Entering edit mode
@richardallenfriedmanbrooklyn-24118
Last seen 3 months ago
United States
Dear List,
AffylmGUI doesn't start in R 4.4.1 although all of the required software is installed. On the same mac, OS 14.6.1 the most recent version of R under which AffylmGUI starts in R4.1.2. Here is a session record:
> library(affylmGUI)
To begin, type affylmGUI()
> affylmGUI()
[1] "Mac OSX:Cannot find Tcl/Tk package \"BWidget\".\taffylmGUI cannot continue.\n\naffylmGUI requires the Tcl/Tk packages, BWidget and Tktable.\nYou must have the toolkit Tcl/Tk installed on your computer.\nTo install the tcl/tk toolkit do the following:\nGo to CRAN (you can use any mirror):\nhttp://cran.r-project.org/bin/macosx/tools/\nDownload tcltk-8.5.5-x11.dmg, install it.\nNote versions shown correct on Jan 18 2013\nIt installs in /usr/local\nRequires Mac OS X 10.4 (Tiger) or higher for 32-bit R\nand Mac OS X 10.5 (Leopard) or higher for 64-bit R.\nYou need the two Tcl/Tk packages called BWidget and Tktable \ninstalled as well.\nDownload BWidget from:\nhttp://sourceforge.net/projects/tcllib/files/BWidget/1.9.5/ or later.\nversion into your Downloads folder.\nUnpack the tar.gz file into /usr/local/lib using \ncd /usr/local/lib\nsudo tar zxvf ~your_username/Downloads/bwidget-1.9.5.tar.gz\nBWidget is written in pure tcl and does not need compiling.\nTktable is written in the C and Tcl languages and the source \nfile needs compiling. The source file is available from:\nhttp://sourceforge.net/projects/tktable/files/tktable/2.10/\nYou need the Apple Dev tools installed. Do:\ntar zxf Tktable2.9.tar.gz\n./configure\nmake\nsudo make install\nNow it will work in R.\n"
Error in affylmGUI() : Error occurred in TclRequire("BWidget")
In addition: Warning message:
In tclRequire(tclPkg) : Tcl package 'BWidget' not found
> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.6.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] affylmGUI_1.78.0
loaded via a namespace (and not attached):
[1] crayon_1.5.3 httr_1.4.7 UCSC.utils_1.0.0 jsonlite_1.8.8 xtable_1.8-4
[6] S4Vectors_0.42.1 statmod_1.5.0 Biostrings_2.72.1 stats4_4.4.1 Biobase_2.64.0
[11] gcrma_2.76.0 IRanges_2.38.1 GenomeInfoDb_1.40.1 BiocManager_1.30.23 compiler_4.4.1
[16] preprocessCore_1.66.0 codetools_0.2-20 R2HTML_2.3.4 limma_3.60.4 affyPLM_1.80.0
[21] XVector_0.44.0 tcltk_4.4.1 R6_2.5.1 GenomeInfoDbData_1.2.12 splines_4.4.1
[26] affy_1.82.0 tkrplot_0.0-27 tools_4.4.1 zlibbioc_1.50.0 BiocGenerics_0.50.0
[31] affyio_1.74.0
>
Please advise.
I hope that affylmGUI is still being supported.
Thanks and best wishes,
Rich
Richard Friedman
Herbert Irving Comprehensive Cancer Center
Columbia University Irving Medical Center
Gordon, Thank you as always for your reply. It turns out that I have Tcl/Tk installed elsewhere than in /usr/local/lib
from R
so that when I try to compile TkTable, I get the following error messages
I guess that I have to reinstall Tcl/Tk in the right place.
Best wishes,
Rich
Dear List, AffylmGUI works fine with R 4.4.1 on Windows. However most of my students have macs. I have installed BWidget and Tktable in the right places but still get the same error message as above: I think that the problem is that Tktable does not compile properly on Sonoma. I have BWidget and TKtable in the proper directory:
When I try to install tktable I get the following error message
Strictly, this is a TKtable problem. However the last entry on the bug report list was 2018. I would appreciate any suggestions. Is it possible for affylmGUI to be made to work with the current Mac OS and R?
Thanks and best wishes,
Rich
Richard Friedman
Columbia University Cancer Center
affylmGUI passes all checks for all platforms, including Mac OS and arm64, for Bioconductor 3.20, so I assume it must work on a Mac:
https://bioconductor.org/checkResults/devel/bioc-LATEST/affylmGUI/
Strangely, the current Bioconductor 3.19 tests don't seem to include Mac, for reasons that I don't understand.
affylmGUI is obviously a tck/tk based package. There is therefore no way that we could make it available for your computer is you're not able to get tcl/tk working.
I no longer have funds to employ affylmGUI programmers, so making substantive changes to the underlying affylmGUI package isn't really possible for me. On the other hand, I can make updates to affylmGUI if you could provide me with a patch that would make it work for the Mac systems.
This is the message that affylmGUI gives if the internal
TclRequirecheck fails on a Mac OS system:Gordon,
I found out what went wrong. The problem was that the xquartz distribution for mac from cran did not include tcltk! I found that by installing tcltk, with homebrew, I was able to get affylmGUI to work. On the command line
Another issue is that in sonoma the Tktable and BWidget files have to be in /opt/R/x86_64/lib/, rather than in /usr/local/lib/, as previously.
Best wishes,
Rich
Glad to hear that you have figured it out. Your experience might help other people with limmaGUI or affylmGUI on MacOS as well.
Gordon,
Thank you as always. I have tried the instructions you gave before my most recent post. The patch is almost certainly beyond my capability but I will look into the matter.
Best wishes,
Rich