From alexl at users.sourceforge.net Tue May 13 09:49:16 2008 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Tue, 13 May 2008 02:49:16 -0700 Subject: [Fedora-r-devel-list] Re: Plans for R-2.7.0? In-Reply-To: <1208957476.12717.151.camel@localhost.localdomain> (Tom Callaway's message of "Wed\, 23 Apr 2008 09\:31\:16 -0400") References: <200804221728.56026.jamatos@fc.up.pt> <1208885860.12717.82.camel@localhost.localdomain> <200804231030.29353.jamatos@fc.up.pt> <1208957476.12717.151.camel@localhost.localdomain> Message-ID: >>>>> "TC" == Tom \"spot\" Callaway writes: TC> On Wed, 2008-04-23 at 02:56 -0700, Alex Lancaster wrote: >> I agree, wait for F-9. Then we can put it through updates-testing, >> have time to push dependent packages that might need rebuilding, >> including (but probably not limited to) rpy. >> >> Meanwhile we could push versions for F-7 & F-8 to updates-testing >> to shake out potential problems. Then push them all to stable >> after F-9 is released. TC> Ehhh, i don't want to break the upgrade path. We'll just sit on TC> this until after F-9. I just noticed that some packages fail to rebuild with R 2.7.0, e.g. http://koji.fedoraproject.org/koji/taskinfo?taskID=606646 the build.log has the following: checking for unpackaged file(s): /usr/lib/rpm/check-files /var/tmp/R-zoo-1.5-3.fc10-root-mockbuild error: Installed (but unpackaged) file(s) found: /usr/share/R/library/zoo/NEWS RPM build errors: Installed (but unpackaged) file(s) found: /usr/share/R/library/zoo/NEWS Does 2.7.0 somehow attempt to compile/provide a NEWS file even if the actual package does not? Alex From alexl at users.sourceforge.net Tue May 13 10:01:39 2008 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Tue, 13 May 2008 03:01:39 -0700 Subject: [Fedora-r-devel-list] Re: Plans for R-2.7.0? In-Reply-To: (Alex Lancaster's message of "Tue\, 13 May 2008 02\:49\:16 -0700") References: <200804221728.56026.jamatos@fc.up.pt> <1208885860.12717.82.camel@localhost.localdomain> <200804231030.29353.jamatos@fc.up.pt> <1208957476.12717.151.camel@localhost.localdomain> Message-ID: <4rbq3ay130.fsf@allele2.eebweb.arizona.edu> >>>>> "AL" == Alex Lancaster writes: >>>>> "TC" == Tom \"spot\" Callaway writes: TC> On Wed, 2008-04-23 at 02:56 -0700, Alex Lancaster wrote: >>> I agree, wait for F-9. Then we can put it through >>> updates-testing, have time to push dependent packages that might >>> need rebuilding, including (but probably not limited to) rpy. >>> >>> Meanwhile we could push versions for F-7 & F-8 to updates-testing >>> to shake out potential problems. Then push them all to stable >>> after F-9 is released. TC> Ehhh, i don't want to break the upgrade path. We'll just sit on TC> this until after F-9. AL> I just noticed that some packages fail to rebuild with R 2.7.0, AL> e.g. AL> http://koji.fedoraproject.org/koji/taskinfo?taskID=606646 AL> the build.log has the following: AL> checking for unpackaged file(s): /usr/lib/rpm/check-files AL> /var/tmp/R-zoo-1.5-3.fc10-root-mockbuild error: Installed (but AL> unpackaged) file(s) found: /usr/share/R/library/zoo/NEWS RPM build AL> errors: Installed (but unpackaged) file(s) found: AL> /usr/share/R/library/zoo/NEWS AL> Does 2.7.0 somehow attempt to compile/provide a NEWS file even if AL> the actual package does not? Actually looking at it a bit closer it seems that R 2.7.0 is a bit smarter about installing the NEWS file if it's present, see: https://bugzilla.redhat.com/show_bug.cgi?id=445635#c11 for more details. This might affect a few packages that don't explicitly include NEWS in their %files list. If this is so, it would probably be useful if the sample spec files in the R packaging guidelines: http://fedoraproject.org/wiki/Packaging/R were also