[Bioc-devel] annotate missing from devel

Thu May 15 18:35:25 CEST 2008

I did see a new version come down via update.packages - Tony can you 
confirm that you are now getting one at your end?

the devel builds seem to be in a bit of a mess, we will be trying to 
address that this week

Marc Carlson wrote:
> I have replaced the useHomology vignette with a newer one that describes 
> the newer inparanoid based packages.
> 
>    Marc
> 
> 
> James W. MacDonald wrote:
>> 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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>>>>>>>>
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>>>>>
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> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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