[Bioc-devel] annotate missing from devel

[James W. MacDonald]

On further examination, the vignette on using the annotation packages is 
still based on the env packages as well. It builds right now because it 
depends on the .db packages, and thus works, but the text is all wrong. 
I'll try to get that updated as well.

Best,

Jim



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
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623