Hi everyone! Now this might be a silly question, but since this is my first time submitting to bioc, please ignore my ignorance. What I?d like to know is this: my package has been accepted, although not yet added to the devel bioc ? is it ok if I change biocLite with BiocManager in the Installation section of readme and vignette now, or should I wait for the addition to the Bioconductor git repo before making any new commits to the master branch? Thanks in advance, Anamaria Elek From: Shepherd, Lori Sent: 31 July 2018 05:51 PM To: jmacdon at u.washington.edu Cc: bioc-devel Subject: Re: [Bioc-devel] EXTERNAL: introducing BiocManager in devel packagepages? We assume most users are using release not devel. So this page is appropriate for the majority users using release 3.7. This page is scheduled to be updated when the next release happens and BiocManager goes live in the Bioc3.8 release. It has been pointed out and we have it as a task to update the useDevel page asap http://www.bioconductor.org/developers/how-to/useDevel/ as this should be updated now for BiocManager. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: James W. MacDonald <jmacdon at uw.edu>
Sent: Tuesday, July 31, 2018 11:24:32 AM
To: Shepherd, Lori
Cc: Tim Triche, Jr.; bioc-devel
Subject: Re: [Bioc-devel] EXTERNAL: introducing BiocManager in devel package pages?
Sent: Tuesday, July 31, 2018 11:24:32 AM
To: Shepherd, Lori
Cc: Tim Triche, Jr.; bioc-devel
Subject: Re: [Bioc-devel] EXTERNAL: introducing BiocManager in devel package pages?
Well, there's this: Package Archives Follow Installation<https://bioconductor.org/install/#install-bioconductor-packages> instructions to use this package in your R session. And the link for the Installation instructions directs you to the page that says to use biocLite. Jim On Tue, Jul 31, 2018 at 10:59 AM, Shepherd, Lori <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>> wrote: Yes DropletUtils has a release and a devel page; as most of the Bioconductor package do. The devel pages have been updated for the BiocManager while the release still are BiocInstaller. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ________________________________ From: Tim Triche, Jr. <tim.triche at gmail.com<mailto:tim.triche at gmail.com>> Sent: Tuesday, July 31, 2018 10:26:31 AM To: Shepherd, Lori Cc: bioc-devel Subject: Re: EXTERNAL: [Bioc-devel] introducing BiocManager in devel package pages? Now I am wondering about my sanity... it seems like perhaps DropletUtils has a release package page too? In any event, looks like things are all set. thanks! --t On Tue, Jul 31, 2018 at 9:21 AM Shepherd, Lori <Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org><mailto:Lori.Shepherd at roswellpark.org<mailto:Lori.Shepherd at roswellpark.org>>> wrote: Where exactly did you see this? It will be up to the package maintainers to update their package documentation (vignettes and such). We have updated the devel package landing pages to include the new BiocManager instructions already: https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html 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 at r-project.org<mailto:bioc-devel-bounces at r-project.org><mailto:bioc-devel-bounces at r-project.org<mailto:bioc-devel-bounces at r-project.org>>> on behalf of Tim Triche, Jr. <tim.triche at gmail.com<mailto:tim.triche at gmail.com><mailto:tim.triche at gmail.com<mailto:tim.triche at gmail.com>>> Sent: Tuesday, July 31, 2018 9:14:24 AM To: bioc-devel Subject: EXTERNAL: [Bioc-devel] introducing BiocManager in devel package pages? So I was looking at DropletUtils and stumbled on this: To install this package, start R and enter: ## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("DropletUtils") It seems like maybe devel might be a sensible place to start migrating users to BiocManager::install(...). Thoughts? --t [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org><mailto:Bioc-devel at r-project.org<mailto: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. 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<mailto:Bioc-devel at r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 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