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 M?nchen Helmholtz Zentrum M?nchen
[Bioc-devel] jupyter installation on merida1
3 messages · Angerer, Philipp, Hervé Pagès
8 days later
Dear maintainers, Is there any progress with this? Any way I can help? Thank you, Philipp ----- Urspr?ngliche Mail ----- Von: "Philipp Angerer" <philipp.angerer at helmholtz-muenchen.de> An: "bioc-devel" <bioc-devel at 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 #!/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 M?nchen _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel Helmholtz Zentrum M?nchen Helmholtz Zentrum M?nchen
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 ----- Urspr?ngliche Mail ----- Von: "Philipp Angerer" <philipp.angerer at helmholtz-muenchen.de> An: "bioc-devel" <bioc-devel at 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 M?nchen
_______________________________________________ Bioc-devel at 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 M?nchen Helmholtz Zentrum M?nchen
Herv? Pag?s 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: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319