[Bioc-devel] [Rd] Is the tcltk failure in affylmGUI related to R bug 15957

[Dan Tenenbaum]

[moving this to bioc-devel]

----- Original Message -----
> From: "Keith Satterley" <keith at wehi.EDU.AU>
> To: r-devel at r-project.org
> Sent: Tuesday, January 13, 2015 9:50:40 PM
> Subject: [Rd] Is the tcltk failure in affylmGUI related to R bug 15957
> 
> I maintain the package affylmGUI. It works when installed on many
> previous versions of R. I have today tested exactly the same code
> under
> R-2.15.3, R-3.0.2, R-3.1.0, R-3.1.1, R-3.1.2 and R-devel.
> 
> I have also tested the versions of affylmGUI downloaded by biocLite
> for
> each version of R and the same result applies.
> 
> I have no errors under 2.15.3, 3.0.2, 3.1.0 and 3.1.1. The following
> error occurs under 3.1.2 and R-devel.
> 
> I run affylmGUI and read a targets file which then causes affylmGUI
> to
> read the specified cel files. On attempting to display the RNA
> targets
> file in a Tk window using the "RNA Targets" option from the "RNA
> Targets" Menu item and the following errors occur:
> 
> Error text box 1: Error in eval(substitute(expr),enclos):could not
> find
> function "<-"   - pressed OK
> Following error text box: Error in paste("::RTcl",n,sep=""): object
> 'n'
> not found   - pressed OK
> Following error text box: Error in assign(name, NULL, environ =
> I$env):
> object 'name' not found   - pressed OK
> Following error text box: Error in paste("set",name, "(0,0)\"\"",sep=
> ""):object 'name' not found   - pressed OK
> 
> This then results in an unfilled Tk window.
> 
> I am testing on a Windows 7, 64 bit environment. My sessionInfo is:
> 
> R version 3.1.2 (2014-10-31)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> locale:
> [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
> LC_MONETARY=English_Australia.1252
> [4] LC_NUMERIC=C LC_TIME=English_Australia.1252
> attached base packages:
>   [1] stats4    parallel  tcltk     stats     graphics  grDevices
> utils     datasets  methods   base
> other attached packages:
>   [1] affylmGUI_1.40.0      AnnotationDbi_1.28.1 GenomeInfoDb_1.2.4
> IRanges_2.0.1         S4Vectors_0.4.0
>   [6] xtable_1.7-4          R2HTML_2.3.1 affyPLM_1.42.0
> preprocessCore_1.28.0 gcrma_2.38.0
> [11] tkrplot_0.0-23        affyio_1.34.0 BiocInstaller_1.16.1
> affy_1.44.0           Biobase_2.26.0
> [16] BiocGenerics_0.12.1   limma_3.22.3
> loaded via a namespace (and not attached):
> [1] Biostrings_2.34.1 DBI_0.3.1         RSQLite_1.0.0 splines_3.1.2
> XVector_0.6.0     zlibbioc_1.12.0
> 
> I think the relevant code that is resulting in the error is generated
> by
> this function in main.R:
> tclArrayVar <- function(){
>      Try(n <- evalq(TclVarCount <- TclVarCount + 1, .TkRoot$env))
>      Try(name <- paste("::RTcl", n,sep = ""))
>      Try(l <- list(env = new.env()))
>      Try(assign(name, NULL, envir = l$env))
>      Try(reg.finalizer(l$env, function(env) tcl("unset", ls(env))))
>      Try(class(l) <- "tclArrayVar")
>      Try(.Tcl(paste("set ",name,"(0,0) \"\"",sep="")))
>      l  ### Investigate this line KS
> } #end of tclArrayVar <- function()
> 
> This code is lines 877-886 in main.R
> 
> Despite the un-investigated last line in this function, it works fine
> in
> earlier versions of R as described above.
> 
> The original programmer has left our division some years ago and I
> have
> maintained the code since then. Consequently my understandings as to
> why
> the code was written the way it was is somewhat limited, so I have
> not
> touched anything unless it was broken.
> 
> My question is, do I need to do something with the affylmGUI code?
> I'd
> appreciate some advice if so.
> 
> Is this failure related to bug 15957
> (https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15957) that
> Duncan
> fixed on 2014-09-08.

Please provide the exact code and files that cause the error.
Dan


> 
> cheers,
> 
> Keith
> ==============================
> Keith Satterley
> Bioinformatics Division
> The Walter & Eliza Hall Institute of Medical Research
> Melbourne, Victoria, Australia
> ==============================
> 
> 
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