[BioC] tcltk package for R 2.14.1
Dan Tenenbaum
dtenenba at fhcrc.org
Wed Jan 25 06:25:26 CET 2012
On Tue, Jan 24, 2012 at 8:35 PM, Chintan Vora - Xcelris
<chintan.vora at xcelrislabs.com> wrote:
> I tried it but its gives me following error
>
>> library(tcltk)
> Error : .onLoad failed in loadNamespace() for 'tcltk', details:
> call: fun(libname, pkgname)
> error: Tcl/Tk support is not available on this system
> In addition: Warning message:
> S3 methods ‘$.tclvar’, ‘$<-.tclvar’, ‘as.character.tclObj’,
> ‘as.character.tclVar’, ‘as.double.tclObj’, ‘as.integer.tclObj’,
> ‘as.logical.tclObj’, ‘as.raw.tclObj’, ‘print.tclObj’, ‘[[.tclArray’,
> ‘[[<-.tclArray’, ‘$.tclArray’, ‘$<-.tclArray’, ‘names.tclArray’,
> ‘names<-.tclArray’, ‘length.tclArray’, ‘length<-.tclArray’, ‘tclObj.tclVar’,
> ‘tclObj<-.tclVar’, ‘tclvalue.default’, ‘tclvalue.tclObj’, ‘tclvalue.tclVar’,
> ‘tclvalue<-.default’, ‘tclvalue<-.tclVar’, ‘close.tkProgressBar’ were
> declared in NAMESPACE but not found
> Error: package/namespace load failed for ‘tcltk’
>
You need to make sure you have the appropriate packages installed on
your system.
You don't specify which Linux distribution you are running, but here
is the list of packages for ubuntu (install with "sudo apt-get install
packageName") courtesy of Hervé Pagès. I should probably make this a
FAQ. Then reinstall R.
Required stuff:
make
libc6-dev
gfortran
gfortran-4.2
g++
g++-4.2
libreadline5-dev
libx11-dev
libxt-dev
Other highly recommended stuff (TeX/LaTeX, tcltk, PNG, JPEG, cairo, Java):
texlive-full
tcl8.5-dev
tk8.5-dev
libxss-dev
libpng12-dev
libjpeg62-dev
libcairo2-dev
gcj
gcj-4.2
Required by some CRAN or Bioconductor packages:
libcurl4-openssl-dev (for RCurl)
libxml2-dev (for XML)
libgtk2.0-dev, libglade2.0-dev (for RGtk2)
libgraphviz-dev (for Rgraphviz)
ggobi (for rggobi)
Really nice to have:
manpages-dev
colorgcc (to activate this: cd /usr/local/bin/ && sudo ln -s
/usr/bin/colorgcc gcc)
Dan
>
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> Regards,
> Chintan Vora
> Sr. Research Associate
> Xcelris Labs Ltd.
> Old Premchandnagar Road,
> Bodakdev, Ahmedabad-380 054 India.
> Tel: +91-79-66197777/66311114
> Fax: +91-79-66309341
> Email: chintan.vora at xcelrislabs.com
> Website: www.xcelrisgenomics.com
>
>
> On 01/23/2012 09:48 PM, Dan Tenenbaum wrote:
>
> On Mon, Jan 23, 2012 at 3:35 AM, Chintan Vora - Xcelris
> <chintan.vora at xcelrislabs.com> wrote:
>
> Hi,
>
> I am trying to install tcltk package for affylmGUI. But I am getting error
>
> > library(BiocInstaller)
> BiocInstaller version 1.2.1, ?biocLite for help
> > biocLite("tcltk")
> BioC_mirror: 'http://www.bioconductor.org'
> Using R version 2.14, BiocInstaller version 1.2.1.
> Installing package(s) 'tcltk'
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
> package 'tcltk' is not available (for R version 2.14.1)
>
> > sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BiocInstaller_1.2.1
>
> loaded via a namespace (and not attached):
> [1] tools_2.14.1
>
> tcltk is a built-in package, included with R.
> You should not need to install it like this;
> library(tcltk)
> should just work.
> Dan
>
>
> --
>
> Regards,
> Chintan Vora
> Sr. Research Associate
> Xcelris Labs Ltd.
> Old Premchandnagar Road,
> Bodakdev, Ahmedabad-380 054 India.
> Tel: +91-79-66197777/66311114
> Fax: +91-79-66309341
> Email: chintan.vora at xcelrislabs.com
> Website: www.xcelrisgenomics.com
>
>
>
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