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List:       bioc-devel
Subject:    Re: [Bioc-devel] =?utf-8?q?CRAN_checks_failed_by_downloading_?= =?utf-8?b?4oCYcmVhY3RvbWUuZGLigJkgcG
From:       Martin Morgan <mtmorgan.bioc () gmail ! com>
Date:       2021-02-26 19:19:57
Message-ID: BN8PR04MB624196A955FC268CD39EFEDDF99D9 () BN8PR04MB6241 ! namprd04 ! prod ! outlook ! com
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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@r-project.org on behalf of florian.jeanneret@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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