[Bioc-devel] Sudden Bioconductor nightly build fail for IsoCorrectoRGUI: cannnot add binding of 'variable' to the base environment

[Martin Morgan]

This is because of a change in base R

  https://github.com/wch/r-source/blob/9ad27a744572fca453665e97110ded41a2680a57/doc/NEWS.Rd#L257

It can be reproduced by using a recent version R-4-1.

Looking at your code, I guess it is at

  https://code.bioconductor.org/browse/IsoCorrectoRGUI/blob/master/R/IsoCorrectionGUI.R#L30

that things start to run into trouble -- probably instead you want to create a 'package local' environment, e.g., 

   isoCorrectionGUIEnvironment <- new.env()

as the very first line in this file, and use that for storing these variables.

Martin



On 5/4/21, 12:36 AM, "Bioc-devel on behalf of Christian Kohler" <bioc-devel-bounces using r-project.org on behalf of christian.kohler using ur.de> wrote:

    Hello BioC community,

    I am the maintainer of the IsoCorrectoRGUI package.
    Starting with April 30th, problems are reported in the Multiple platform 
    build/check report for BioC3.13 (Linux, Windows Server as well as macOS) 
    though IsoCorrectoRGUIs code base did not change since end of October 2020.

    The relevant part of the error message is shown below:

    * checking examples ... ERROR
    Running examples in ‘IsoCorrectoRGUI-Ex.R’ failed
    The error most likely occurred in:

     > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
     > ### Name: IsoCorrectionGUI
     > ### Title: Graphical User Interface for IsoCorrectoR
     > ### Aliases: IsoCorrectionGUI
     >
     > ### ** Examples
     >
     >
     >  IsoCorrectionGUI()
    Error in baseEnvRef$continueIsoCorrection <- TRUE :
       cannot add binding of 'continueIsoCorrection' to the base environment
    Calls: IsoCorrectionGUI -> initGUI
    Execution halted

    Frankly speaking, at the moment I have no clue why the CHECK procedure 
    fails from one day to the next. Does this reflect a conflict with R 
    4.1.0 alpha internals?
    Any insight would be greatly appreciated as the deadline for passing R 
    CMD check is in a couple of days.

    If anyone knows why this could be happening or if it is likely to sort 
    itself in the next build please let me know.


    Thanks,

    Christian

    _______________________________________________
    Bioc-devel using r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/bioc-devel