From pingoufc4 at yahoo.fr Wed Oct 3 23:09:33 2007 From: pingoufc4 at yahoo.fr (pingou) Date: Thu, 04 Oct 2007 01:09:33 +0200 Subject: [Fedora-r-devel-list] How to handle already installed libraries ? In-Reply-To: <46F97F7F.8030704@yahoo.fr> References: <46F97F7F.8030704@yahoo.fr> Message-ID: <4704212D.8050403@yahoo.fr> Hi all, I have just realized that I made a mistake sending my new question instead I send the previous one... My apologizes for that. Please find here, the original question. Speaking with some people on the #R chan on irc (freenode) one question shows up, What happened if a library is installed by RPM but was already installed before through the R cmd install command ? Which one of the 2 libraries is used ? Quite some libraries that I have made are noarch libraries, I install them in /usr/share whereas the r cmd install install them in /usr/lib. Which mean that we can have twice the same library. Then, I was wondering whether we should include a way to check for the presence of a library before install it. What do you think of it ?? Other question, in the case that the library has not been installed at the right place should we remove it ? (before install it through the rpm) Best regards, ~pingou ___________________________________________________________________________ Yahoo! Mail r?invente le mail ! D?couvrez le nouveau Yahoo! Mail et son interface r?volutionnaire. http://fr.mail.yahoo.com From pertusus at free.fr Wed Oct 3 23:18:12 2007 From: pertusus at free.fr (Patrice Dumas) Date: Thu, 4 Oct 2007 01:18:12 +0200 Subject: [Fedora-r-devel-list] How to handle already installed libraries ? In-Reply-To: <4704212D.8050403@yahoo.fr> References: <46F97F7F.8030704@yahoo.fr> <4704212D.8050403@yahoo.fr> Message-ID: <20071003231812.GA2602@free.fr> On Thu, Oct 04, 2007 at 01:09:33AM +0200, pingou wrote: > Hi all, > > Which one of the 2 libraries is used ? I guess that R has a search path with both locations? > Quite some libraries that I have made are noarch libraries, I install > them in /usr/share whereas the r cmd install install them in /usr/lib. /usr/share is the right place for noarch libraries. > Then, I was wondering whether we should include a way to check for the > presence of a library before install it. We shouldn't. > Other question, in the case that the library has not been installed at > the right place should we remove it ? (before install it through the rpm) We shouldn't either. If the user mixes rpm installed and hand installed softwares he should know what he is doing, doing things automatically is not right when we don't know the user intentions. Now maybe there could be some facilities in R in fedora to help user install his stuff in a specific path (for example /usr/local/lib or /usr/local/share) in order not to install stuff in directories that are traditionnally under rpm conrol, like /usr/lib and /usr/share. But I don't know if it is feasible, nor easy, and I am not sure that it is desirable either. -- Pat From jamatos at fc.up.pt Thu Oct 4 07:01:10 2007 From: jamatos at fc.up.pt (=?iso-8859-1?q?Jos=E9_Matos?=) Date: Thu, 4 Oct 2007 08:01:10 +0100 Subject: [Fedora-r-devel-list] Plans for R 2.6 Message-ID: <200710040801.11025.jamatos@fc.up.pt> Hi, now that R 2.6 is out what is the work plan? :-) https://stat.ethz.ch/pipermail/r-announce/2007/000832.html Regards, -- Jos? Ab?lio From pingoufc4 at yahoo.fr Thu Oct 4 10:07:45 2007 From: pingoufc4 at yahoo.fr (pingou) Date: Thu, 04 Oct 2007 12:07:45 +0200 Subject: [Fedora-r-devel-list] How to handle already installed libraries ? In-Reply-To: <20071003231812.GA2602@free.fr> References: <46F97F7F.8030704@yahoo.fr> <4704212D.8050403@yahoo.fr> <20071003231812.GA2602@free.fr> Message-ID: <4704BB71.10207@yahoo.fr> Patrice Dumas wrote: > On Thu, Oct 04, 2007 at 01:09:33AM +0200, pingou wrote: >> Hi all, >> Other question, in the case that the library has not been installed at >> the right place should we remove it ? (before install it through the rpm) > > We shouldn't either. > Maybe the new feature of R 2.6 could help on that point... > R CMD INSTALL --preclean cleans up the sources after a > previous installation (as if that had used --clean) before > attempting to install. Should we use it ? (in the sense that now that R implements it) Regards, ~Pingou [1]https://stat.ethz.ch/pipermail/r-announce/2007/000832.html ___________________________________________________________________________ Yahoo! Mail r?invente le mail ! D?couvrez le nouveau Yahoo! Mail et son interface r?volutionnaire. http://fr.mail.yahoo.com From pertusus at free.fr Thu Oct 4 10:41:05 2007 From: pertusus at free.fr (Patrice Dumas) Date: Thu, 4 Oct 2007 12:41:05 +0200 Subject: [Fedora-r-devel-list] How to handle already installed libraries ? In-Reply-To: <4704BB71.10207@yahoo.fr> References: <46F97F7F.8030704@yahoo.fr> <4704212D.8050403@yahoo.fr> <20071003231812.GA2602@free.fr> <4704BB71.10207@yahoo.fr> Message-ID: <20071004104105.GA4111@free.fr> On Thu, Oct 04, 2007 at 12:07:45PM +0200, pingou wrote: > > > Maybe the new feature of R 2.6 could help on that point... > > > R CMD INSTALL --preclean cleans up the sources after a > > previous installation (as if that had used --clean) before > > attempting to install. > > Should we use it ? (in the sense that now that R implements it) Then R CMD INSTALL --preclean would be called in a pre script or the like? rpm already takes care of removing old files? -- Pat From pingoufc4 at yahoo.fr Thu Oct 4 10:50:13 2007 From: pingoufc4 at yahoo.fr (pingou) Date: Thu, 04 Oct 2007 12:50:13 +0200 Subject: [Fedora-r-devel-list] How to handle already installed libraries ? In-Reply-To: <20071004104105.GA4111@free.fr> References: <46F97F7F.8030704@yahoo.fr> <4704212D.8050403@yahoo.fr> <20071003231812.GA2602@free.fr> <4704BB71.10207@yahoo.fr> <20071004104105.GA4111@free.fr> Message-ID: <4704C565.3020203@yahoo.fr> Patrice Dumas wrote: > On Thu, Oct 04, 2007 at 12:07:45PM +0200, pingou wrote: >> Maybe the new feature of R 2.6 could help on that point... >> >>> R CMD INSTALL --preclean cleans up the sources after a >>> previous installation (as if that had used --clean) before >>> attempting to install. >> Should we use it ? (in the sense that now that R implements it) > > Then R CMD INSTALL --preclean would be called in a pre script or the > like? rpm already takes care of removing old files? > I was more thinking to change our command >R CMD INSTALL %{packname} -l %{buildroot}%{_datadir}/R/library to something like >R CMD INSTALL --preclean %{packname} -l %{buildroot}%{_datadir}/R/library I have the feeling that it will not solve the problems of the two libraries, but I might help to clean before updated... ~pingou ___________________________________________________________________________ Yahoo! Mail r?invente le mail ! D?couvrez le nouveau Yahoo! Mail et son interface r?volutionnaire. http://fr.mail.yahoo.com From pertusus at free.fr Thu Oct 4 11:33:29 2007 From: pertusus at free.fr (Patrice Dumas) Date: Thu, 4 Oct 2007 13:33:29 +0200 Subject: [Fedora-r-devel-list] How to handle already installed libraries ? In-Reply-To: <4704C565.3020203@yahoo.fr> References: <46F97F7F.8030704@yahoo.fr> <4704212D.8050403@yahoo.fr> <20071003231812.GA2602@free.fr> <4704BB71.10207@yahoo.fr> <20071004104105.GA4111@free.fr> <4704C565.3020203@yahoo.fr> Message-ID: <20071004113329.GC4490@free.fr> On Thu, Oct 04, 2007 at 12:50:13PM +0200, pingou wrote: > >R CMD INSTALL %{packname} -l %{buildroot}%{_datadir}/R/library > to something like > >R CMD INSTALL --preclean %{packname} -l %{buildroot}%{_datadir}/R/library > > I have the feeling that it will not solve the problems of the two > libraries, but I might help to clean before updated... What is cleaned in that case? Things below 1. %{buildroot}%{_datadir}/R/library or 2. %{_datadir}/R/library Or 3. in source? In case 1. I can't see the interest of doing it, in case 2. it is very wrong, and in case 3. I also can't see what it would be needed for. Doing it in pre script may have more sense, but once again the user should do it by hand, it shouldn't be automatic. -- Pat From pingoufc4 at yahoo.fr Thu Oct 4 11:36:57 2007 From: pingoufc4 at yahoo.fr (pingou) Date: Thu, 04 Oct 2007 13:36:57 +0200 Subject: [Fedora-r-devel-list] How to handle already installed libraries ? In-Reply-To: <20071004113329.GC4490@free.fr> References: <46F97F7F.8030704@yahoo.fr> <4704212D.8050403@yahoo.fr> <20071003231812.GA2602@free.fr> <4704BB71.10207@yahoo.fr> <20071004104105.GA4111@free.fr> <4704C565.3020203@yahoo.fr> <20071004113329.GC4490@free.fr> Message-ID: <4704D059.7080601@yahoo.fr> Patrice Dumas wrote: > > Doing it in pre script may have more sense, but once again the user > should do it by hand, it shouldn't be automatic. > Then I believe that we should just leave things as they are now :) ___________________________________________________________________________ Yahoo! Mail r?invente le mail ! D?couvrez le nouveau Yahoo! Mail et son interface r?volutionnaire. http://fr.mail.yahoo.com From tcallawa at redhat.com Thu Oct 4 13:30:02 2007 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Thu, 04 Oct 2007 09:30:02 -0400 Subject: [Fedora-r-devel-list] Plans for R 2.6 In-Reply-To: <200710040801.11025.jamatos@fc.up.pt> References: <200710040801.11025.jamatos@fc.up.pt> Message-ID: <1191504602.3634.17.camel@localhost.localdomain> On Thu, 2007-10-04 at 08:01 +0100, Jos? Matos wrote: > Hi, > now that R 2.6 is out what is the work plan? :-) > https://stat.ethz.ch/pipermail/r-announce/2007/000832.html I'm going to package it up today for F-7, F-8 and devel (I'm going to request an F-8 branch, so it gets picked up as a 0-day update). I'll throw an email out to this list when the package is built. ~spot From jamatos at fc.up.pt Thu Oct 4 15:08:19 2007 From: jamatos at fc.up.pt (=?utf-8?q?Jos=C3=A9_Matos?=) Date: Thu, 4 Oct 2007 16:08:19 +0100 Subject: [Fedora-r-devel-list] Plans for R 2.6 In-Reply-To: <1191504602.3634.17.camel@localhost.localdomain> References: <200710040801.11025.jamatos@fc.up.pt> <1191504602.3634.17.camel@localhost.localdomain> Message-ID: <200710041608.19760.jamatos@fc.up.pt> On Thursday 04 October 2007 14:30:02 Tom "spot" Callaway wrote: > I'll throw an email out to this list when the package is built. OK. Thanks. > ~spot -- Jos? Ab?lio From tcallawa at redhat.com Thu Oct 4 20:38:14 2007 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Thu, 04 Oct 2007 16:38:14 -0400 Subject: [Fedora-r-devel-list] Plans for R 2.6 In-Reply-To: <200710041608.19760.jamatos@fc.up.pt> References: <200710040801.11025.jamatos@fc.up.pt> <1191504602.3634.17.camel@localhost.localdomain> <200710041608.19760.jamatos@fc.up.pt> Message-ID: <1191530294.3634.50.camel@localhost.localdomain> On Thu, 2007-10-04 at 16:08 +0100, Jos? Matos wrote: > On Thursday 04 October 2007 14:30:02 Tom "spot" Callaway wrote: > > I'll throw an email out to this list when the package is built. > > OK. Thanks. They're all built. I'm going to go push the update for