[Bioc-devel] annotate missing from devel

Wed May 14 15:55:45 CEST 2008

My bad. Marc is going to fix the vignette, and in the meantime I stuck 
an extension on the old vignette so it would be ignored in the build 
process. However, I didn't change the depends field to remove 
hsahomology and xlahomology.

Fixed now.

Best,

Jim

Tony Chiang wrote:
> I definitely agree with you; but as it is not my package I don't think the
> maintainers would appreciate me fiddling with it. Herve told us that the
> Vignette was broken, and both Jim and Marc said they would update it within
> a week or so. I guess my e-mail was just a gentle reminder (I know Jim and
> Marc are both busy). Until the vignette is fixed and the changes committed
> to svn, biocLite won't work.
> 
> Tony
> 
> On Wed, May 14, 2008 at 2:16 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 
>> 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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-- 
James W. MacDonald, M.S.
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Affymetrix and cDNA Microarray Core
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