[Bioc-devel] annotate missing from devel

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.

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

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