Developer Meeting in Lausanne CH 4.+5. April 2007

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Wolfgang Huber ★ 13k

@wolfgang-huber-3550

Last seen 14 days ago

EMBL European Molecular Biology Laborat…

Dear Bioconductors, there will be a Bioconductor Developers' Meeting on 4.+5. April 2007 in Lausanne, Switzerland. Local organizer is Darlene Goldstein and the Vital IT centre. Mark your calendars. Details of the programme will be announced soon, but it will include tutorials on the new Biobase classes (eSet), Sweave and authoring documents for reproducible research, new database interfaces for large datasets, advanced R programming, and of course and most importantly possibilities for feedback and interactions between package authors, and with the "core infrastructure" people. Happy Christmas! Wolfgang -- ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber

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ADD COMMENT • link updated 17.3 years ago by Lina Hultin-Rosenberg ▴ 180 • written 17.3 years ago by Wolfgang Huber ★ 13k

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Lina Hultin-Rosenberg ▴ 180

@lina-hultin-rosenberg-1802

Last seen 9.6 years ago

Dear all, I have been using biomaRt to connect to ensembl and have previously done that without any problems. Now when I tried again today I run into problems, see code and error message below. I have also provided the output from sessionInfo() below. I would greatly appreciate some help with this, probably easily solved, problem! ______________________________________________________________________ > library(biomaRt) > ensembl = useMart("ensembl") Error in validObject(.Object) : invalid class "Mart" object: invalid object for slot "vschema" in class "Mart": got class "NULL", should be or extend class "character" > sessionInfo() Version 2.3.1 (2006-06-01) i686-pc-linux-gnu attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" other attached packages: biomaRt RCurl XML "1.6.3" "0.6-2" "0.99-8" ______________________________________________________________________ ____ Sincerely, Lina Rosenberg ________________________________ Lina Hultin Rosenberg Msc Molecular Biotechnology Evolutionary Biology Department Uppsala University Norbyv?gen 18 752 36 Uppsala Phone: +46-18-4716444 Email: lina.hultin.rosenberg at ebc.uu.se

ADD COMMENT • link 17.3 years ago Lina Hultin-Rosenberg ▴ 180

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Lina, Please update your R and your biomaRt to a more recent version. Ensembl is an online resource that regularly has new releases that change its content (and just has one this week), and hence the biomaRt package needed changes to keep pace with it. Best wishes Wolfgang Lina Hultin-Rosenberg wrote: > Dear all, > > I have been using biomaRt to connect to ensembl and have previously done > that without any problems. Now when I tried again today I run into problems, > see code and error message below. I have also provided the output from > sessionInfo() below. > > I would greatly appreciate some help with this, probably easily solved, > problem! > > ______________________________________________________________________ >> library(biomaRt) >> ensembl = useMart("ensembl") > Error in validObject(.Object) : invalid class "Mart" object: invalid object > for slot "vschema" in class "Mart": got class "NULL", should be or extend > class "character" > >> sessionInfo() > Version 2.3.1 (2006-06-01) > i686-pc-linux-gnu > > attached base packages: > [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" > [7] "base" > > other attached packages: > biomaRt RCurl XML > "1.6.3" "0.6-2" "0.99-8" > ____________________________________________________________________ ______ > > Sincerely, > Lina Rosenberg > > ________________________________ > Lina Hultin Rosenberg > Msc Molecular Biotechnology > Evolutionary Biology Department > Uppsala University > Norbyv?gen 18 > 752 36 Uppsala > Phone: +46-18-4716444 > Email: lina.hultin.rosenberg at ebc.uu.se > > _______________________________________________ > 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 -- ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber

ADD REPLY • link 17.3 years ago Wolfgang Huber ★ 13k

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