Seems unlikely that that particular bug is involved. I seem to recall some
change related to inadvertent variable capture in .TkRoot$env (?). At any rate,
we currently have
> parent.env(.TkRoot$env)
<environment: R_EmptyEnv>
which used to be
> parent.env(.TkRoot$env)
<environment: R_GlobalEnv>
as a result, this won't work any more because R_EmptyEnv has no operators and
functions in it:
> evalq(x <- 1, .TkRoot$env)
Error in eval(substitute(expr), envir, enclos) :
could not find function "<-"
and consequently, you conk out at
Try(n <- evalq(TclVarCount <- TclVarCount + 1, .TkRoot$env))
which presumably needs to be recoded in the same way as the current code in
tclVar():
> tclVar
function (init = "")
{
n <- .TkRoot$env$TclVarCount <- .TkRoot$env$TclVarCount +
1L
name <- paste0("::RTcl", n)
l <- list(env = new.env())
assign(name, NULL, envir = l$env)
reg.finalizer(l$env, function(env) tcl("unset", ls(env)))
class(l) <- "tclVar"
tclvalue(l) <- init
l
}
(The whole thing looks a bit odd: Your function clones a fair bit of tclVar,
wrapping each line in Try() for no apparent reason (or?), with the apparent
purpose of doing something that seems quite similar to what tclArray() already
does...)
-pd
> On 14 Jan 2015, at 06:50 , Keith Satterley <ke...@wehi.edu.au> wrote:
>
> I maintain the package affylmGUI. It works when installed on many previous
> versions of R. I have today tested exactly the same code under R-2.15.3,
> R-3.0.2, R-3.1.0, R-3.1.1, R-3.1.2 and R-devel.
>
> I have also tested the versions of affylmGUI downloaded by biocLite for each
> version of R and the same result applies.
>
> I have no errors under 2.15.3, 3.0.2, 3.1.0 and 3.1.1. The following error
> occurs under 3.1.2 and R-devel.
>
> I run affylmGUI and read a targets file which then causes affylmGUI to read
> the specified cel files. On attempting to display the RNA targets file in a
> Tk window using the "RNA Targets" option from the "RNA Targets" Menu item and
> the following errors occur:
>
> Error text box 1: Error in eval(substitute(expr),enclos):could not find
> function "<-" - pressed OK
> Following error text box: Error in paste("::RTcl",n,sep=""): object 'n' not
> found - pressed OK
> Following error text box: Error in assign(name, NULL, environ = I$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.
>
> cheers,
>
> Keith
> ==============================
> Keith Satterley
> Bioinformatics Division
> The Walter & Eliza Hall Institute of Medical Research
> Melbourne, Victoria, Australia
> ==============================
>
>
> ______________________________________________________________________
> The information in this email is confidential and =\ i...{{dropped:21}}
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