[Bioc-devel] annotate missing from devel

[Sean Davis]

On Wed, May 14, 2008 at 9:05 AM, Tony Chiang <tchiang at fhcrc.org> wrote:
> Hi Sean,
>
> I know...I have all bioconductor source files checked out. There are some
> folks here who want to use some of my packages that depend on packages which
> depend on annotate. For the short term, it is fine to install manually with
> the vignette being somewhat broken. I just wanted to make my life a little
> easier and tell them to grab it via biocLite rather than having them install
> svn, etc. It has been about a week since others brought it up, and I just
> wanted to know about an ETA so I can tell them.

If the only issue is the vignette, then the best bet might be to
remove that particular vignette for now and replace it when it is
complete?

Sean

> On Wed, May 14, 2008 at 1:39 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>> 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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>>
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