Dear Michael, I was looking up the status of the cran2deb effort and notice that you now have a PPA where new packages are landing and being built for Ubuntu. It looks like this is still a work in progress, but is already a fantastic resource for me and I hope it is something that you can continue to operate. I'm now installing many of these packages but some things I need are missing. I'm hoping I can get these built and contribute my results and any other bug fixes I make back to you. As the Bio-Linux maintainer and a contributor to Debian-Med I'm very familiar with DEB building and general Ubuntu hacking. I'm not an R user but I know the basics (and I'm supporting several big time R users here who can help me out). As far as I'm aware, the packages on cran2deb4ubuntu will have been built from a selection of auto-generated sources spat out from cran2deb. There used to be a page where these could be downloaded but I can't find it any more (or am I just going blind?). Is there somewhere I can snag the source packages used for the PPA? Should I just download and run cran2deb myself to obtain them? Also, what's the best way to contribute back to you? FYI, the first packages on my hitlist are (mostly from bioconductor): pcaMethods (should be easy) bitseq (I just packaged the standalone version - https://launchpad.net/~tbooth/+archive/ppa1/+packages) samr biomaRt (probably a PITA, not looked yet) Cheers, TIM -- Tim Booth <tbooth at ceh.ac.uk> NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705
Hi Tony, Yes, this might be a good thing to tackle in Kiel. How much effort would it be to do a rebuild against the latest CRAN/Bioconductor packages? Could this be done before the meeting so we have up-to-date source packages to tinker with? Cheers, TIM On Mon, 2013-02-11 at 12:44 +0000, Tony Travis wrote:> On 11/02/13 12:31, Tim Booth wrote: > > [...] > > As far as I'm aware, the packages on cran2deb4ubuntu will have been > > built from a selection of auto-generated sources spat out from cran2deb. > > There used to be a page where these could be downloaded but I can't find > > it any more (or am I just going blind?). Is there somewhere I can snag > > the source packages used for the PPA? Should I just download and run > > cran2deb myself to obtain them? Also, what's the best way to contribute > > back to you? > > Hi, Tim. > > The "c2d" that Steffen and me put up on the RINH Beowulf server after > the Debian-Med sprint in Travemuende is still there, but has been > neglected since I left the University of Aberdeen: > > http://bioinformatics.rri.sari.ac.uk/cran2deb/ > > I could revisit this with you at the Sprint in Kiel if you want? > > Bye, > > Tony.-- Tim Booth <tbooth at ceh.ac.uk> NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705
On Mon, 11 Feb 2013, Tony Travis wrote:> On 11/02/13 14:40, Dirk Eddelbuettel wrote: > >[...] > >Do you guys know about Don Armstrong's builder? Effectively the successor to > >my cran2deb efforts: > > > > http://debian-r.debian.net > > Thanks for the heads-up about Don's builder.I'm trying to keep it up to date, but there are definitely some packages missing. If there are particular ones that you need which aren't built, let me know, and I can go through and get them built. Don Armstrong -- Unix, MS-DOS, and Windows NT (also known as the Good, the Bad, and the Ugly). -- Matt Welsh http://www.donarmstrong.com http://rzlab.ucr.edu
Hello,> On Mon, 11 Feb 2013, Mathieu Basille wrote: > > To be complete, I found a third package that was unavailable to > > installation through aptitude, although it was listed in the Debian > > R Package Archive: extrafont [1], although the dependencies > > extrafontdb and Rttf2pt1 were available and installed without any > > problem. See my system info in the previous message. > > Right. If the binary package doesn't exist, this usually means that > there was a failure of the package build for some reason. I have to > then go back through, see why the binary build failed, and fix the > database so that the source package gets the proper changes for the > next go-round. [Unfortunately, I still haven't fixed cran2deb to pull > the source package from the archive if it exists instead of trying to > rebuild it, but eventually I'll get to that point. In the meantime, > you can just let me know the package name, and I'll look into it > specifically instead of getting to it as I have extra time.]With so many flavours of distributions and backports with slightly different library names etc., or just with all those conflicting updates kicking in without prior notice, we just have to accept that it takes an awful lot of time and monitoring to curate all those packages. I came to the conclusion that a) this is too much work for a spare time activity and b) that quite a lot of how to do it right is similar to how Debian/Ubuntu already works. The PPA concepts is something that Debian wants to have for quite some Google-summer-of-codes back and I completely agree that it fits well also with cran2deb. What was missing when I last looked at cran2deb was an inter-distributional/inter-release specification of how build- and run-time-dependencies should be speficied. That added, and with a common server, there is little speaking against just working on the same code base, from what I oversee. Many greetings Steffen