[Bioc-devel] annotate missing from devel

Marc Carlson mcarlson at fhcrc.org
Wed May 14 23:23:19 CEST 2008 

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
>>>>>>>>>
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Bioc-devel at stat.math.ethz.ch mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>
>>>>>>        [[alternative HTML version deleted]]
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel at stat.math.ethz.ch mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>
>>>>        [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at stat.math.ethz.ch mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>
>>     [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

More information about the Bioc-devel mailing list