[Bioc-devel] ncdf deprecation

Dan Tenenbaum dtenenba at fredhutch.org
Fri Dec 4 19:19:30 CET 2015

Hi Stephanie and Hervé,

ncdf has been added to the extra repos for BioC 3.2

I hesitate to add it to the extra repos for devel (3.3). If we don't add it, then we will start getting build errors as soon as ncdf is removed from CRAN (well actually, it will happen the next time we update R on the devel build machines after ncdf is removed, unless we uninstall it manually). IMO this is a good thing as it will alert maintainers that they need to make the appropriate changes to their packages.

I think it would be great for all maintainers of packages that depend on ncdf to start making the appropriate changes (RNetCDF or ncdf4 instead) sooner rather than later, in devel, then nobody will have to scramble to get this done when ncdf is removed from CRAN.


----- Original Message -----
> From: "Hervé Pagès" <hpages at fredhutch.org>
> To: "Stephanie M. Gogarten" <sdmorris at u.washington.edu>, "bioc-devel" <bioc-devel at r-project.org>
> Sent: Tuesday, December 1, 2015 12:14:33 AM
> Subject: Re: [Bioc-devel] ncdf deprecation

> Hi Stephanie,
> Thanks for the heads-up. Yes we'll add ncdf to the "extra" repos for
> BioC 3.2 and probably to 3.3 too. That will prevent BioC 3.2 from
> breaking when ncdf is removed from CRAN and also give some extra time
> to developers to modify their package in devel (BioC 3.3) to use ncdf4
> instead.
> Cheers,
> H.
> On 11/30/2015 03:42 PM, Stephanie M. Gogarten wrote:
>> I was notified today that the ncdf package is deprecated and will be
>> removed from CRAN in January. Since this date does not correspond with a
>> Bioconductor release, is it possible to add ncdf to the Bioconductor
>> "extra" repository for the duration of this release? I will modify
>> GWASTools to use the ncdf4 package, but such a major change does not
>> seem appropriate to introduce into the release branch.
>> The Bioconductor packages TargetSearch and xcms are affected as well as
>> GWASTools.
>> thanks,
>> Stephanie
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> --
> Hervé Pagès
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> E-mail: hpages at fredhutch.org
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> Fax:    (206) 667-1319
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