updated accordingly, as many people use those as templates to create new R packages. Alex From tcallawa at redhat.com Tue May 13 13:55:40 2008 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Tue, 13 May 2008 09:55:40 -0400 Subject: [Fedora-r-devel-list] Re: Plans for R-2.7.0? In-Reply-To: <4rbq3ay130.fsf@allele2.eebweb.arizona.edu> References: <200804221728.56026.jamatos@fc.up.pt> <1208885860.12717.82.camel@localhost.localdomain> <200804231030.29353.jamatos@fc.up.pt> <1208957476.12717.151.camel@localhost.localdomain> <4rbq3ay130.fsf@allele2.eebweb.arizona.edu> Message-ID: <1210686940.1920.12.camel@localhost.localdomain> On Tue, 2008-05-13 at 03:01 -0700, Alex Lancaster wrote: > This might affect a few packages that don't > explicitly include NEWS in their %files list. If this is so, it would > probably be useful if the sample spec files in the R packaging > guidelines: Good catch, I've updated the guidelines. ~spot From pingou at pingoured.fr Sat May 17 11:23:20 2008 From: pingou at pingoured.fr (pingou) Date: Sat, 17 May 2008 13:23:20 +0200 Subject: [Fedora-r-devel-list] Re: Plans for R-2.7.0? In-Reply-To: <1208957476.12717.151.camel@localhost.localdomain> References: <200804221728.56026.jamatos@fc.up.pt> <1208885860.12717.82.camel@localhost.localdomain> <200804231030.29353.jamatos@fc.up.pt> <1208957476.12717.151.camel@localhost.localdomain> Message-ID: <482EC028.5050808@pingoured.fr> Tom "spot" Callaway wrote: > On Wed, 2008-04-23 at 02:56 -0700, Alex Lancaster wrote: > >> I agree, wait for F-9. Then we can put it through updates-testing, >> have time to push dependent packages that might need rebuilding, >> including (but probably not limited to) rpy. >> >> Meanwhile we could push versions for F-7 & F-8 to updates-testing to >> shake out potential problems. Then push them all to stable after F-9 >> is released. > > Ehhh, i don't want to break the upgrade path. We'll just sit on this > until after F-9. > What about pushing it now ? :) I have started to look at the new bioconductor release, some of them will require R >= 2.7.0. Cheers Pierre From tcallawa at redhat.com Sat May 17 13:09:12 2008 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Sat, 17 May 2008 09:09:12 -0400 Subject: [Fedora-r-devel-list] Re: Plans for R-2.7.0? In-Reply-To: <482EC028.5050808@pingoured.fr> References: <200804221728.56026.jamatos@fc.up.pt> <1208885860.12717.82.camel@localhost.localdomain> <200804231030.29353.jamatos@fc.up.pt> <1208957476.12717.151.camel@localhost.localdomain> <482EC028.5050808@pingoured.fr> Message-ID: <1211029752.3801.148.camel@localhost.localdomain> On Sat, 2008-05-17 at 13:23 +0200, pingou wrote: > Tom "spot" Callaway wrote: > > On Wed, 2008-04-23 at 02:56 -0700, Alex Lancaster wrote: > > > >> I agree, wait for F-9. Then we can put it through updates-testing, > >> have time to push dependent packages that might need rebuilding, > >> including (but probably not limited to) rpy. > >> > >> Meanwhile we could push versions for F-7 & F-8 to updates-testing to > >> shake out potential problems. Then push them all to stable after F-9 > >> is released. > > > > Ehhh, i don't want to break the upgrade path. We'll just sit on this > > until after F-9. > > > > What about pushing it now ? :) > > I have started to look at the new bioconductor release, some of them > will require R >= 2.7.0. It is now in testing for all active releases (F-7, F-8, F-9): https://admin.fedoraproject.org/updates/F7/pending/rpy-0.4.6-25.fc7,R-2.7.0-2.fc7.1 https://admin.fedoraproject.org/updates/F8/pending/rpy-1.0.1-4.fc8,R-2.7.0-2.fc8.1 https://admin.fedoraproject.org/updates/F9/pending/rpy-1.0.1-6.fc9,R-2.7.0-2.fc9.1 I'm not sure why these haven't pushed yet, I did them several days ago. ~spot