Hi all,

I am getting an error when I call biocLite(type="source") for R-2.5 alpha
but not when I call the same function for R-2.6. What is strange is that it
seems that R-2.6 is basically doing the same thing at the moment as
R-2.5alpha, so I can't figure out what is going on here. The error
comes when
biocLite tries to install the "tkWidgets" package:

----
> biocLite("tkWidgets", type="source")
Running biocinstall version 2.0.3 with R version 2.5.0 (currently in alpha)
Your version of R requires version 2.0 of Bioconductor (currently in alpha
too).
trying URL 'http://bioconductor.org/packages/2.0/bioc/src/contrib/tkWidgets_1.13.3.tar.gz
'
Content type 'application/x-gzip' length 304935 bytes
opened URL
==================================================
downloaded 297Kb

* Installing *source* package 'tkWidgets' ...
** R
** inst
** preparing package for lazy loading
Loading required package: widgetTools
Loading Tcl/Tk interface ... Error in fun(...) : Can't find a usable
init.tcl in the following directories:
    @TCL_IN_FRAMEWORK@ @TCL_IN_FRAMEWORK@



This probably means that Tcl wasn't installed properly.

Error : .onLoad failed in 'loadNamespace' for 'tcltk'
Error in fun(...) : Package tcltk unavailalbe!
Error : .onLoad failed in 'loadNamespace' for 'widgetTools'
Error: package 'widgetTools' could not be loaded
Execution halted
ERROR: lazy loading failed for package 'tkWidgets'
** Removing
'/Library/Frameworks/R.framework/Versions/2.5/Resources/library/tkWidgets'
------

But when I make the same call in the R-2.6 I have installed...I get things
working smoothly:

------
> biocLite("tkWidgets", type="source")
Running biocinstall version 2.1.2 with R version 2.6.0 (under development)
WARNING: Your version of R will TEMPORARILY USE version 2.0 of Bioconductor
(currently
in alpha stage, and targeting R 2.5.0) until we start the devel cycle for
Bioconductor 2.1
trying URL 'http://bioconductor.org/packages/2.0/bioc/src/contrib/tkWidgets_1.13.3.tar.gz
'
Content type 'application/x-gzip' length 304935 bytes
opened URL
==================================================
downloaded 297Kb

* Installing *source* package 'tkWidgets' ...
** R
** inst
** preparing package for lazy loading
Loading required package: widgetTools
Loading Tcl/Tk interface ... done
Loading required package: DynDoc
** help
 >>> Building/Updating help pages for package 'tkWidgets'
     Formats: text html latex example
  DPExplorer                        text    html    latex   example
  WName                             text    html    latex   example
  appendSepDir                      text    html    latex   example
  args2XML                          text    html    latex   example
  argsWidget                        text    html    latex   example
  colInfo-class                     text    html    latex   example
  dataViewer                        text    html    latex   example
  dbArgsWidget                      text    html    latex   example
  eExplorer                         text    html    latex   example
  fileBrowser                       text    html    latex   example
  fileWizard                        text    html    latex   example
  getLightTW                        text    html    latex   example
  getWvalues                        text    html    latex   example
  guess.sep                         text    html    latex   example
  hasChar                           text    html    latex   example
  importPhenoData                   text    html    latex   example
  importWizard                      text    html    latex   example
  listSelect                        text    html    latex   example
  objNameToList                     text    html    latex   example
  objViewer                         text    html    latex   example
  objectBrowser                     text    html    latex   example
  pExplorer                         text    html    latex   example
  pickFiles                         text    html    latex   example
  pickItems                         text    html    latex   example
  pickObjs                          text    html    latex   example
  setArgsList                       text    html    latex   example
  stdType                           text    html    latex   example
  tkMIAME                           text    html    latex
  tkSampleNames                     text    html    latex
  tkphenoData                       text    html    latex
  vExplorer                         text    html    latex   example
  values.Widget                     text    html    latex   example
  widgetRender                      text    html    latex   example
** building package indices ...
* DONE (tkWidgets)

The downloaded packages are in
        /private/tmp/RtmpfLaQSg/downloaded_packages
-----------

Sorry for the long output...but this does seem weird and I am kind of
surprised at the result. It might be worth mentioning that I built
R-2.6from source by checking out the lastest R-devel from subversion
while I
downloaded R-2.5 alpha from the att site. I will attach the output for the
respective sessionInfo() calls:

----------
> sessionInfo()
R version 2.5.0 alpha (2007-04-08 r41093)
i386-apple-darwin8.9.1

locale:
C

attached base packages:
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
[7] "base"
------------

------------
> sessionInfo()
R version 2.6.0 Under development (unstable) (2007-04-08 r41095)
i386-apple-darwin8.9.1

locale:
C

attached base packages:
[1] "tcltk"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
[7] "methods"   "base"

other attached packages:
     marray   tkWidgets      DynDoc widgetTools       limma
   "1.13.2"    "1.13.3"    "1.13.2"    " 1.11.2"    "2.9.17"
-------------

Thanks,
--Tony

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