On Sun, Sep 21, 2014 at 11:07 AM, Martin Morgan <mtmor...@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 > > >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
