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List:       bioc-devel
Subject:    [Bioc-devel] =?windows-1252?q?CRAN_checks_failed_by_downloading_?= =?windows-1252?q?=91reactome=2Edb
From:       JEANNERET Florian <florian.jeanneret () cea ! fr>
Date:       2021-02-17 19:50:03
Message-ID: B5E45C0E60EA8A4ABB55290696B3466C1A30450A () EXDAG0-A3 ! intra ! cea ! fr
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Hello all !

I need some help to "build my package" using reactome.db for reactomePA functions.

In fact, builds and remote downloads have failed for Ubuntu but not for Windows 10 at \
reactome.db downloading. The same appears when I try to download reactome.db alone.

Archive downloading [url][1] works manually from Bioconductor page.

With this command:

    BiocManager::install("reactome.db")

I get these messages:

    Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
    Installing package(s) 'reactome.db'
    essai de l'URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/reactome.db_1.70.0.tar.gz'
  Content type 'application/x-gzip' length 454979427 bytes (433.9 MB)
    ========================================
    downloaded 348.9 MB

    Error in download.file(url, destfile, method, mode = "wb", ...) :
      download from 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/reactome.db_1.70.0.tar.gz' \
failed  De plus : Warning messages:
    1: In download.file(url, destfile, method, mode = "wb", ...) :
      downloaded length 365895769 != reported length 454979427
    2: In download.file(url, destfile, method, mode = "wb", ...) :
      URL 'https://bioconductor.org/packages/3.11/data/annotation/src/contrib/reactome.db_1.70.0.tar.gz': \
Timeout of 60 seconds was reached  Warning in download.packages(pkgs, destdir = tmpd, \
available = available,  :  download of package ‘reactome.db’ failed
    Installation path not writeable, unable to update packages: littler, boot, class, \
                cluster,
      codetools, foreign, KernSmooth, MASS, Matrix, mgcv, nlme, nnet, spatial


______

In case of personal use, I can change the timeout option:

    options(timeout = 300)  # five minutes



But in case of package building, this warning is an issue, so how should we manage it \
?

For CRAN checks for instance on Ubuntu,
I get in logs:

    ...
    trying URL 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/reactome.db_1.74.0.tar.gz'
  Content type 'application/x-gzip' length 430092992 bytes (410.2 MB)
    ==================================================
    downloaded 410.2 MB
    ...

Then:

    * installing *source* package ‘reactome.db’ ...
    ** using staged installation
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** testing if installed package can be loaded from temporary location
    ** testing if installed package can be loaded from final location
    ** testing if installed package keeps a record of temporary installation path
    * creating tarball
    Build timed out (after 20 minutes). Marking the build as failed.
    Build was aborted

Again a question of time, so my question is, how to manage this ? Or this package \
could be a part of  Bioconductor despite this warning ?

Complete logs are here : \
https://builder.r-hub.io/status/original/MOANI_0.99.0.tar.gz-20213007616144e596072fe64e5e7127


Any ideas ?
Thanks !


  [1]: https://bioconductor.org/packages/3.12/data/annotation/src/contrib/reactome.db_1.74.0.tar.gz


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