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

Simon Urbanek simon.urbanek at r-project.org
Sat Jun 23 15:14:01 CEST 2012 

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,                  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
>> 
>> 
> 
> David Winsemius, MD
> West Hartford, CT
> 
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