[Bioc-devel] jupyter installation on merida1

Angerer, Philipp ph|||pp@@ngerer @end|ng |rom he|mho|tz-muenchen@de
Thu Dec 12 13:24:41 CET 2019

Dear maintainers,

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

Thank you,

----- 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: 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
$ 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,

Helmholtz Zentrum München

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