You might also supply a patch to the maintainer. A reasonable example how to do that being found here: http://ariejan.net/2007/07/03/how-to-create-and-apply-a-patch-with- subversion/ Best, Jim Vincent Carey wrote: > The short answer is 'no', nothing official. The long answer is that dealing > with such improvements is up to the maintainer of the specific package > affected. If the maintainer is identified in the package DESCRIPTION, > contact him/her directly. If you don't see a maintainer identified > (bioconductor devel team, for example, is listed as the package maintainer) > you could contact any of the developers directly. For example, you could > write to me. > > On Wed, May 12, 2010 at 12:39 PM, Mike Dewar <mike.dewar at="" columbia.edu="">wrote: > >> Hello, >> >> If I make some improvements to a piece of code included in Bioconductor, is >> there an 'official' way of submitting the improvements for future inclusion? >> >> Cheers, >> >> Mike Dewar >> >> >> - - - >> Dr Michael Dewar >> Postdoctoral Research Scientist >> Applied Mathematics >> Columbia University >> http://www.columbia.edu/~md2954/ <http: www.columbia.edu="" %7emd2954=""/> >> >> _______________________________________________ >> 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 >> > > [[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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

Hello, I asked a question last week about how to submit patches. After hacking on the code ('annotationTools') for a while I realised (http://biostar.stackexchange.com/questions/1054/homology- bioconductor) that it was either the wrong package for the job or, what I think is more likely, a package that had been largely superseded by another package ('biomaRt'). So I have a new question, or maybe it's a suggestion: is there a way to mark packages for removal, or to add something to their entry in bioconductor that says "this package has been largely replaced by this other package"? I should say that I feel rather mean asking this question, and it shouldn't reflect badly on the authors of the package in question. It's just had their been a pointer on the annotationTools package that said "these days, you should maybe check out 'biomaRt'" I would have saved myself quite a lot of time. And I guess, in such a rapidly evolving area, and with such a large code base, this sort of thing will be required sooner or later? Cheers, Mike Dewar On 13 May 2010, at 12:26, Vincent Carey wrote: > The short answer is 'no', nothing official. The long answer is that dealing with such improvements is up to the maintainer of the specific package affected. If the maintainer is identified in the package DESCRIPTION, contact him/her directly. If you don't see a maintainer identified (bioconductor devel team, for example, is listed as the package maintainer) you could contact any of the developers directly. For example, you could write to me. > > On Wed, May 12, 2010 at 12:39 PM, Mike Dewar <mike.dewar@columbia.edu> wrote: > Hello, > > If I make some improvements to a piece of code included in Bioconductor, is there an 'official' way of submitting the improvements for future inclusion? > > Cheers, > > Mike Dewar > > > - - - > Dr Michael Dewar > Postdoctoral Research Scientist > Applied Mathematics > Columbia University > http://www.columbia.edu/~md2954/ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > - - - Dr Michael Dewar Postdoctoral Research Scientist Applied Mathematics Columbia University http://www.columbia.edu/~md2954/ [[alternative HTML version deleted]]

Mike, if you have improvements to the code of annotationTools, you can contact me and I will be happy to try and incorporate them. My current email address is the package DESCRIPTION file that you can display using packageDescription("annotationTools"). You implied in your post on BioStar that column indices into annotation files are hard-coded in annotationTools functions. When designing them I actually tried to allow for flexibility in file format and provided the corresponding options, like e.g. for getGENEID idCol: column in annotation table containing the gene IDs. Or for getHOMOLOG clusterCol: column in homology/orthology table containing homology/orthology cluster IDs. speciesCol: column in homology/orthology table containing species IDs. idCol: column in homology/orthology table containing gene IDs. I set the default values to match the format of Affymetrix files (for annotation functions) or HomoloGene file (for getHOMOLOG for instance). However these file formats might have changed since then. If this is the case, I will change the default values. Alex ________________________________________ From: Vincent Carey [stvjc@channing.harvard.edu] Sent: Monday, May 17, 2010 11:16 AM To: Mike Dewar Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] code improvements On Mon, May 17, 2010 at 10:49 AM, Mike Dewar <mike.dewar at="" columbia.edu="">wrote: > Hello, > > I asked a question last week about how to submit patches. > > After hacking on the code ('annotationTools') for a while I realised ( > http://biostar.stackexchange.com/questions/1054/homology- bioconductor) > that it was either the wrong package for the job or, what I think is more > likely, a package that had been largely superseded by another package > ('biomaRt'). > > So I have a new question, or maybe it's a suggestion: is there a way to > mark packages for removal, or to add something to their entry in > bioconductor that says "this package has been largely replaced by this other > package"? > We do remove packages. When package functionalities decay, R supports a Deprecated/Defunct annotation/user redirection process, and this is used in Bioconductor when appropriate. > > I should say that I feel rather mean asking this question, and it shouldn't > reflect badly on the authors of the package in question. It's just had their > been a pointer on the annotationTools package that said "these days, you > should maybe check out 'biomaRt'" I would have saved myself quite a lot of > time. And I guess, in such a rapidly evolving area, and with such a large > code base, this sort of thing will be required sooner or later? > > Your judgment on the duplication of annotationTools functionality by biomaRt seems to me overbroad. The annotationTools vignette shows various functionalities that are not supported by biomaRt. I see no reason that the two should not coexist. Cheers, > > Mike Dewar > > On 13 May 2010, at 12:26, Vincent Carey wrote: > > The short answer is 'no', nothing official. The long answer is that > dealing with such improvements is up to the maintainer of the specific > package affected. If the maintainer is identified in the package > DESCRIPTION, contact him/her directly. If you don't see a maintainer > identified (bioconductor devel team, for example, is listed as the package > maintainer) you could contact any of the developers directly. For example, > you could write to me. > > On Wed, May 12, 2010 at 12:39 PM, Mike Dewar <mike.dewar at="" columbia.edu="">wrote: > >> Hello, >> >> If I make some improvements to a piece of code included in Bioconductor, >> is there an 'official' way of submitting the improvements for future >> inclusion? >> >> Cheers, >> >> Mike Dewar >> >> >> - - - >> Dr Michael Dewar >> Postdoctoral Research Scientist >> Applied Mathematics >> Columbia University >> http://www.columbia.edu/~md2954/ <http: www.columbia.edu="" %7emd2954=""/> >> >> _______________________________________________ >> 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 >> > > > - - - > Dr Michael Dewar > **Postdoctoral Research Scientist > Applied Mathematics > Columbia University > http://www.columbia.edu/~md2954/ <http: www.columbia.edu="" %7emd2954=""/> > > > > > > > [[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