Hi,

I can't install Ringo on R 2.8.0 and Bioconductor 2.2, with (R 2.7.1 I
have no problems):

Error in setMethod("update", signature = c("cher"), function(object,
...) { : 
  no existing definition for function "update"

See below for full transcript and sessionInfo.

Although I can of course use the old version as well, any help on this
would be much appreciated!

All the best,
Mikko


> getBioC("Ringo")
Running biocinstall version 2.2.9 with R version 2.8.0 
Your version of R requires version 2.2 of BioConductor.
trying URL
'http://bioconductor.org/packages/2.2/bioc/src/contrib/Ringo_1.4.0.tar.g
z'
Content type 'application/x-gzip' length 937239 bytes (915 Kb)
opened URL
==================================================
downloaded 915 Kb

* Installing *source* package 'Ringo' ...
** libs
g++ -I/usr/local/lib64/R-2.8.0/lib64/R/include  -I/usr/local/include
-fpic  -g -O2 -c mmeansd.cpp -o mmeansd.o
g++ -I/usr/local/lib64/R-2.8.0/lib64/R/include  -I/usr/local/include
-fpic  -g -O2 -c mmedian.cpp -o mmedian.o
gcc -std=gnu99 -I/usr/local/lib64/R-2.8.0/lib64/R/include
-I/usr/local/include    -fpic  -g -O2 -c region_overlap.c -o
region_overlap.o
gcc -std=gnu99 -I/usr/local/lib64/R-2.8.0/lib64/R/include
-I/usr/local/include    -fpic  -g -O2 -c ringo_init.c -o ringo_init.o
g++ -shared -L/usr/local/lib64 -o Ringo.so mmeansd.o mmedian.o
region_overlap.o ringo_init.o   
** R
** inst
** preparing package for lazy loading
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: geneplotter
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: xtable
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: limma
Loading required package: vsn
Loading required package: affy
Loading required package: RColorBrewer
Loading required package: SparseM
Package SparseM (0.78) loaded.  To cite, see citation("SparseM")

Attaching package: 'SparseM'


        The following object(s) are masked from package:stats :

         model.response 


        The following object(s) are masked from package:base :

         backsolve,
         chol 

Error in setMethod("update", signature = c("cher"), function(object,
...) { : 
  no existing definition for function "update"
Error: unable to load R code in package 'Ringo'
Execution halted
ERROR: lazy loading failed for package 'Ringo'
** Removing '/usr/local/lib64/R-2.8.0/lib64/R/library/Ringo'
The downloaded packages are in
        /tmp/RtmpTe1ANE/downloaded_packages
Updating HTML index of packages in '.Library'
Warning message:
In install.packages(pkgs = pkgs, repos = repos, dependencies =
dependencies,  :
  installation of package 'Ringo' had non-zero exit status

> sessionInfo()
R version 2.8.0 (2008-10-20) 
x86_64-unknown-linux-gnu 

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U
TF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=
C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATI
ON=C

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


loaded via a namespace (and not attached):
[1] tcltk_2.8.0 tools_2.8.0



Mikko Arvas
VTT Technical Research Centre of Finland
Protein Production Team
E-mail     mikko.arvas@vtt.fi
Phone    +385-(0)40-754 1857
Fax        +358-(0)20-722 7071
Address  Tietotie 2 
               PL 1000 
               02044 VTT
               Finland
Web pages:
VTT: www.vtt.fi
Protein Production:
http://www.vtt.fi/palvelut/cluster4/topic4_3/Proteiinin_tuotto.jsp



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