[Bioc-devel] annotate missing from devel

[Sean Davis]

On Wed, May 14, 2008 at 8:00 AM, Tony Chiang <tchiang at fhcrc.org> wrote:
> Hi all,
>
> Will there be an ETA on a fix for this problem? There seems to be many
> packages that I cannot load because they depend on annotate.

Tony,

The package appears to install just fine for me doing (from the
command line--your mileage may vary):

svn export https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/annotate
R CMD INSTALL annotate

This is on a unix-like system (Mac) and of course requires an svn
client and build tools for your system but, once installed, it will
allow installation of those other packages.

Hope that helps in the short term.

Sean

> On Wed, May 7, 2008 at 10:56 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
>
>> Hi Jim,
>>
>> I was planning to write a short vignette to replace the broken hsahomology
>> one (since we have previously deprecated that).  I was going to replace it
>> with one that demonstrates how you can use the newer inparanoid packages.  I
>> just have not had time to do it yet.  Please let me know if you have this
>> tackled already, but if not it is already on my "to do " list.  In the
>> meantime, dropping the broken vignette that describes a defunct package
>> seems like a step in the right direction.
>>
>>
>>   Marc
>>
>>
>>
>>
>>
>> James W. MacDonald wrote:
>>
>> > Hi Herve,
>> >
>> > Herve Pages wrote:
>> >
>> > > Hi Kasper,
>> > >
>> > > Kasper Daniel Hansen wrote:
>> > >
>> > > > The checks seems fine but I cannot obtain it with biocLite under
>> > > > 2.8.0
>> > > >
>> > >
>> > > The "orange" builds (i.e. the builds for R-2.7/BioC-2.2) look fine for
>> > > annotate:
>> > >
>> > >
>> > > http://bioconductor.org/checkResults/2.2/bioc-LATEST/annotate/lamb1-buildsrc.html
>> > >
>> > > but not the "aquarium" builds (i.e. the builds for R-2.8/BioC-2.3):
>> > >
>> > >
>> > > http://bioconductor.org/checkResults/2.3/bioc-LATEST/annotate/wilson1-buildsrc.html
>> > >
>> > > Therefore annotate will not be pushed to the BioC 2.3 public repo
>> > > until someone
>> > > fixes its vignette.
>> > >
>> >
>> > Unfortunately that vignette is unfixable - it is based on the old
>> > Homologene/env packages, so will need to be almost completely rewritten to
>> > use the new InParanoid/SQLite packages.
>> >
>> > I should be able to replace it with something reasonable either this
>> > week or the next. In the meantime I will just rename it so it won't
>> > interfere with the build.
>> >
>> > Best,
>> >
>> > Jim
>> >
>> >
>> >
>> > > Cheers,
>> > > H.
>> > >
>> > > PS: The general page for all our builds is:
>> > >
>> > >  http://bioconductor.org/checkResults/
>> > >
>> > >
>> > >
>> > > > Kasper
>> > > >
>> > > > _______________________________________________
>> > > > Bioc-devel at stat.math.ethz.ch mailing list
>> > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> > > >
>> > >
>> > > _______________________________________________
>> > > Bioc-devel at stat.math.ethz.ch mailing list
>> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> > >
>> >
>> >
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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