[BioC] SVGAnnotation

Uwe Ligges ligges at statistik.tu-dortmund.de
Fri Nov 5 20:29:28 CET 2010

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 of XMLSchema that we host is also outdated), they don't contain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:

>> 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. ;-)
If it is expected to do a better job, we'd need to add the build stamp 
into the PACKAGES database.

Best wishes,

> Cheers,
> H.
>> Best wishes,
>> Uwe
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