Hi. Thanks for pointing that out. Yes we are aware the installation page isn't updated yet and will update the page shortly.
Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Joris Meys <joris.m...@ugent.be> Sent: Thursday, June 21, 2018 4:06:11 AM To: Ramos Perez, Marcel Cc: bioc-devel Subject: Re: [Bioc-devel] BiocManager now on CRAN Dear Marcel, A big thanks to you and the entire bioconductor team. I will spread the word among my colleagues. I also noticed that the installation instructions aren't adapted yet on the bioconductor site ( https://www.bioconductor.org/install/). Probably I'm just rushing here and you are working on it, but I thought to inform you anyway as our courses link to that website for official installation instructions. Cheers Joris On Wed, Jun 20, 2018 at 6:23 PM, Marcel Ramos <marcel.ra...@roswellpark.org> wrote: > Dear bioc-devs, > > > A month ago we notified you about our "next generation" changes to > BiocInstaller. > > Thanks to all beta testers and those who provided feedback and > suggestions for a new package name. > > > I am pleased to inform you that BiocManager is now on CRAN: > https://cran.r-project.org/web/packages/BiocManager/index.html > > > As mentioned in our last email, you can now install BiocManager using: > > ``` > install.packages("BiocManager") > BiocManager::install("YourPackageNameHere") > ``` > > Action Item: > > - Please modify the vignettes in your bioc-devel packages to > reflect the use of BiocManager > > > After the next couple of weeks or so, we will be identifying packages in > bioc-devel (3.8) that still > mention BiocInstaller / biocLite. > > > Best regards, > Marcel > > Bioconductor Core Team > Roswell Park Cancer Institute > Dept. of Biostatistics & Bioinformatics > Elm & Carlton Streets > Buffalo, New York 14263 > > > On 05/09/2018 06:11 PM, Martin Morgan wrote: > > Developers -- > > > > A preliminary heads-up and request for comments. > > > > Almost since project inception, we've used the commands > > > > source("https://bioconductor.org/biocLite.R";) > > biocLite(pkgs) > > > > to install packages. This poses security risks (e.g., typos in the > > url) and deviates from standard R package installation procedures. > > > > > > We'd like to move to a different system where a base package, call it > > 'BiocManager', is installed from CRAN and used to install Bioconductor > > packages > > > > if (!"BiocManager" %in% rownames(installed.packages())) > > install.packages("BiocManager") > > BiocManager::install(pkgs) > > > > This establishes a secure chain from user R session to Bioconductor > > package installation. It is also more consistent with base R package > > installation procedures. > > > > BiocManager exposes four functions > > > > - install() or update packages > > > > - version() version of Bioconductor in use > > > > - valid() are all Bioconductor packages from the same Bioconductor > > version? > > > > - repositories() url location for Bioconductor version-specific > > repositories > > > > install() behaves like biocLite(), using the most current version of > > Bioconductor for the version of R in use. It stores this state using a > > Bioconductor package 'BiocVersion', which is nothing more than a > > sentinel for the version in use. One can also 'use devel' or a > > particular version of Bioconductor (consistent with the version of R) > > with > > > > BiocManager::install(version = "3.8") # or the synonym "devel" > > > > > > We intend to phase this in over several release cycles, and to > > continue to support the traditional biocLite() route for versions > > before BiocManager becomes available. > > > > We also intend to change the overall versioning of 'Bioconductor' > > itself, where releases are always even (3.8, 3.10, 3.12, ...) and > > 'devel' always odd. > > > > Obviously this is a large change, eventually requiring updates to many > > locations on our web site and individual vignettes. > > > > > > Of course the key question is the name of the 'BiocManager' package. > > It cannot easily be 'BiocInstaller', because of the differences in way > > CRAN and Bioconductor version packages. Some possible names are > > ' > > BiocInstall::install() > > BiocPackages::install() > > BiocManager > > BiocMaestro > > > > > > Your comments are welcome... > > > > Martin > > > > > > This email message may contain legally privileged and/or...{{dropped:2}} > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > This email message may contain legally privileged and/or...{{dropped:4}} > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Joris Meys Statistical consultant Department of Data Analysis and Mathematical Modelling Ghent University Coupure Links 653, B-9000 Gent (Belgium) <https://maps.google.com/?q=Coupure+links+653,%C2%A0B-9000+Gent,%C2%A0Belgium&entry=gmail&source=g> tel: +32 (0)9 264 61 79 ----------- Biowiskundedagen 2017-2018 http://www.biowiskundedagen.ugent.be/ ------------------------------- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php [[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. 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