[Bioc-devel] CRAN packages depending on broken Bioc 3.11 packages may be archived

[Kasper Daniel Hansen]

Or remove the graph dependency

On Tue, Nov 26, 2019 at 3:16 PM James W. MacDonald <jmacdon using uw.edu> wrote:

> Hi Lori,
>
> Let me know if you don't hear from Benilton. It shouldn't be much work to
> fix oligo - we could convert to using Gviz for the graphic that is
> currently using GenomeGraphs. I can make the change next week if necessary.
>
> Best,
>
> Jim
>
>
>
> On Tue, Nov 26, 2019 at 12:57 PM Shepherd, Lori <
> Lori.Shepherd using roswellpark.org> wrote:
>
> > typo -  heatplus and topGO have responded directly.
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Comprehensive Cancer Center
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> > ________________________________
> > From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of
> > Shepherd, Lori <Lori.Shepherd using RoswellPark.org>
> > Sent: Tuesday, November 26, 2019 12:54 PM
> > To: Henrik Bengtsson <henrik.bengtsson using gmail.com>;
> > bioc-devel using r-project.org <bioc-devel using r-project.org>
> > Subject: Re: [Bioc-devel] CRAN packages depending on broken Bioc 3.11
> > packages may be archived
> >
> > All of these package have been notified from the Bioconductor side as
> > well.  We hope the maintainers will respond shortly.
> > heatmap and topGO  have responded directly and are working on fixes.  I
> > hope the others are too.
> >
> >
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Comprehensive Cancer Center
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> > ________________________________
> > From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Henrik
> > Bengtsson <henrik.bengtsson using gmail.com>
> > Sent: Tuesday, November 26, 2019 12:47 PM
> > To: bioc-devel using r-project.org <bioc-devel using r-project.org>
> > Subject: [Bioc-devel] CRAN packages depending on broken Bioc 3.11
> packages
> > may be archived
> >
> > In case it's not known, paraphrasing from CRAN notification email,
> > CRAN [sic!] packages:
> >
> >   TROM, demi, diffMeanVar, maGUI, metaboGSE
> >
> > risk being archived on December 7 because broken Bioconductor
> dependencies:
> >
> >   Heatplus, missMethyl, oligo, oligoClasses, topGO
> >
> > prevent pdInfoBuilder from being installed.
> >
> > I don't maintain any of the above - I'm just the messenger.
> >
> > /Henrik
> >
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
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-- 
Best,
Kasper

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