I have faced the same issue as described in this post and I agree with Aaron, that it would be nice if the doc on the website where extended to specify the version as in "BiocManager::install(version='3.10’)"
Best, Nico > On 15 Nov 2019, at 00:32, Aaron Lun > <infinite.monkeys.with.keyboa...@gmail.com> wrote: > > 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 > <lori.sheph...@roswellpark.org> 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 Bioconductor version '3.9' is out-of-date; the current release version '3.10' 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 <jakob.theor...@ndcn.ox.ac.uk> >> Sent: Wednesday, November 13, 2019 3:59 PM >> To: Aaron Lun <infinite.monkeys.with.keyboa...@gmail.com>; Shepherd, Lori >> <lori.sheph...@roswellpark.org> >> Cc: bioc-devel@r-project.org <bioc-devel@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-boun...@r-project.org> on behalf of Aaron Lun >> <infinite.monkeys.with.keyboa...@gmail.com> >> Sent: 13 November 2019 18:56 >> To: Shepherd, Lori <lori.sheph...@roswellpark.org> >> Cc: bioc-devel@r-project.org <bioc-devel@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.sheph...@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-boun...@r-project.org> on behalf of Jakob >>> Theorell <jakob.theor...@ndcn.ox.ac.uk> >>> Sent: Wednesday, November 13, 2019 11:06 AM >>> To: bioc-devel@r-project.org <bioc-devel@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 >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org 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]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> _______________________________________________ >> Bioc-devel@r-project.org 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. > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
