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Question: Ringo install fails on R 2.8.0
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gravatar for Mikko Arvas
9.0 years ago by
Mikko Arvas90
European Union
Mikko Arvas90 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 > 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@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]]
ADD COMMENTlink modified 9.0 years ago by laurent140 • written 9.0 years ago by Mikko Arvas90
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gravatar for laurent
9.0 years ago by
laurent140
United States
laurent140 wrote:
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.t ar.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_N AME= > C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFI CATI > 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 9.0 years ago by laurent140
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@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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 9.0 years ago by Mikko Arvas90
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