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.ange...@helmholtz-muenchen.de> > An: "bioc-devel" <bioc-devel@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 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cpIYbv1AiHTjF5Nik5CJ68U9_TmpbwrPvf-oYdGq4f4&s=ILPGAvIGyD5FCK0Qm7sJTwxXxn-24Kt_FOgjqogsF-0&e= > > 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
