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

Sat Jun 23 08:28:29 CEST 2012

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.)

-- 
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