[Bioc-devel] CRAN checks failed by downloading ‘reactome.db’ package (WARNING Ubuntu, OK for Windows)

[Martin Morgan]

If you mean package building on your own machine, you could add the options(timeout = 300L) to a file 
'.Rprofile' in your 'HOME' directory; that way the timeout is set for all your R sessions, including the one that is building the package.

The Bioconductor build system already has reactome.db installed, so it will not 'count' toward the time it takes to build and check your package. Be sure that your package has reactome.db in the Suggests: field, then it is not necessary to download it in your vignette / examples; it will already be installed.

The next release of BiocManager, which should happen very soon now, should set the longer timeout for package downloads.

Martin

On 2/17/21, 2:50 PM, "Bioc-devel on behalf of JEANNERET Florian" <bioc-devel-bounces using r-project.org on behalf of florian.jeanneret using cea.fr> wrote:

    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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