From keith at wehi.EDU.AU  Wed Jan 14 06:50:40 2015
From: keith at wehi.EDU.AU (Keith Satterley)
Date: Wed, 14 Jan 2015 16:50:40 +1100
Subject: [Rd] Is the tcltk failure in affylmGUI related to R bug 15957
Message-ID: <54B603B0.9090607@wehi.edu.au>

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
==============================


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[Rd] Is the tcltk failure in affylmGUI related to R bug 15957
Keith Satterley