From pingou at pingoured.fr Mon Feb 9 10:41:02 2009 From: pingou at pingoured.fr (Pierre-Yves) Date: Mon, 09 Feb 2009 11:41:02 +0100 Subject: [Fedora-r-devel-list] %files section Message-ID: <4990083E.6020501@pingoured.fr> Dear list, Still in the process of finding a way to create a ready-to-build spec file I have had some though on the %files section. I will probably change the actual format of the %files to : %files %defattr(-, root, root, -) %dir %{_libdir}/R/library/%{packname} %{_libdir}/R/library/%{packname}/* %exclude %{_libdir}/R/library/%{packname}/doc %exclude %{_libdir}/R/library/%{packname}/DESCRIPTION %exclude %{_libdir}/R/library/%{packname}/html %exclude %{_libdir}/R/library/%{packname}/latex/ %exclude %{_libdir}/R/library/%{packname}/man/ %doc %{_libdir}/R/library/%{packname}/doc %doc %{_libdir}/R/library/%{packname}/DESCRIPTION %doc %{_libdir}/R/library/%{packname}/html %doc %{_libdir}/R/library/%{packname}/latex/ %doc %{_libdir}/R/library/%{packname}/man/ I can (more or less) easily check which documentation files are there while it's much harder to check which files/folders are generated by the build (ie: R-ex, data, demo...) How does it sound to you ?? Thanks for your feedback, Regards, Pierre From jamatos at fc.up.pt Mon Feb 9 12:45:56 2009 From: jamatos at fc.up.pt (=?iso-8859-1?q?Jos=E9_Matos?=) Date: Mon, 9 Feb 2009 12:45:56 +0000 Subject: [Fedora-r-devel-list] %files section In-Reply-To: <4990083E.6020501@pingoured.fr> References: <4990083E.6020501@pingoured.fr> Message-ID: <200902091245.57212.jamatos@fc.up.pt> On Monday 09 February 2009 10:41:02 Pierre-Yves wrote: > Dear list, > > Still in the process of finding a way to create a ready-to-build spec > file I have had some though on the %files section. > > I will probably change the actual format of the %files to : > %files > %defattr(-, root, root, -) > %dir %{_libdir}/R/library/%{packname} > %{_libdir}/R/library/%{packname}/* Aren't two lines equivalent to %{_libdir}/R/library/%{packname}/ > How does it sound to you ?? It seems OK but the rpm syntax always feels to me as weird and in line with TeX that still does several passes into one document because at the time the engine was designed memory was a prime consideration. ;-) > Thanks for your feedback, > Regards, > > Pierre -- Jos? Ab?lio From pingou at pingoured.fr Wed Feb 18 15:35:15 2009 From: pingou at pingoured.fr (Pierre-Yves) Date: Wed, 18 Feb 2009 16:35:15 +0100 Subject: [Fedora-r-devel-list] Metadata packages Message-ID: <499C2AB3.9030607@pingoured.fr> Dear list, While I have started to package R libraries I needed the package R-BSgenome.Dmelanogaster.FlyBase.r51 and R-BSgenome.Celegans.UCSC.ce2 as dependencies, there are nowadays not needed any more and their size and interest make me dubious of their interest. Is anyone here using them ? If so I will invest time to build the new dependencies and the latest version, else I think I will orphan them. Stupid question, but is there anyone here using one of the bioconductor package ? (except Alex who I know test them ;-) ) Thanks && regards, Pierre From pingou at pingoured.fr Wed Feb 18 16:31:40 2009 From: pingou at pingoured.fr (Pierre-Yves) Date: Wed, 18 Feb 2009 17:31:40 +0100 Subject: [Fedora-r-devel-list] %files section In-Reply-To: <200902091245.57212.jamatos@fc.up.pt> References: <4990083E.6020501@pingoured.fr> <200902091245.57212.jamatos@fc.up.pt> Message-ID: <499C37EC.1040903@pingoured.fr> Jos? Matos wrote: > Aren't two lines equivalent to > %{_libdir}/R/library/%{packname}/ Yes they are so I changed :) But while testing on some packages I found something I don't fully understand: %files %defattr(-, root, root, -) #noarch %{_datadir}/R/library/%{packname}/ %exclude %{_datadir}/R/library/%{packname}/doc %exclude %{_datadir}/R/library/%{packname}/DESCRIPTION %exclude %{_datadir}/R/library/%{packname}/html %exclude %{_datadir}/R/library/%{packname}/latex/ %exclude %{_datadir}/R/library/%{packname}/man/ %doc %{_datadir}/R/library/%{packname}/doc %doc %{_datadir}/R/library/%{packname}/DESCRIPTION %doc %{_datadir}/R/library/%{packname}/html %doc %{_datadir}/R/library/%{packname}/latex/ %doc %{_datadir}/R/library/%{packname}/man/ With this section rpmlint returns a warning that there is no docs. Which is indeed true, in the rpm if I open it I cannot find the DESCRIPTION file nor the other folders. %files %defattr(-, root, root, -) #noarch %{_datadir}/R/library/%{packname}/ %exclude %{_datadir}/R/library/%{packname}/doc %exclude %{_datadir}/R/library/%{packname}/DESCRIPTION %exclude %{_datadir}/R/library/%{packname}/html %exclude %{_datadir}/R/library/%{packname}/latex/ %exclude %{_datadir}/R/library/%{packname}/man/ %doc %{_datadir}/R/library/%{packname}/doc %doc %{_datadir}/R/library/%{packname}/DESCRIPTION %doc %{_datadir}/R/library/%{packname}/html %doc %{_datadir}/R/library/%{packname}/latex/ %doc %{_datadir}/R/library/%{packname}/man/ %doc %{_datadir}/R/library/%{packname}/NEWS %doc %{_datadir}/R/library/%{packname}/COPYING %doc %{_datadir}/R/library/%{packname}/CONTENTS %doc %{_datadir}/R/library/%{packname}/NAMESPACE %doc %{_datadir}/R/library/%{packname}/INDEX With this section, rpmlint is happy and don't say anything anymore, but I still can't find the DESCRIPTION file of the man folder So is it normal ? Shouldn't rpm/rpmlint give a warning/error when I try to %exclude and files that are not found or when I try to set them as %doc ? Some lights would be appreciate :) Thanks, Regards, Pierre From tcallawa at redhat.com Wed Feb 18 16:40:13 2009 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Wed, 18 Feb 2009 11:40:13 -0500 Subject: [Fedora-r-devel-list] %files section In-Reply-To: <499C37EC.1040903@pingoured.fr> References: <4990083E.6020501@pingoured.fr> <200902091245.57212.jamatos@fc.up.pt> <499C37EC.1040903@pingoured.fr> Message-ID: <499C39ED.9000805@redhat.com> On 2009-02-18 at 11:31:40 -0500, Pierre-Yves wrote: > Shouldn't rpm/rpmlint give a warning/error when I try to %exclude and > files that are not found or when I try to set them as %doc ? Probably. I'm guessing you can't %exclude a file, then include it as %doc. ~spot From pingou at pingoured.fr Thu Feb 19 08:24:41 2009 From: pingou at pingoured.fr (Pierre-Yves) Date: Thu, 19 Feb 2009 09:24:41 +0100 Subject: [Fedora-r-devel-list] %files section In-Reply-To: <499C39ED.9000805@redhat.com> References: <4990083E.6020501@pingoured.fr> <200902091245.57212.jamatos@fc.up.pt> <499C37EC.1040903@pingoured.fr> <499C39ED.9000805@redhat.com> Message-ID: <499D1749.9040708@pingoured.fr> Tom "spot" Callaway wrote: > On 2009-02-18 at 11:31:40 -0500, Pierre-Yves wrote: >> Shouldn't rpm/rpmlint give a warning/error when I try to %exclude and >> files that are not found or when I try to set them as %doc ? > > Probably. I'm guessing you can't %exclude a file, then include it as %doc. But if I include the directory, include the files as %doc and then %exclude them from the directory (see below) then I got the " File listed twice: " error :/ Regards, Pierre ------------------------------------------------------ This is what I meant: %{_datadir}/R/library/%{packname}/ %doc %{_datadir}/R/library/%{packname}/latex %doc %{_datadir}/R/library/%{packname}/html %doc %{_datadir}/R/library/%{packname}/DESCRIPTION %doc %{_datadir}/R/library/%{packname}/man %exclude %{_datadir}/R/library/%{packname}/latex %exclude %{_datadir}/R/library/%{packname}/html %exclude %{_datadir}/R/library/%{packname}/DESCRIPTION %exclude %{_datadir}/R/library/%{packname}/man From tcallawa at redhat.com Thu Feb 19 13:03:47 2009 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Thu, 19 Feb 2009 08:03:47 -0500 Subject: [Fedora-r-devel-list] %files section In-Reply-To: <499D1749.9040708@pingoured.fr> References: <4990083E.6020501@pingoured.fr> <200902091245.57212.jamatos@fc.up.pt> <499C37EC.1040903@pingoured.fr> <499C39ED.9000805@redhat.com> <499D1749.9040708@pingoured.fr> Message-ID: <499D58B3.4060804@redhat.com> On 2009-02-19 at 3:24:41 -0500, Pierre-Yves wrote: > Tom "spot" Callaway wrote: >> On 2009-02-18 at 11:31:40 -0500, Pierre-Yves wrote: >>> Shouldn't rpm/rpmlint give a warning/error when I try to %exclude and >>> files that are not found or when I try to set them as %doc ? >> >> Probably. I'm guessing you can't %exclude a file, then include it as >> %doc. > > But if I include the directory, include the files as %doc and then > %exclude them from the directory (see below) then I got the " File > listed twice: " error :/ Yes, see, what I'm saying is that you cannot mix %doc and %exclude. ~spot From alexl at users.sourceforge.net Sat Feb 21 08:54:52 2009 From: alexl at users.sourceforge.net (Alex Lancaster) Date: Sat, 21 Feb 2009 01:54:52 -0700 Subject: [Fedora-r-devel-list] Re: Metadata packages In-Reply-To: <499C2AB3.9030607@pingoured.fr> (Pierre-Yves's message of "Wed\, 18 Feb 2009 16\:35\:15 +0100") References: <499C2AB3.9030607@pingoured.fr> Message-ID: >>>>> "P" == Pierre-Yves writes: P> Dear list, While I have started to package R libraries I needed the P> package R-BSgenome.Dmelanogaster.FlyBase.r51 and P> R-BSgenome.Celegans.UCSC.ce2 as dependencies, there are nowadays P> not needed any more and their size and interest make me dubious of P> their interest. P> Is anyone here using them ? If so I will invest time to build the P> new dependencies and the latest version, else I think I will orphan P> them. P> Stupid question, but is there anyone here using one of the P> bioconductor package ? (except Alex who I know test them ;-) ) I'm sure there are others outside this list who use them. We should probably consider publicizing their existence a little more widely. By the way, do we now have the "minimal" or "base" set of bioconductor packages in Fedora? We should update the feature page with the list of unpackaged R modules if there are any: https://fedoraproject.org/wiki/Features/Bioconductor#Scope Alex From pingou at pingoured.fr Sat Feb 21 10:00:37 2009 From: pingou at pingoured.fr (Pierre-Yves) Date: Sat, 21 Feb 2009 11:00:37 +0100 Subject: [Fedora-r-devel-list] Re: Metadata packages In-Reply-To: References: <499C2AB3.9030607@pingoured.fr> Message-ID: <1235210437.3671.2.camel@pingouGreen.localdomain> On Sat, 2009-02-21 at 01:54 -0700, Alex Lancaster wrote: > I'm sure there are others outside this list who use them. We should > probably consider publicizing their existence a little more widely. > By the way, do we now have the "minimal" or "base" set of bioconductor > packages in Fedora? We should update the feature page with the list > of unpackaged R modules if there are any: > > https://fedoraproject.org/wiki/Features/Bioconductor#Scope No, there is not yet new packages done, but I was thinking on starting this project a bit more, that's why I was trying to get R2spec able to generate "ready-to-build" spec files but since I can not play with %doc and %exclude at the same time to be able to include the whole folder well we'll have to do without :) I will probably ask for some reviews on R package on the bugzilla later this week. Thanks for your interest, Regards, P.Yves