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List:       bioc-devel
Subject:    Re: [Bioc-devel] ncdf deprecation
From:       Dan Tenenbaum <dtenenba () fredhutch ! org>
Date:       2015-12-04 18:19:30
Message-ID: 910407019.1318446.1449253170674.JavaMail.zimbra () fredhutch ! org
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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.

Thanks,
Dan




----- Original Message -----
> From: "Hervé Pagès" <hpages@fredhutch.org>
> To: "Stephanie M. Gogarten" <sdmorris@u.washington.edu>, "bioc-devel" \
>                 <bioc-devel@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@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@fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
> 
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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