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[Bioc-devel] Question about "Warning: '.local' is deprecated."

3 messages · Martin Morgan, Jakob Theorell

Original
Jakob Theorell
# 
Dear all,
In one of my packages, flowSpecs, I have over the last weeks gotten this warning message:


* checking examples ... WARNING
Found the following significant warnings:

  Warning: '.local' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.

I am trying my best to check the ?Deprecated pages, but I find them quite uninformative, and the specific deprecation help does not take me further either, it only says:
Warning message:
'.local' is deprecated.
See help("Deprecated")

And most annoying of all: there are no .local calls in the package since weeks back. Very thankful for any input that can straighten this out.
Best regards

Jakob Theorell, MD/PhD
Autoimmune Neurology Group
Nuffield Department of Clinical Neurosciences
University of Oxford
Phone: +447597976151
Martin Morgan
# 
I would suggest forcing warnings to errors

    options(warn=2)

and then when the now-error occurs using

    traceback()

to see what is wrong -- I think this is a call to a deprecated S4 method, and what you'd really like is the method signature.

Martin

?On 4/27/20, 2:58 AM, "Bioc-devel on behalf of Jakob Theorell" <bioc-devel-bounces at r-project.org on behalf of jakob.theorell at ndcn.ox.ac.uk> wrote:

    Dear all,
    In one of my packages, flowSpecs, I have over the last weeks gotten this warning message:


    * checking examples ... WARNING
    Found the following significant warnings:

      Warning: '.local' is deprecated.
    Deprecated functions may be defunct as soon as of the next release of
    R.
    See ?Deprecated.

    I am trying my best to check the ?Deprecated pages, but I find them quite uninformative, and the specific deprecation help does not take me further either, it only says:

    > .Deprecated(old = ".local")
    Warning message:
    '.local' is deprecated.
    See help("Deprecated")

    And most annoying of all: there are no .local calls in the package since weeks back. Very thankful for any input that can straighten this out.
    Best regards

    Jakob Theorell, MD/PhD
    Autoimmune Neurology Group
    Nuffield Department of Clinical Neurosciences
    University of Oxford
    Phone: +447597976151






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Jakob Theorell
# 
Thank you!
Found it: "flowCore::description" is old, "flowCore::keyword" is replacement.
Best regards
Jakob