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

[David Winsemius]

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

-- 
David Winsemius, MD
Heritage Laboratories
West Hartford, CT