[R-SIG-Mac] packages, R-patched and RC [Was: Importing Excel files]

Prof Brian Ripley ripley at stats.ox.ac.uk
Sat Jun 23 06:50:11 CEST 2012

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.

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,                  ripley at stats.ox.ac.uk
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

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