packages updated their 
dependencies and the eb should be update as well.


Best

Yann


Le 18.10.2021 à 13:46, Strube, Alexandre a écrit :

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 
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 
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



--

Logo UNIGE  Yann Sagon
Référent HPC

Division du système et des technologies de l'information et de la 
communication

Université de Genève | 24 rue Général-Dufour
Tél 022 379 77 37 | Bureau 151

www.unige.ch/stic

Re: [easybuild] Biopython-1.78-intel-2020a-Python-3.8.2.eb failed : yaff 1.4.2 requires h5py, which is not installed.

2021-10-18 Thread Strube, Alexandre 
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  
> 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 
> 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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