[Bioc-devel] jupyter installation on merida1

[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" <philipp.angerer using helmholtz-muenchen.de>
> An: "bioc-devel" <bioc-devel using r-project.org>
> 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&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cpIYbv1AiHTjF5Nik5CJ68U9_TmpbwrPvf-oYdGq4f4&s=C96Pdpt7hGdREMh3Vp7MV4DVbc6nI7xJApJ1bdoZw1U&e=
> 
> * 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&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cpIYbv1AiHTjF5Nik5CJ68U9_TmpbwrPvf-oYdGq4f4&s=5JnZPiSkkIS2byivvXDZh-o7-oN4XgGijLVwPLRpvdY&e=
> 
> Thank you so much,
> Philipp
> 
> Helmholtz Zentrum München
> 
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> 
> Helmholtz Zentrum München
> 

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