On Jun 23, 2012, at 2:28 AM, David Winsemius wrote: > > On Jun 23, 2012, at 12:50 AM, Prof Brian Ripley wrote: > >> Other messages say this is a temporary snafu on the Mac builder, which will >> be resolved once it percolates through CRAN: the master is OK already. > > Then I must be confused. I thought this was the master: > >> http://stat.ethz.ch/CRAN/bin/macosx/leopard/contrib/2.15 > > (I normally use the CMU, Berkeley or Fred-Hutch mirrors, but I tried the > ETH-Z site as well. The Mac R build was obtained from the att.research site > minutes before the posting.
... and that (R.research.att.com) is also the source for Mac R + package binaries (and those only). CRAN master syncs from there and in turn other mirrors sync from the CRAN master. Cheers, Simon > ) > > -- > David. >> >> On 23/06/2012 05:09, David Winsemius wrote: >>> >>> On Jun 20, 2012, at 8:14 AM, Prof Brian Ripley wrote: >>> >>>> On 20/06/2012 11:20, peter dalgaard wrote: >>>>> >>>>> On Jun 19, 2012, at 23:29 , Prof Brian Ripley wrote: >>>>> >>>>>> On 19/06/2012 17:35, Simon Urbanek wrote: >>>>>>> On Jun 19, 2012, at 5:36 AM, peter dalgaard wrote: >>>>>>> >>>>>>>> >>>>>>>> On Jun 19, 2012, at 01:16 , Colstat wrote: >>>>>>>> >>>>>>>>> I think the error says it "package Œgdata‚ was built under R >>>>>>>>> version 2.15.1" and you have R 2.5.10. >>>>>>>>> >>>>>>>>> Update your R first, let me know if it doesn't work. >>>>>>>> >>>>>>>> 2.15.1 is announced for Friday... I think it's a bit of a >>>>>>>> glitch that CRAN is already automatically providing packages >>>>>>>> for it, but you are of course more than welcome to test the >>>>>>>> prereleases (from http://R.research.att.com/). >>>>>>>> >>>>>>>> I suppose that this comes about from building packages with >>>>>>>> R-patched, which transitions directly into the prereleases for >>>>>>>> the next version. >>>>>>>> >>>>>>> >>>>>>> Yes, this is a side-effect of that. I wonder what we can do about >>>>>>> it - I used to build packages with released versions only, but >>>>>>> then people complained that patched had fixes for some things >>>>>>> they needed... >>>>>> >>>>>> We could simply not update the version of R-patched used during the >>>>>> beta/RC periods: they are after all only about 10 days. >>>>> >>>>> Yes, that would handle the formal issue of the version number >>>>> conflict. >>>>> >>>>> However, there's a deeper issue which got highlighted by the >>>>> identical() debacle in April-June: It seems that we can't guarantee >>>>> ABI compatibility throughout the R-branch series (e.g., everything >>>>> labeled 2.15.x). We try to ensure that the modified versions of R >>>>> will run packages built with a previous version, but the other way >>>>> around might not work. If that sort of thing happens in R-patched, >>>>> midway between releases, then users could find themselves blocked >>>>> from installing packages until they update to R-patched, which could >>>>> be undesirable in corporate or educational settings. >>>> >>>> Note this only applies to binary packages: people can always install >>>> from the sources (trivially for 'gdata' since it has no compiled code). >>>> >>>> My understanding is that the Windows' policy is to stick with the >>>> current 2.15.x release: 2.15.0 is currently used but once 2.15.1 is >>>> out packages will be built with 2.15.1 (and re-built if their >>>> dependencies change). >>>> >>>> The 'debacle' was Bioconductor's lack of understanding of the >>>> assumptions of their own distribution model. As we said at the time, >>>> if you want to provide binary packages that work under all of 2.15.x, >>>> you need to prepare them with 2.15.0. But as Simon points out, that >>>> may stop binary packages being provided for some recent source packages. >>>> >>>> Note that there are other issues here: as we have seen in the last >>>> week, updates and downdates to a recommended package such as Matrix >>>> have required other packages to be re-installed. It is not just the >>>> version of R that is relevant but also what other packages were >>>> installed at the time the binary package was prepared. >>>> >>>> We may need to work harder to get people to understand that binary >>>> packages have 'use at your own risk' status. >>> >>> Do the foregoing observations explain why I am unable to get any access >>> to the binary CRAN indexes using the MacGUI installer? I've tried with >>> three different repositories, so I do not think it is due to a scheduled >>> weekend maintenance problem: >>> >>> Warning: unable to access index for repository >>> http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15 >>> Warning: unable to access index for repository >>> http://stat.ethz.ch/CRAN/bin/macosx/leopard/contrib/2.15 >>> Warning: unable to access index for repository >>> http://cran.cnr.Berkeley.edu/bin/macosx/leopard/contrib/2.15 >>> > >>> >>> I _can_ see the source directories and install source packages, so it >>> seems not to be a connectivity issue. >>> >>> I started seeing this with R 2.15.0 , so I updated, but it continues: >>> >>> > sessionInfo() >>> R version 2.15.1 RC (2012-06-20 r59589) >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> loaded via a namespace (and not attached): >>> [1] tools_2.15.1 >>> >>> The problem persists in a non-GUI session: >>> >>> > available.packages() >>> --- Please select a CRAN mirror for use in this session --- >>> Loading Tcl/Tk interface ... done >>> Warning: unable to access index for repository >>> http://cran.fhcrc.org/bin/macosx/leopard/contrib/2.15 >>> Package Version Priority Depends Imports LinkingTo Suggests Enhances >>> OS_type License Archs File Repository >>> >> >> >> -- >> Brian D. Ripley, [email protected] >> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ >> University of Oxford, Tel: +44 1865 272861 (self) >> 1 South Parks Road, +44 1865 272866 (PA) >> Oxford OX1 3TG, UK Fax: +44 1865 272595 >> >> > > David Winsemius, MD > West Hartford, CT > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