F-7 into testing now. ~spot From pingoufc4 at yahoo.fr Thu Oct 25 22:52:13 2007 From: pingoufc4 at yahoo.fr (pingou) Date: Fri, 26 Oct 2007 00:52:13 +0200 Subject: [Fedora-r-devel-list] Guidelines and R cmd check Message-ID: <47211E1D.9010400@yahoo.fr> Dear all Please find here the answer that I had from somebody from the bioconductor-devel mailing list. The subject was (originally) more or less related to the R CMD check that we use by default on the spec : >A lot of packages also use a Suggest field (e.g. Biobase suggests ALL, >Biostrings suggests BSgenome.Celegans.UCSC.ce2). Most of the times, >people >don't need the suggested stuff. It could be that this stuff is only >used in >the vignette or in some of the man pages (in the example section). >That's the case for Biostrings. Forcing people to install all the stuff >suggested by Biostrings (by putting it in the Depends field) would be a >bad idea. First it would introduce circular dependencies. Second it >would >force them to download gigabytes of data that they don't need! > >All this to say that I don't think that people using the RPM version of >Bioconductor should be forced to install the suggested stuff. Packaging quite some libraries from that repository, I would say that the resolution of the dependences is quite an important issue for that repository. I addition, I believe that he is true when he stands that most of the suggest dependences are only of interest for examples or so... My question is then, should we stick to the present packaging guidelines or should we take this into account ? I agree that the r cmd check make sure that all the dependencies are present, but make sure that they are is (to my opinion) also a packager and reviewer job, and is also quite easy with the DESCRIPTION file. What is your opinion on that point ? Thanks for your help, Best regards ~pingou ___________________________________________________________________________ Yahoo! Mail r?invente le mail ! D?couvrez le nouveau Yahoo! Mail et son interface r?volutionnaire. http://fr.mail.yahoo.com From tcallawa at redhat.com Fri Oct 26 13:08:55 2007 From: tcallawa at redhat.com (Tom "spot" Callaway) Date: Fri, 26 Oct 2007 09:08:55 -0400 Subject: [Fedora-r-devel-list] Guidelines and R cmd check In-Reply-To: <47211E1D.9010400@yahoo.fr> References: <47211E1D.9010400@yahoo.fr> Message-ID: <1193404135.3400.11.camel@localhost.localdomain> On Fri, 2007-10-26 at 00:52 +0200, pingou wrote: > I agree that the r cmd check make sure that all the dependencies are > present, but make sure that they are is (to my opinion) also a > packager > and reviewer job, and is also quite easy with the DESCRIPTION file. > > What is your opinion on that point ? I say, use your best judgement. If the dependencies are really "suggestions", then don't force them as BuildRequires/Requires just to make R CMD CHECK happy. Comment out the check, and explain why in a spec file comment. ~spot From jamatos at fc.up.pt Fri Oct 26 17:30:03 2007 From: jamatos at fc.up.pt (=?utf-8?q?Jos=C3=A9_Matos?=) Date: Fri, 26 Oct 2007 18:30:03 +0100 Subject: [Fedora-r-devel-list] Guidelines and R cmd check In-Reply-To: <1193404135.3400.11.camel@localhost.localdomain> References: <47211E1D.9010400@yahoo.fr> <1193404135.3400.11.camel@localhost.localdomain> Message-ID: <200710261830.03436.jamatos@fc.up.pt> On Friday 26 October 2007 14:08:55 Tom "spot" Callaway wrote: > I say, use your best judgement. If the dependencies are really > "suggestions", then don't force them as BuildRequires/Requires just to > make R CMD CHECK happy. Comment out the check, and explain why in a spec > file comment. I agree. > ~spot -- Jos? Ab?lio