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
