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.