TCL/TK in R
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Bogdan ▴ 620
@bogdan-2367
Last seen 25 days ago
Palo Alto, CA, USA

Dear all,

I would like to have TLC/TK support in R in order to install some packages like UMI4Cats. Would you please let me know what I shall do in this regard ? Thanks a lot !

> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua 
       TRUE        TRUE        TRUE       FALSE        TRUE       FALSE 
   http/ftp     sockets      libxml        fifo      cledit       iconv 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
        NLS     profmem       cairo         ICU long.double     libcurl 
       TRUE       FALSE        TRUE        TRUE        TRUE        TRUE

~ Bogdan

TCL/TK • 396 views
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This isn't really a Bioconductor question, so you might get a faster response on a more general R forum. Which operating system are you running?

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Mike Mike. I am using Ubuntu 16.04 that has TclTk support that is built-in.

In R I have also installed the package "tcltk2" although no success.

The TclTk needs to be recognized by in R in order to install a BioC library, that is UMI4Cats .

http://bioconductor.org/packages/release/bioc/html/UMI4Cats.html

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Are you compiling R from source, or installing from the Ubuntu repositories via apt-get install ? I think the output of capabilities() is defined by what's available when R is compiled. If you're building it yourself, maybe you need to rebuild having installed tk-dev and tcl-dev.

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Thank you Mike. On my Ubuntu machine, before compiling R, I had tcl-dev and tk-dev already at the latest version.

*tk-dev is already the newest version (8.6.0+9).

tcl-dev is already the newest version (8.6.0+9).*

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@james-w-macdonald-5106
Last seen 1 day ago
United States

As Mike already pointed out, this isn't a Bioconductor question. You could ask on R-help but they will most likely tell you that it's already documented and you should read that.

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Hi James, thank you for your suggestions. I have re-installed R having the option --with-tcltk and BioC and did not help.

Would you know, is there any online resource that provides R (and BioC) already installed that I could potential use instead of struggling with my own machine. Thanks !

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You could take a look at the Bioconductor docker containers at https://www.bioconductor.org/help/docker/

They have tcltk support available:

-> % docker run -it --entrypoint=Rscript bioconductor/bioconductor_docker:RELEASE_3_13 -e 'capabilities()'
       jpeg         png        tiff       tcltk         X11        aqua 
       TRUE        TRUE        TRUE        TRUE       FALSE       FALSE 
   http/ftp     sockets      libxml        fifo      cledit       iconv 
       TRUE        TRUE        TRUE        TRUE       FALSE        TRUE 
        NLS       Rprof     profmem       cairo         ICU long.double 
      FALSE        TRUE        TRUE        TRUE        TRUE        TRUE 
    libcurl 
       TRUE
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Thanks a lot Mike ! It has been very helpful !

A question though : shall I run : docker run -it --user rstudio bioconductor/bioconductor_docker:devel R

and install UMI4Cats, obviously, a lot of other libraries are installed.

How can I save the docker container that contains the additional libraries that I have installed ?

thank you !

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