[Bioc-devel] change the codes in Bio

Tue Oct 23 11:47:13 CEST 2018

Hi, Bioconductor core team, 
I have changed the codes from the master repository, and how can I push the change to the Bioconductor repository for this package? The package is in the check report for BioC 3.8,

Irene  

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Today's Topics:

   1. Re: BiocManager now on CRAN (Shepherd, Lori)

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Message: 1
Date: Thu, 21 Jun 2018 11:03:36 +0000
From: "Shepherd, Lori" <Lori.Shepherd using RoswellPark.org>
To: "Ramos Perez, Marcel" <Marcel.RamosPerez using RoswellPark.org>,
        "Joris.Meys using ugent.be" <Joris.Meys using ugent.be>
Cc: bioc-devel <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] BiocManager now on CRAN
Message-ID:
        <MW2PR12MB2364F36A14B8DF8F5BE020C0F9760 using MW2PR12MB2364.namprd12.prod.outlook.com>

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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-bounces using r-project.org> on behalf of Joris Meys <Joris.Meys using 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.Ramos using 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 using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
>
> This email message may contain legally privileged and/or...{{dropped:4}}
>
> _______________________________________________
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>

--
Joris Meys
Statistical consultant

Department of Data Analysis and Mathematical Modelling
Ghent University
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