________________________________
From: Jakob Theorell <jakob.theorell at ndcn.ox.ac.uk>
Sent: Wednesday, November 13, 2019 3:59 PM
To: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>; Shepherd, Lori <Lori.Shepherd at RoswellPark.org>
Cc: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] BiocManager not installing latest release version of DepecheR
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 at r-project.org> on behalf of Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
Sent: 13 November 2019 18:56
To: Shepherd, Lori <Lori.Shepherd at roswellpark.org>
Cc: bioc-devel at r-project.org <bioc-devel at 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 at 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 at r-project.org> on behalf of Jakob Theorell <jakob.theorell at ndcn.ox.ac.uk>
Sent: Wednesday, November 13, 2019 11:06 AM
To: bioc-devel at r-project.org <bioc-devel at 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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