Hi, i'm Miguel and i'm working in a new version of the genArise software. Since it was writed for R 2.3.x, a lot of thing have changed now. First we updated it, and now it works fine with windows vista and 7. But we have a great problem, it looks like all the code uses S3 classes. I've read that BioConductor now requires a structured code in all packages, and also all should use S4 classes. I'm not shure if all the .R files are ok, and a great problem is that genArise has problems using tcltk. Can anyone tell me if it's necessary to update genArise structure ? Or it can be submitted to bioC again without changes? Thanks a lot! Miguel Angel Carvajal IFC, UNAM Mexico

Hi Miguel -- On 08/16/2010 05:35 PM, mcarvajal at ifc.unam.mx wrote: > Hi, i'm Miguel and i'm working in a new version of the genArise > software. Since it was writed for R 2.3.x, a lot of thing have changed now. > > First we updated it, and now it works fine with windows vista and 7. But > we have a great problem, it looks like all the code uses S3 classes. > I've read that BioConductor now requires a structured code in all > packages, and also all should use S4 classes. We encourage new package authors to use S4 classes. But genArise is already in the Bioconductor repository, so it is not required in this case. > I'm not shure if all the .R files are ok, and a great problem is that > genArise has problems using tcltk. Can anyone tell me if it's necessary > to update genArise structure ? Or it can be submitted to bioC again > without changes? Because genArise is already in Bioconductor, the package maintainer can just update the code using svn. They don't have to re-submit the package. Some instructions are at http://bioconductor.org/developers/index.html and http://bioconductor.org/developers/source-control/ I don't think you're listed as the maintainer, and you may not have the correct permissions to check in your changes. If that's the case, then please let me know, cc'ing the original maintainer so that I know it's ok with them that you are taking over the package. (email me off-list if you need clarification with this). These sorts of questions should be sent to the Bioc-devel mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel where we can have more technical conversations. It might also make sense to communicate off-list if there are big changes that you'd like help with. If you provide more information, we can try to help with tcltk. Martin > > Thanks a lot! > Miguel Angel Carvajal > IFC, UNAM > Mexico > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793