[Bioc-devel] new error(?) related to annotation: illuminaHumanv1CHR is deprecated

[Vincent Carey]

On Sun, Sep 21, 2014 at 11:07 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:

> On 09/21/2014 07:44 AM, Vincent Carey wrote:
>
>> this is coming out of the build system for GGtools ... not easy to find as
>> the
>>
>> problem seems to cause emission of megabytes of warnings
>>
>>
>> illuminaHumanv1CHR is deprecated as the data is better accessed from
>>
>>    another location. Please use an appropriate TxDb object or package for
>>
>>    this kind of data.
>>
>>
>> i don't see the deprecation in the doc for illuminaHumanv1.db and i cannot
>>
>> get a get() to throw it.  i also don't see this on the devel version
>> package landing page
>>
>
> Marc will likely reply on Monday. But the intention is that the CHR bimaps
> in *db packages Marc curates are being deprecated. The deprecation itself
> occurs in AnnotationDbi, I think. The reason is the lack of provenance for
> this information -- what genome build does it refer to? -- and its
> availability from other sources (i.e., the TxDb packages) with provenance.
>
>
Nice to hear about the streamlining and improved provenance.  I confess I
don't
see how to get a probe-chr mapping out of TxDb -- is there something new in
there?
A select operation that can resolve queries about manufacturer identifiers?


> > illuminaHumanv1CHR
> illuminaHumanv1CHR is deprecated as the data is better accessed from
>   another location. Please use an appropriate TxDb object or package for
>   this kind of data.
> CHR map for chip illuminaHumanv1 (object of class "ProbeAnnDbBimap")
>
> I think this is currently a message, but should be a warning.
>
> AnnotationDbi is not building successfully, so its biocLite() version and
> landing page are not in sync with an svn checkout (used by the build
> system); to replicate on your own system requires an svn install, at least
> until AnnotationDbi builds successfully.
>

OK, so I can get the message now.  But I think more details need to be
supplied if
we are to drop references to *CHR.


>
> I guess the megabytes of warnings come from code in GGtools or elsewhere;
> maybe there's a


Indeed.  Perhaps unrelated to this.

convenient way of aggregating them (hopefully before throwing the warning,
> since that can be quite expensive).
>
> Martin
>
>
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