subject:"\\\\\\\[Bioc\\\\\\\-devel\\\\\\\] jupyter installation on merida1"

Re: [Bioc-devel] jupyter installation on merida1

2019-12-12 Thread Pages, Herve

Hi Philipp,

I've updated python3 (from 3.6 to 3.7) and jupyter on merida1. Now we have:

   merida1:~ biocbuild$ python3 --version
   Python 3.7.3

   merida1:~ biocbuild$ which jupyter
   /usr/local/bin/jupyter

   merida1:~ biocbuild$ jupyter --version
   jupyter core : 4.6.1
   jupyter-notebook : 6.0.2
   qtconsole: 4.6.0
   ipython  : 7.10.1
   ipykernel: 5.1.3
   jupyter client   : 5.3.4
   jupyter lab  : not installed
   nbconvert: 5.6.1
   ipywidgets   : 7.5.1
   nbformat : 4.4.0
   traitlets: 4.3.3

which is exactly the same as on celaya2.

Best,
H.


On 12/12/19 04:24, Angerer, Philipp wrote:
> Dear maintainers,
> 
> Is there any progress with this? Any way I can help?
> 
> Thank you,
> Philipp
> 
> - Ursprüngliche Mail -
> Von: "Philipp Angerer" 
> An: "bioc-devel" 
> Gesendet: Mittwoch, 4. Dezember 2019 10:58:44
> Betreff: [Bioc-devel] jupyter installation on merida1
> 
> Dear BioConductor maintainers,
> 
> The buildbots almost seem able to build my package’s vignettes again, but the 
> jupyter installation on merida1 still doesn’t seem quite right: 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_release_bioc-2DLATEST_destiny_merida1-2Dbuildsrc.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=cpIYbv1AiHTjF5Nik5CJ68U9_TmpbwrPvf-oYdGq4f4=C96Pdpt7hGdREMh3Vp7MV4DVbc6nI7xJApJ1bdoZw1U=
> 
> * creating vignettes ... ERROR
> --- re-building ‘DPT.ipynbmeta’ using nbconvert
> Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = 
> env, :
> running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' [...] 'DPT.ipynb' 
> 2>&1' had status 126
> Call failed. Output:
> sh: /usr/local/bin/jupyter: /usr/local/opt/python3/bin/python3.6: bad 
> interpreter: No such file or directory
> 
> Exit status 126 means “The thing you tried to execute is not executable or 
> doesn’t exist”. The message looks like sh tries to find the binary referenced 
> in the shebang of /usr/local/bin/jupyter, and fails. I assume jupyter has 
> been installed with an interpreter that no longer exists, and now its shebang 
> points into the void? I guess the following is true for your system:
> 
> $ head -n1 /usr/local/bin/jupyter
> #!/usr/local/opt/python3/bin/python3.6
> $ ls /usr/local/opt/python3/bin/python3.6
> No such file or directory (os error 2)
> 
> Anyway, it would be amazing if someone could fix jupyter’s installation on 
> that system (until jupyter nbconvert --help works). The vignette engine 
> trying to use it (nbconvertR) has extensive INSTALL instructions that might 
> help: 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.rstudio.com_web_packages_nbconvertR_INSTALL=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=cpIYbv1AiHTjF5Nik5CJ68U9_TmpbwrPvf-oYdGq4f4=5JnZPiSkkIS2byivvXDZh-o7-oN4XgGijLVwPLRpvdY=
> 
> Thank you so much,
> Philipp
> 
> Helmholtz Zentrum München
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=cpIYbv1AiHTjF5Nik5CJ68U9_TmpbwrPvf-oYdGq4f4=ILPGAvIGyD5FCK0Qm7sJTwxXxn-24Kt_FOgjqogsF-0=
> 
> Helmholtz Zentrum München
> 
> Helmholtz Zentrum München
> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] jupyter installation on merida1

2019-12-12 Thread Angerer, Philipp

Dear maintainers,

Is there any progress with this? Any way I can help?

