I would assume that "BiocManager::install()" won't update an existing set of BioC packages unless explicitly prompted. If that's the case, shouldn't the instructions at http://bioconductor.org/install/ specify "BiocManager::install(version='3.10')"?
On Wed, Nov 13, 2019 at 1:04 PM Shepherd, Lori <[email protected]> wrote: > > BiocManager should recognize versions automatically for the version of R. I > believe we had a message that would be displayed in this case where there was > a more recent version available > Something along the lines of: > Bioconductor version '3.9' is out-of-date; the current release version '3.10' > is available with R version '3.6'; see https://bioconductor.org/install > > It is broken in this latest version of BiocManager but will be correct > shortly. > > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > ________________________________ > From: Jakob Theorell <[email protected]> > Sent: Wednesday, November 13, 2019 3:59 PM > To: Aaron Lun <[email protected]>; Shepherd, Lori > <[email protected]> > Cc: [email protected] <[email protected]> > 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 <[email protected]> on behalf of Aaron Lun > <[email protected]> > Sent: 13 November 2019 18:56 > To: Shepherd, Lori <[email protected]> > Cc: [email protected] <[email protected]> > 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 > <[email protected]> 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 <[email protected]> on behalf of Jakob > > Theorell <[email protected]> > > Sent: Wednesday, November 13, 2019 11:06 AM > > To: [email protected] <[email protected]> > > 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 > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > [email protected] mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > This email message may contain legally privileged and/or confidential > > information. If you are not the intended recipient(s), or the employee or > > agent responsible for the delivery of this message to the intended > > recipient(s), you are hereby notified that any disclosure, copying, > > distribution, or use of this email message is prohibited. If you have > > received this message in error, please notify the sender immediately by > > e-mail and delete this email message from your computer. Thank you. > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > [email protected] mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
