What is the mechanism for contributing an R package to Bioconductor? I would like information on license agreements, an email address to send the source code to, and any other guidelines. I could not find that information on the web site. Thank you for your assistance. Sincerely, David Bickel http://www.mcg.edu/research/biostat/bickel.html David R. Bickel, Assistant Professor Medical College of Georgia Office of Biostatistics and Bioinformatics Tel.: 706-721-4697; Fax: 706-721-6294 dbickel@mail.mcg.edu or bickel@prueba.info

>>>>> "david" == David R Bickel <dbickel@mail.mcg.edu> writes: david> What is the mechanism for contributing an R package to Bioconductor? I would david> like information on license agreements, an email address to send the source david> code to, and any other guidelines. I could not find that information on the david> web site. Thank you for your assistance. I think it depends on what you intend to do. Contribution of a single package, to be put on the can be done provided that it passes "muster": 1. an open source license must be used 2. contains a vignette written in SWeave describing usage. 3. should be using the Biobase tools or other S4 classes when appropriate. -------------- from the FAQ --------------- How can I create a Bioconductor compliant package? This is very simple. Your package must pass R's CMD check process without warnings or errors. It must work with the current version of R (this will be a number no less than R 1.5). It must contain a directory inst/docs that contains LaTeX documentation of your package. The documentation here is intended to describe the over all functionality of your package. This is separate and in addition to documenting the functions in your package in the standard way. It would be nice if you used some of the Bioconductor classes and methods. Especially those in the Biobase and annotate packages. ------------------------------------------ Feel free to post more questions, if any remain. -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics U. of Washington Biostatistics rossini@u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org -------------- http://software.biostat.washington.edu/ ---------------- FHCRC: M: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX (my tuesday/wednesday/friday locations are completely unpredictable.)

Hi David .... > What is the mechanism for contributing an R package to Bioconductor? I would > like information on license agreements, an email address to send the source > code to, and any other guidelines. I could not find that information on the > web site. Thank you for your assistance. Well, I was going to give the quick answer to see the FAQ, especially http://www.bioconductor.org/what.html#R%20and%20Bioconductor. However, this seems to be incomplete, especially to answer some of your questions. I could have sworn most of this was *somewhere*, but I guess this shows that I need to do some page updating :) Anyhow, to answer your questions: - Licenses: Contributed packages are expected to be licensed under an open source license. We heavily encourage the use of the LGPL for any sort of "infrastructure" packages (ie: non-leaf, packages that are intended to be used by other packages), although "leaf" type packages are more up to you. - Email: Send either a description/link to the Bioconductor list or you can email me directly either the same information or the package itself. - Other guidelines: See that link I put above, specifically the "How can I create an Bioconductor compliant package?" subsection. If you have any other questions, feel free to shout. Thanks for your interest! -Jeff