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

[Christian Kohler]

Dear Martin,

thank you very much for the quick help.

I'll try it this way.

BTW: I could have read the NEWS file by my own before asking, sorry for 
that.


Best

Christian

On 04.05.21 12:21, Martin Morgan wrote:
> 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
>
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