News: Bioconductor 3.8 is released
4
gravatar for Valerie Obenchain
12 months ago by
United States
Valerie Obenchain6.7k wrote:
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
news bioconductor release • 559 views
ADD COMMENTlink modified 11 months ago by restat1100 • written 12 months ago by Valerie Obenchain6.7k

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 REPLYlink written 12 months ago by Diego Diez750

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 REPLYlink written 12 months ago by Jenny Drnevich1.9k

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Bioconductor version '3.7' is out-of-date; the current release version '3.8' is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 REPLYlink written 12 months ago by Martin Morgan ♦♦ 24k
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 REPLYlink modified 12 months ago by Martin Morgan ♦♦ 24k • written 12 months ago by Jenny Drnevich1.9k
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