Thank you,
Philipp

- Ursprüngliche Mail -
Von: "Philipp Angerer" 
An: "bioc-devel" 
Gesendet: Mittwoch, 4. Dezember 2019 10:58:44
Betreff: [Bioc-devel] jupyter installation on merida1

Dear BioConductor maintainers, 

The buildbots almost seem able to build my package’s vignettes again, but the 
jupyter installation on merida1 still doesn’t seem quite right: 
http://bioconductor.org/checkResults/release/bioc-LATEST/destiny/merida1-buildsrc.html

* creating vignettes ... ERROR
--- re-building ‘DPT.ipynbmeta’ using nbconvert
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = 
env, :
running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' [...] 'DPT.ipynb' 2>&1' 
had status 126
Call failed. Output:
sh: /usr/local/bin/jupyter: /usr/local/opt/python3/bin/python3.6: bad 
interpreter: No such file or directory

Exit status 126 means “The thing you tried to execute is not executable or 
doesn’t exist”. The message looks like sh tries to find the binary referenced 
in the shebang of /usr/local/bin/jupyter, and fails. I assume jupyter has been 
installed with an interpreter that no longer exists, and now its shebang points 
into the void? I guess the following is true for your system:

$ head -n1 /usr/local/bin/jupyter
#!/usr/local/opt/python3/bin/python3.6
$ ls /usr/local/opt/python3/bin/python3.6
No such file or directory (os error 2)

Anyway, it would be amazing if someone could fix jupyter’s installation on that 
system (until jupyter nbconvert --help works). The vignette engine trying to 
use it (nbconvertR) has extensive INSTALL instructions that might help: 
https://cran.rstudio.com/web/packages/nbconvertR/INSTALL

Thank you so much,
Philipp

Helmholtz Zentrum München

___ 
Bioc-devel@r-project.org mailing list 
https://stat.ethz.ch/mailman/listinfo/bioc-devel 

Helmholtz Zentrum München

Helmholtz Zentrum München

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] jupyter installation on merida1

2019-12-04 Thread Angerer, Philipp




Dear BioConductor maintainers, 

The buildbots almost seem able to build my package’s vignettes again, but the 
jupyter installation on merida1 still [ 
http://bioconductor.org/checkResults/release/bioc-LATEST/destiny/merida1-buildsrc.html
 | doesn’t seem quite right ] : 
* creating vignettes ... ERROR 
--- re-building ‘DPT.ipynbmeta’ using nbconvert 
Warning in system2("jupyter", shQuote(args), carg, carg, wait = TRUE, env = 
env,  : 
running command 'PYTHONPATH=.:.: 'jupyter' 'nbconvert' [...] 'DPT.ipynb' 2>&1' 
had status 126 
Call failed. Output: 
sh: /usr/local/bin/jupyter: /usr/local/opt/python3/bin/python3.6: bad 
interpreter: No such file or directory 


Exit status 126 means “The thing you tried to execute is not executable or 
doesn’t exist”. The message looks like sh tries to find the binary referenced 
in the shebang of /usr/local/bin/jupyter, and fails. I assume jupyter has been 
installed with an interpreter that no longer exists, and now its shebang points 
into the void? I guess the following is true for your system: 
$ head -n1 /usr/local/bin/jupyter 
#!/usr/local/opt/python3/bin/python3.6 
$ ls /usr/local/opt/python3/bin/python3.6 
No such file or directory (os error 2) 


Anyway, it would be amazing if someone could fix jupyter’s installation on that 
system (until jupyter nbconvert --help works). The vignette engine trying to 
use it (nbconvertR) [ https://cran.rstudio.com/web/packages/nbconvertR/INSTALL 
| has extensive INSTALL instructions ] that might help! 


Thank you so much, 
Philipp 

Helmholtz Zentrum München


Helmholtz Zentrum München


[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] jupyter installation on merida1

Re: [Bioc-devel] jupyter installation on merida1

[Bioc-devel] jupyter installation on merida1

3 matches

Site Navigation

Mail list logo

Footer information