[BioC] Ringo install fails on R 2.8.0

[Arvas Mikko]

Hi,

You are right, it works fine with latest biocLite(). I tried biocLite
orginally too, but I forgot to source the latest version, stupid of me.

Thanks!

All the best,
Mikko 

-----Original Message-----
From: laurent [mailto:lgautier at gmail.com] 
Sent: 11. marraskuuta 2008 14:00
To: Arvas Mikko
Cc: bioconductor at stat.math.ethz.ch; toedling at ebi.ac.uk
Subject: Re: [BioC] Ringo install fails on R 2.8.0



On Tue, 2008-11-11 at 13:55 +0200, Arvas Mikko wrote:
> 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
> 

isn't the recommended way of installing packages:

source(url("http://www.bioconductor.org/biocLite.R"))
biocLite("Ringo")


> > 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_NAM
> E= 
> C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICA
> TI
> 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 at 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
> 
> 
> 
> 	[[alternative HTML version deleted]]
> 
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