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News:Bioconductor 3.8 is released

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Valerie Obenchain ★ 6.8k

@valerie-obenchain-4275

Last seen 2.9 years ago

United States

Thanks to all developers and community members for contributing to the project!

Please see the full release announcement here:

   https://www.bioconductor.org/news/bioc_3_8_release/

The Bioconductor Team

bioconductor news release News • 1.9k views

ADD COMMENT • link updated 6.0 years ago by restat110 • 0 • written 6.1 years ago by Valerie Obenchain ★ 6.8k

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I found that because I was using already BiocManager with Bioc 3.7 I had to use BiocManager::install(version = "3.8") in order to upgrade to Bioc 3.8.

ADD REPLY • link 6.1 years ago Diego Diez ▴ 760

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Yes - I happen to be teaching a workshop tomorrow on Bioconductor, and the new way to upgrade to BioC took me a while to find. Previously, biocLite() would check and give a message that a newer version of Bioconductor was available for your version of R, but it doesn't like BiocManager::install() has that check in place (yet?)!

ADD REPLY • link 6.1 years ago Jenny Drnevich ★ 2.0k

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If you had transitioned to BiocManager already for version 3.7, the following message shows up

$ bioc-3.7
> library(BiocManager)
Bioconductor version 3.7 (BiocManager 1.30.3), ?BiocManager::install for help
Bioconductor version '3.7' is out-of-date; the current release version '3.8' is
  available with R version '3.5'; see https://bioconductor.org/install

I guess BiocInstaller is silent about upgrading; we'll look in to that...

ADD REPLY • link 6.1 years ago Martin Morgan 25k

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Ah – now I see the message! You have to explicitly load the BiocManager package. The main install page and all the package landing pages call the install via BiocManager::install(), which as you said is silent. Probably would be good to add the warning to this as well when you get the chance. As always, thanks for all the work that you & the Bioconductor team do! Happy Halloween, Jenny

ADD REPLY • link updated 6.1 years ago by Martin Morgan 25k • written 6.1 years ago by Jenny Drnevich ★ 2.0k