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[R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission maGUI 2.3

dhamma pal 
0Ok, thanks.
I have tried all suggested by you. But no package or function detected to
be dependent on BiocInstaller or Bioclite.
I have tested on both windows and linux OSs, but none shown any warning
related to these deprecated packages. Everything working fine on my PCs but
not able to pass through CRAN check at the CRAN organisation.
On Mon, 12 Nov 2018, 5:45 pm Martin Morgan <mtmorgan.bioc at gmail.com wrote:

            

      
      
      
    

        

      
      
    

        
On 12 Nov 2018 5:45 pm, "Martin Morgan" <mtmorgan.bioc at gmail.com> wrote:

        
I cannot tell whether this will be helpful or not. It looks to me like the
warning occurs when one of your dependencies uses BiocInstaller. You could
create a database of all available packages

  chooseCRANmirror()
  chooseBioCmirror()
  db = available.packages()

find the installation dependencies of your package dependencies

  flds = c("Depends", "Imports", "LinkingTo")
  pkgs = read.dcf("DESCRIPTION", flds)[, flds]
  pkgs = trimws(unlist(strsplit(pkgs, ","), use.names = FALSE))
  pkgs = pkgs[!is.na(pkgs)]

and discover which references BiocInstaller

  deps = tools::package_dependencies(pkgs, db, recursive = TRUE)
  unlist(deps)["BiocInstaller" %in% unlist(deps)]

But actually when I run this with version 2.2 of your package I don't see a
dependency on BiocInstaller (other than in your own package).

Martin


?On 11/11/18, 9:55 PM, "R-package-devel on behalf of dhamma pal" <
r-package-devel-bounces at r-project.org on behalf of dhammapalb at uohyd.ac.in>
wrote:

    The latest version donot use BIOCINSTALLER or bioclite, still getting a
    warning.

    Errors are not detected in the current version, i.e. 2.3 version of
maGUI.
    But errors are getting reported in the earlier version i.e., 2.2 which
is
    not the making the current version to pass through the CRAN. I have
tried
    to submit the corrected  package with version 2.2 to rectify the errors,
    but getting overriden error. Now how to ugrade maGUI to 2.3?
    Thanks in advance.


    ---------- Forwarded message ---------
    From: <ligges at statistik.tu-dortmund.de>
    Date: Thu, 8 Nov 2018, 1:12 pm
    Subject: [CRAN-pretest-archived] CRAN submission maGUI 2.3
    To: <dhammapalb at uohyd.ac.in>
    Cc: <CRAN-submissions at r-project.org>


    Dear maintainer,

    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_20181108_081501/Windows/00check.log
    >
    Status: 1 WARNING, 1 NOTE
    Debian: <

https://win-builder.r-project.org/incoming_pretest/maGUI_2.3_20181108_081501/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>

    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_20181108_081501/
    >
    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 at 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.


    ______________________________________________
    R-package-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-package-devel

  
  


  

    

      Message-ID:
      <CACApb-EmZD+QfzozTB82b-s6AM0Hyw7vupxwvFbH3-OL9+YOGg@mail.gmail.com>
    

    

      In-Reply-To:
      <MWHPR05MB3582D8704C86C6193CB15266F9C10@MWHPR05MB3582.namprd05.prod.outlook.com>
    

    

      

        
          
            
          
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Thread (3 messages)

  

  

    
            
        dhamma pal
        
        CRAN submission maGUI 2.3
      
      Nov 11
    
    
      
            
        Martin Morgan
        
        CRAN submission maGUI 2.3
      
      Nov 12
    
    
      
            
        dhamma pal
        
        CRAN submission maGUI 2.3
      
      Nov 14