[Bioc-devel] Biobase 1.15.33 depends on ALL problem

Keith Satterley keith at wehi.EDU.AU
Fri Sep 7 05:52:01 CEST 2007

To Martin & Seth in particular,

I need to clarify the message I wrote a three hours ago. Not all my problems 
were solved. I had downloaded /bin/windows/base/R-2.6.0alpha-win32.exe from my 
local mirror(unimelb.edu.au) and used biocLite.

I was a little premature. The library("affy") command worked fine now, no errors 
like this:
"... but >= c(1, 12, 0) is required by ...".

However, when running affylmGUI and loading data from Affymetrix files, I 
received the same error message that Lauro Samoy Van Dyck had, Namely:

Error in .nextMethod(e1, e2)...

The version of Biobase I had installed with biocLite into the latest 
R-2.6.0alpha was 1.15.30. On compiling and installing version 1.15.33 of 
Biobase, the nextMethod(e1, e2) error has been fixed. I'm now don't have any 
problems running affylmGUI.

My sessionInfo is:
 > sessionInfo()
R version 2.6.0 alpha (2007-09-05 r42787)
attached base packages:
  [1] splines   tools     tcltk     stats     graphics  grDevices datasets 
utils     methods
[10] base
other attached packages:
  [1] R2HTML_1.58            xtable_1.5-1           hgu95av2_1.17.0 
  [5] hgu95av2cdf_1.17.0     gcrma_2.9.1            matchprobes_1.9.10 
  [9] affy_1.15.7            preprocessCore_0.99.12 affyio_1.5.8 
[13] limma_2.11.11



Keith Satterley wrote:
> Hi Martin and Seth,
> Thanks for your prompt responses. I downloaded a binary R-2.6.0alpha a couple of 
> hours ago (about 15:00hours, Thursday, Seattle time). I then used biocLite to 
> install all the packages I usually install and all works well now,
> thanks,
> Keith
> Seth Falcon wrote:
>> Martin Morgan <mtmorgan at fhcrc.org> writes:
>>> Thanks Keith for the report.
>>> You've entered a bit of a twilight zone, and the sailing will be a bit
>>> rough.
>>> The underlying problem involves changes in R, not Biobase. I don't
>>> know the details, but a series of changes between R r42739 and 42758
>>> use a different way of representing package versions. It looks like
>>> your R lies in the middle of this. I am speculating that the unusual
>>> errors about package version mismatches relate to this; these problems
>>> do not occur on more recent R on linux; there might be
>>> windows-specific issues, which I will investigate later today.
>>> Usually, the solution would be 'update R'. You'll want to be careful,
>>> though, to update R to R-alpha, rather than R-devel, as R-devel has
>>> branched in preparation for the release in October. The problem is
>>> that R-alpha is available as *source*; if you are used to downloading
>>> the binary version of R-devel, then you'll end up with R-2.7.0dev
>>> (which we do not intend to be able to support with biocLite for at
>>> least a couple of weeks).
>> A Windows binary for R-alpha will be available Real Soon Now.  I
>> expect it will be on our CRAN mirror http://cran.fhcrc.org sometime on
>> Saturday if not before.
>> + seth
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