[moving this to bioc-devel] ----- Original Message ----- > From: "Keith Satterley" <ke...@wehi.edu.au> > To: r-de...@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 > ============================== > > > ______________________________________________________________________ > The information in this email is confidential and > intend...{{dropped:4}} > > ______________________________________________ > r-de...@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel