[Bioc-devel] best way to transition users to new version of package

2015-05-27 Thread Robert M. Flight
I am the author and maintainer of the categoryCompare package on Bioconductor. As I and others have used it over the years, I am seeing that there are a lot of design mistakes in the code, and that it was not extensible in it's current form. Therefore, I decided to do a complete rewrite starting

Re: [Bioc-devel] missing font causes build warning on bioc release packages

2015-05-27 Thread Dan Tenenbaum
Hi, - Original Message - From: Ludwig Geistlinger ludwig.geistlin...@bio.ifi.lmu.de To: bioc-devel@r-project.org Sent: Wednesday, May 27, 2015 6:54:33 AM Subject: [Bioc-devel] missing font causes build warning on bioc release packages Dear Bioc Team, As far as I am

[Bioc-devel] Meta-information about bioc and bioc-package releases

2015-05-27 Thread Gabe Becker
Hey all, I've been wondering if bioc could offer a way to query information about itself similar - though not necessarily identical - to what Gabor Csardi's (cc'ed) crandb offers http://www.r-pkg.org/services#api http://www.r-pkg.org/services#api Basically, I would really like two things, in

Re: [Bioc-devel] best way to transition users to new version of package

2015-05-27 Thread Wolfgang Huber
Robert with the packages cellHTS, cellHTS2 and DESeq, DESeq2 (and with the functions vsn, vsn2 in the vsn package) I three times chose route 1, and am generally happy about it. In due time, you can deprecate and then defunct the old one. Option 2 seems needlessly disruptive (potentially). A

Re: [Bioc-devel] Meta-information about bioc and bioc-package releases

2015-05-27 Thread Gabe Becker
Dan, Thanks for the quick response. Unfortunately I am hoping for something I can access with base R, including older versions, which precludes https and curl. Is there any way to have a public facing url that hosts that file, or a webservice which returns it directly? Best, ~G On Wed, May 27,

Re: [Bioc-devel] Meta-information about bioc and bioc-package releases

2015-05-27 Thread Dan Tenenbaum
- Original Message - From: Gabe Becker becker.g...@gene.com To: Dan Tenenbaum dtene...@fredhutch.org Cc: Gabe Becker becker.g...@gene.com, csardi gabor csardi.ga...@gmail.com, bioc-devel@r-project.org Sent: Wednesday, May 27, 2015 3:32:35 PM Subject: Re: [Bioc-devel]