[Bioc-devel] List of Deprecated Packages Bioc 3.11

[Paul Shannon]

Hi Lori,

Is there a replacement for the athaliana package, org.At.tair.db?  We sometimes use this in our work.

 - Paul

> On Nov 18, 2019, at 6:24 AM, Shepherd, Lori <Lori.Shepherd using RoswellPark.org> wrote:
> 
> The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly. The current list of deprecated packages for Bioc 3.11 is as follows:
> 
> Maintainer requested deprecation:
> 
>  *   Software:
> 
>     *   QUALIFIER
>     *   motifRG
>     *   triform
>  *   Annotation:
> 
>     *   org.At.tair.db
>     *   hom.At.inp.db
>     *   hom.Ce.inp.db
>     *   hom.Dm.inp.db
>     *   hom.Dr.inp.db
>     *   hom.Hs.inp.db
>     *   hom.Mm.inp.db
>     *   hom.Rn.inp.db
>     *   hom.Sc.inp.db
>     *   KEGG.db (use KEGGREST instead)
> 
> Unresponsive/not-maintained packages:
> 
>  *   Software:
> 
>     *   SELEX
>     *   CTDquerier
> 
> The follow Annotation packages were deprecated in 3.10 and removed from 3.11 but not previously announced.
> 
>  *   MafDb.ESP6500SI.V2.SSA137.hs37d5
>  *   MafDb.EXP6500SI.V2.SSA137.GRCh38
> 
> We will be sending emails out to packages that have been broken across all platforms for an extended period of time as those are packages that are up for immediate deprecation if not corrected in a timely fashion.
> 
> Thank you
> 
> 
> 
> 
> Lori Shepherd
> 
> Bioconductor Core Team
> 
> Roswell Park Comprehensive Cancer Center
> 
> Department of Biostatistics & Bioinformatics
> 
> Elm & Carlton Streets
> 
> Buffalo, New York 14263
> 
> 
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