[BioC] SVGAnnotation

[Hervé Pagès]

On 11/05/2010 12:29 PM, Uwe Ligges wrote:
>
>
> On 05.11.2010 20:25, Hervé Pagès wrote:
>> Hi Uwe,
>>
>> On 11/05/2010 06:04 AM, Uwe Ligges wrote:
>>> Hi,
>>>
>>> the binary of SVGAnnotation in
>>> BioC/packages/2.7/extra/bin/windows/contrib/2.12/SVGAnnotation_0.6-0.zip
>>>
>>> is declared to be built under R-2.10.x (rather than R-2.12.x)
>>
>> Thanks for telling us!
>>
>> We host a few Omegahat packages in our extra repo and we try to
>> host the latest versions. This SVGAnnotation Windows binary is
>> the latest version currently available at Omegahat.
>>
>> Unfortunately Omegahat binary packages are often lagging behind
>> the source packages (when they are available at all). For example,
>> for the current release, there is only 1 Windows binary at the
>> moment (out of 84 source packages):
>>
>> http://www.omegahat.org/R/bin/windows/contrib/2.12/PACKAGES
>>
>> In the case of SVGAnnotation and XMLSchema (the Windows binary
>> of XMLSchema that we host is also outdated), they don't contain
>> native code so I should be able to produce updated binaries without
>> too many problems.
>
> I see.
>
> A recent XMLSchema binary is on CRAN extras:
> http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.12/
>
>
>>>
>>> which causes update.packages(checkBuilt=TRUE) to reinstall it again and
>>> again under Windows.
>>
>> It sounds like update.packages(checkBuilt=TRUE) could do a better job.
>> Generally speaking why would an "update tool" replace something by
>> something that is identical?
>
>
> Well, since update.packages assumes that packages in ./2.12/ have been
> built with R-2.12.x which is not that unreasonable. ;-)

Yes it's a fair assumption. Even though sometimes it's not the case.
Beside us dropping old binaries in our ./2.12/, the CRAN repository
currently has a symlink from 2.13 to 2.12 so right now packages in
./2.13/ have not been built with R-2.13.x
I wonder what update.packages(checkBuilt=TRUE) would do for R-devel
users on Windows (I didn't try)...

H.


> If it is expected to do a better job, we'd need to add the build stamp
> into the PACKAGES database.
>
> Best wishes,
> Uwe
>
>
>
>> Cheers,
>> H.
>>
>>>
>>> Best wishes,
>>> Uwe
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319