[R-SIG-Mac] cannit get list of binary packages from the GUI

Simon Urbanek simon.urbanek at r-project.org
Sat Mar 17 14:59:32 CET 2012 

On Mar 17, 2012, at 7:06 AM, David Winsemius wrote:

> 
> On Mar 16, 2012, at 7:21 PM, Simon Urbanek wrote:
> 
>> 
>> On Mar 16, 2012, at 8:55 AM, Prof Brian Ripley wrote:
>> 
>>> On 16/03/2012 12:31, Ken knoblauch wrote:
>>>> Federico Calboli<f.calboli<at>  imperial.ac.uk>  writes:
>>>>> Apologies, I forgot to say, I have R 2.14.2, latest 64-bit GUI
>>>> from http://r.research.att.com/, OS 10.7.3
>>>>>> I just noticed the following weird issue.  If I go to the menu
>>>> 'Packages and Data',  select 'Package
>>>>> Installer' the installer goes up, but when I tell it to give the
>>>> list of binaries available (I like to keep up
>>>>> to date, and check every couple of days) the list comes up empty.
>>>> The list for CRAN sources, and for
>>>>> Bioconductor binaries work fine.
>>>>>> 
>>>>>> I tried to change the mirror, but it does not make a difference.
>>>>>> 
>>>>>> Am I the only one with the problem? what's going on?
>>>> 
>>>> I second this observation.
>>> 
>>> What is going on is that http://cran.r-project.org/bin/macosx/leopard/contrib/2.14/ has an empty PACKAGES file.  Given that it hadn't been updated for a couple of weeks on Weds, you may just need to be patient.  But in any case, only Simon can fix this as only he has sufficient access to the package builder. So reporting to Simon is always going to be the most effective way forward for similar problems.
>>> 
>> 
>> Hmm... it's not empty on the master machine -- use http://r.research.att.com as the mirror - it should work ...
>> 
> 
> Could PACKAGES file be in some damaged state that R cannot process? When I change the repository to that value  in the R64 GUI and try to see either either the binary versions or the source versions of contributed packages in the Package Installer I get these warnings at the console:
> 
> Warning: unable to access index for repository  http://r.research.att.com/bin/macosx/leopard/contrib/2.14
> 
> Warning: unable to access index for repository  http://r.research.att.com/src/contrib
> 

That is really odd - in particular because the src/contrib one is really just an rsync from CRAN so it is not processed on my side at all. Could it be some proxy or internet setting that is different in Firefox and your R? Or some intermittent Internet problem?

Both directories are populated by rsync and it moves files atomically so there should never be an incomplete file ...

I checked on the master site and there are PACKAGES in all directories:

urbanek at ix:/R/cran/bin/macosx/leopard/contrib$ ls -l 2.1?/PACKAGES*
-rw-r--r-- 1 urbanek urbanek 305553 Jul  2  2010 2.10/PACKAGES
-rw-r--r-- 1 urbanek urbanek  86929 Jul  2  2010 2.10/PACKAGES.gz
-rw-r--r-- 1 urbanek urbanek 346594 Jan 20  2011 2.11/PACKAGES
-rw-r--r-- 1 urbanek urbanek  99277 Jan 20  2011 2.11/PACKAGES.gz
-rw-r--r-- 1 urbanek urbanek 630019 Sep 23 04:03 2.12/PACKAGES
-rw-r--r-- 1 urbanek urbanek 152152 Sep 23 04:03 2.12/PACKAGES.gz
-rw-r--r-- 1 urbanek urbanek 691386 Feb 13 10:50 2.13/PACKAGES
-rw-r--r-- 1 urbanek urbanek 165741 Feb 13 10:50 2.13/PACKAGES.gz
-rw-r--r-- 1 urbanek urbanek 702359 Mar 17 05:07 2.14/PACKAGES
-rw-r--r-- 1 urbanek urbanek 168453 Mar 17 05:07 2.14/PACKAGES.gz
-rw-r--r-- 1 urbanek urbanek 676374 Mar 17 05:08 2.15/PACKAGES
-rw-r--r-- 1 urbanek urbanek 155935 Mar 17 05:08 2.15/PACKAGES.gz

and the last two are updated by the nightly script (on the build machine, so, again, those are moved atomically). I'll double-check the builds, but everything seems just fine ...

Thanks,
Simon

> I am able to see the .tgz packages at http://r.research.att.com/bin/macosx/leopard/contrib/2.14/ with Firefox.
> 
> I am able to get a list of source packages (but not binary) to display in the Package Installer if I use a different repository. And I am able to install binary packages with ... for example:
> 
> install.packages("actuar", repo="http://r.research.att.com", type="mac.binary.leopard")
> 
> (Which updated an existing version to the current version.)
> 
> Admittedly I am running a somewhat behind the times version, but this is completely different behavior than it has exhibited up to a few days ago.
> 
> -- 
> David Winsemius, MD
> 
> R version 2.14.0 Patched (2011-11-13 r57650)
> 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] splines   stats     grDevices utils     datasets  graphics
> [7] methods   base
> 
> other attached packages:
> [1] rms_3.4-0        Hmisc_3.9-2      survival_2.36-10
> [4] sos_1.3-1        brew_1.0-6       lattice_0.20-0
> 
> loaded via a namespace (and not attached):
> [1] cluster_1.14.1 grid_2.14.0    tools_2.14.0
> 
> 
> 
>> Few days ago the build machine has lost network connectivity due to a faulty ethernet cable, so maybe it has thrown off mirroring, that's the closest I can get to an explanation...
>> 
>> 
>>> Perhaps this can encourage people to test 2.15.0 beta?  Its binary package repository does have a populated PACKAGES file.
>>> 
>> 
>> Yes, we can't stress is often enough that we need people to test betas, reporting bugs after the release is too late!
>> 
>> Thanks,
>> Simon
>> 
>> 
>>>> 
>>>> 
>>>>>> --
>>>>>> Federico C. F. Calboli
>>>>>> Neuroepidemiology and Ageing Research
>>>>>> Imperial College, St. Mary's Campus
>>>>>> Norfolk Place, London W2 1PG
>>>>>> 
>>>>>> Tel +44 (0)20 75941602   Fax +44 (0)20 75943193
>>>>>> 
>>>>>> f.calboli [.a.t] imperial.ac.uk
>>>>>> f.calboli [.a.t] gmail.com
>>>> 
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>>> 
>>> -- 
>>> 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
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>> 
>>> 
>> 
>> _______________________________________________
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> 
> David Winsemius, MD
> West Hartford, CT
> 
>

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