[Bioc-devel] BiocManager not installing latest release version of DepecheR

[Jakob Theorell]

Yes, this sounds like a very good solution. Thank you all for your input, and I hope this silly mistake of mine might have some positive consequence.
Best
Jakob
________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Aaron Lun <infinite.monkeys.with.keyboards using gmail.com>
Sent: 13 November 2019 18:56
To: Shepherd, Lori <Lori.Shepherd using roswellpark.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] BiocManager not installing latest release version of DepecheR

Perhaps the installation instructions on each package's landing page
should explicitly specify 'version=3.10' (or whatever happens to be
the latest release) in the install() call. This avoids ambiguities
with using the latest version when the current and previous releases
are on the same version of R.

-A

On Wed, Nov 13, 2019 at 8:25 AM Shepherd, Lori
<Lori.Shepherd using roswellpark.org> wrote:
>
> It looks like you are still installing release 3.9 versions of packages.  The latest version is release 3.10.
>
> If you do
> BiocManager::version()
> Does it show "3.9"  or "3.10"?
>
> I'm betting "3.9"
>
> You can do
>
> BiocManager::install(version="3.10")
> BiocManager::install()
>
>
> To update all packages to 3.10 versions
>
>
> Cheers,
>
>
> 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 Jakob Theorell <jakob.theorell using ndcn.ox.ac.uk>
> Sent: Wednesday, November 13, 2019 11:06 AM
> To: bioc-devel using r-project.org <bioc-devel using r-project.org>
> Subject: [Bioc-devel] BiocManager not installing latest release version of DepecheR
>
> Dear all,
> This is probably a mistake on my side, but I just now tried to install the last release version of DepecheR (for which I am the maintainer), and although the source package on BioConductor is 1.2, this is the text I get from BiocManager when installing:
>
> Bioconductor version 3.9 (BiocManager 1.30.9), R 3.6.1 (2019-07-05)
> Installing package(s) 'DepecheR'
> trying URL 'https://bioconductor.org/packages/3.9/bioc/bin/macosx/el-capitan/contrib/3.6/DepecheR_1.0.3.tgz'
>
> This is clearly the old version, that does not contain all the updates that the source package contains. Have I missed something I should have done to prevent this and what can I in that case do now?
> Best regards
> Jakob Theorell, MD/PhD
> Autoimmune Neurology Group
> Nuffield Department of Clinical Neurosciences
> University of Oxford
>
>
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