[Bioc-devel] BiocManager not installing latest release version of DepecheR
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.Shepherd at 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this case where there was a more recent version available Something along the lines of: Bioconductor version '3.9' is out-of-date; the current release version '3.10' is available with R version '3.6'; see https://bioconductor.org/install It is broken in this latest version of BiocManager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.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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel at 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.