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
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