HI Colin , 

Thanks very much for looking into that, 

As you said the following combination works as expected:, much
appreciated.

 

 

> sessionInfo()

R version 2.6.0 Under development (unstable) (2007-06-26 r42066) 

i386-pc-mingw32 

 

locale:

LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MON
ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252

 

attached base packages:

[1] tools     stats     graphics  grDevices utils     datasets  methods


[8] base     

 

other attached packages:

[1] annaffy_1.10.0       KEGG_2.0.0           GO_2.0.0            

[4] affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.0        

[7] Biobase_1.16.0      

 

loaded via a namespace (and not attached):

[1] AnnotationDbi_1.0.4 DBI_0.2-3           RSQLite_0.6-3      

> 

 

________________________________

From: Colin A. Smith [mailto:colin@colinsmith.org] 
Sent: Tuesday, 9 October 2007 2:20 PM
To: Paul Leo
Cc: bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] annaffy - saveHTML changed behaviour in newer
versions



I tried installing R 2.7.0 (devel) on my PPC Mac and ran into several
errors that are probably not worth trying to work around at this stage
in R 2.7.0 development. I tried your set of commands with R 2.6.0 and
annaffy 1.10.0 and got the correct output. My best guess is that R 2.7.0
is broken right now and causing the problems. I probably won't look into
trying to resolve problems with annaffy/R 2.7.0 for several months,
until development stabilizes.



For now, stick with R 2.6.0 and the release version of annaffy. One
important note: any aafTable objects you have saved from a version of
annaffy prior to 1.9.2 will have unexpected results when you try to use
them in R 2.6.0. The new R release adds an additional requirement for S4
method dispatch that versions of annaffy prior to 1.9.2 did not take
care of.



-Colin



On Oct 8, 2007, at 18:21 , Paul Leo wrote:





Thanks Colin, 

That would be great! I tried one other test also after my email. I
loaded the old version of annaffy that worked under R2.5 into R2.7. The
same "bad" behaviour resulted. I suspected the problems came from the
merge commands .... Which is probably less commonly used with annaffy...
However my tested included using exactly the same data_table object in
both R versions just before using the saveHTML command (saved workspace
under R2.5 loaded into R2.7 and just the saveHTML was run : same
effect). Hope that info is of some use...

 Attached is the output.


	[[alternative HTML version deleted]]

