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

[Martin Morgan]

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.

 > 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.

I guess the megabytes of warnings come from code in GGtools or elsewhere; maybe 
there's a convenient way of aggregating them (hopefully before throwing the 
warning, since that can be quite expensive).

Martin

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