Question

Error: Bioconductor version '3.8' requires R version '3.5'

1

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romanowska.j ▴ 10

@romanowskaj-20711

Last seen 5.6 years ago

Hi, I have been using bioconductor for a while now, but today suddenly I got this error message when trying to run BiocManager::install()

Error: Bioconductor version '3.8' requires R version '3.5'; see https://bioconductor.org/install

I have R 3.6, so I have no idea why this error appears. I've also re-installed BiocManager, but this didn't help.

software error • 15k views

ADD COMMENT • link updated 5.6 years ago by Mike Smith ★ 6.6k • written 5.6 years ago by romanowska.j ▴ 10

Martin Morgan · Accepted Answer · 2019-05-06

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Mike Smith ★ 6.6k

@mike-smith

Last seen 1 day ago

EMBL Heidelberg

It looks like maybe you've updated R, but are using the same library of packages that were installed when running R 3.5. If you're now using R 3.6 then you want to be using Bioconductor version 3.9. Try running the following to update everything to the newer version of Bioconductor:

BiocManager::install(version = "3.9")

ADD COMMENT • link 5.6 years ago Mike Smith ★ 6.6k

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I am having the same problems after installing R 3.6. BiocManager version is 3.9 but I am unable to upgrade any bioconductor package. Even using BiocUpgrade fails.

> BiocManager::install(version = "3.9")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26)
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help
> biocLite("phyloseq")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.6.0 (2019-04-26).
Installing package(s) ‘phyloseq’
also installing the dependencies ‘Rhdf5lib’, ‘zlibbioc’, ‘rhdf5’, ‘S4Vectors’, ‘IRanges’, ‘XVector’, ‘Biobase’, ‘biomformat’, ‘Biostrings’, ‘multtest’

Warning: unable to access index for repository https://bioconductor.org/packages/3.7/bioc/bin/macosx/el-capitan/contrib/3.6:
  cannot open URL 'https://bioconductor.org/packages/3.7/bioc/bin/macosx/el-capitan/contrib/3.6/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.7/data/annotation/bin/macosx/el-capitan/contrib/3.6:
  cannot open URL 'https://bioconductor.org/packages/3.7/data/annotation/bin/macosx/el-capitan/contrib/3.6/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.7/data/experiment/bin/macosx/el-capitan/contrib/3.6:
  cannot open URL 'https://bioconductor.org/packages/3.7/data/experiment/bin/macosx/el-capitan/contrib/3.6/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.7/workflows/bin/macosx/el-capitan/contrib/3.6:
  cannot open URL 'https://bioconductor.org/packages/3.7/workflows/bin/macosx/el-capitan/contrib/3.6/PACKAGES'
Packages which are only available in source form, and may need compilation of C/C++/Fortran:
  ‘Rhdf5lib’ ‘zlibbioc’ ‘rhdf5’ ‘S4Vectors’ ‘IRanges’ ‘XVector’ ‘Biobase’ ‘Biostrings’ ‘multtest’
Do you want to attempt to install these from sources? (Yes/no/cancel) no
> biocLite("BiocUpgrade")
Upgrade all packages to Bioconductor version 3.8? [y/n]: 
y
Installing package into ‘/Users/eugenioparente/Library/R/3.6/library’
(as ‘lib’ is unspecified)
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help
'BiocInstaller' changed to version 1.30.0
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.6.0 (2019-04-26).

ADD REPLY • link updated 5.6 years ago by Martin Morgan 25k • written 5.6 years ago by parenteeug • 0

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You do not need to use source("https://bioconductor.org/biocLite.R") or biocLite() any more - these have been been deprecated for a while now.

There's more information at http://bioconductor.org/install/ but to summarise you can install a package using BiocManager::install() e.g.

BiocManager::install("phyloseq")

ADD REPLY • link 5.6 years ago Mike Smith ★ 6.6k

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biocLite is used for the R older version of R (<3.5).

ADD REPLY • link 5.6 years ago ravisaroch • 0

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Thanks, I've actually restarted my PC and tried re-installing once more and it worked. Sometimes one just needs to tell the problem out loud and the solution appears ;)

ADD REPLY • link 5.6 years ago romanowska.j ▴ 10