[R-pkg-devel] Regarding maGUI package error

[Martin Morgan]

On Windows, likely the warning about BiocInstaller comes from a package dependency, rather than your package.

Somehow this seems like a CRAN misconfiguration or perhaps workaround to accommodate packages that need to be fixed. The warning message comes when loading BiocInstaller (BiocInstaller has been replaced by BiocManager, which is a standard CRAN package). The development version of R should be using the development version of Bioconductor. BiocInstaller was removed from the development version of Bioconductor, so the warning message should not appear -- any package trying to load BiocInstaller should simply fail.

Martin Morgan

On 2/20/19, 2:06 AM, "R-package-devel on behalf of dhamma pal" <r-package-devel-bounces using r-project.org on behalf of dhammapalb using uohyd.ac.in> wrote:

    Hi.
    Following is the check results from CRAN server, though I didn't get any
    warning on my PC.
    
    package maGUI_2.3.tar.gz does not pass the incoming checks automatically,
    please see the following pre-tests:
    Windows: <
    https://win-builder.r-project.org/incoming_pretest/maGUI_2.3_20190217_181340/Windows/00check.log
    >
    Status: 1 WARNING, 1 NOTE
    Debian: <
    https://win-builder.r-project.org/incoming_pretest/maGUI_2.3_20190217_181340/Debian/00check.log
    >
    Status: 1 NOTE
    
    Last released version's CRAN status: ERROR: 2
    See: <https://CRAN.R-project.org/web/checks/check_results_maGUI.html
    <https://cran.r-project.org/web/checks/check_results_maGUI.html>>
    
    CRAN Web: <https://cran.r-project.org/package=maGUI>
    
    Please fix all problems and resubmit a fixed version via the webform.
    If you are not sure how to fix the problems shown, please ask for help on
    the R-package-devel mailing list:
    <https://stat.ethz.ch/mailman/listinfo/r-package-devel>
    If you are fairly certain the rejection is a false positive, please
    reply-all to this message and explain.
    
    More details are given in the directory:
    <
    https://win-builder.r-project.org/incoming_pretest/maGUI_2.3_20190217_181340/
    >
    The files will be removed after roughly 7 days.
    
    No strong reverse dependencies to be checked.
    
    Best regards,
    CRAN teams' auto-check service
    Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
    Check: CRAN incoming feasibility, Result: NOTE
      Maintainer: 'Dhammapal Bharne <dhammapalb using uohyd.ac.in>'
    
      New submission
    
      Package was archived on CRAN
    
      CRAN repository db overrides:
        X-CRAN-Comment: Archived on 2018-11-01 as check warnings were not
          corrected despite a month's notice.
    
        Needed change for BioC 3.8
    
    Flavor: r-devel-windows-ix86+x86_64
    Check: whether package can be installed, Result: WARNING
      Found the following significant warnings:
        Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the
    'BiocManager' CRAN
      See 'd:/RCompile/CRANincoming/R-devel/maGUI.Rcheck/00install.out' for
    details.
    
    Flavor: r-devel-windows-ix86+x86_64
    Check: Overall checktime, Result: NOTE
      Overall checktime 11 min > 10 min
    
    
    On Wed, 20 Feb 2019, 2:36 am Duncan Murdoch <murdoch.duncan using gmail.com wrote:
    
    > On 19/02/2019 11:47 a.m., dhamma pal wrote:
    > > Dear all.
    > > The current version of the maGUI package is 2.2 which got errors after
    > the
    > > upgradation of R version.
    > >
    > > Therefore I was trying to submit new version 2.3 of the package but
    > getting
    > > warnings of the previous version of 2.2 at the CRAN incoming Precheck
    > > server.
    > >
    > > To resolve this, Do I need to upload the corrected package with the 2.2
    > > version?
    > > or How to rectify the errors of the previous version the packages at the
    > > CRAN repository?
    > >
    > > Note: The error message is that "BiocInstaller and biocLite packages are
    > > depreciated. Use BiocManager instead." Therefore I have replaced these
    > > packages with BiocManager package. But now It couldn't upload at CRAN
    > > because of the errors in the previous version.
    >
    > I suspect your interpretation of the messages you've received could be
    > incorrect.  Could you post a copy of it if it came by email, or a link
    > if it's on a web page?
    >
    > One reason you may have trouble uploading a revision is that you were
    > unresponsive to requests for fixes in the previous one, and your package
    > has been archived:  see
    >
    > https://cran.r-project.org/web/packages/maGUI/index.html
    >
    > and
    >
    >
    > https://cran-archive.r-project.org/web/checks/2018-11-01_check_results_maGUI.html
    >
    > The stuff about the Bioconductor packages is shown as warnings, but you
    > also have errors.  Did you fix everything?
    >
    > Duncan Murdoch
    >
    
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