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] Sudden Bioconductor nightly build fail for IsoCorrectoRGUI: cannnot add binding of 'variable' to the base environment
4 messages · Martin Morgan, Christian Kohler
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 at r-project.org on behalf of christian.kohler at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
1 day later
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 at r-project.org on behalf of christian.kohler at 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 at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
3 days later
Dear Martin, IsoCorrectoRGUI now successfully passes the Multiple platform build/check report for BioC3.13, yeah ! Many thanks for your help. 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 at r-project.org on behalf of christian.kohler at 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 at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel