Question

Cannot install Bioconductor Packages. Cannot install BiocManager.

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reventropy2003 ▴ 10

@reventropy2003-14321

Last seen 6.2 years ago

It looks like the new release has moved away from biocLite and is now using the BiocManager. R is telling me that the package is not available for version 3.4.1. The version of R I'm using is only a year old and I'd rather not upgrade to an unstable release. Is there a workaround?

software error bioconductor biocmanager • 11k views

ADD COMMENT • link updated 6.2 years ago by shepherl 4.1k • written 6.2 years ago by reventropy2003 ▴ 10

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For previous versions of R / Bioconductor, the 'old fashioned' approach of using biocLite() should still work. What are you trying to do?

ADD REPLY • link 6.2 years ago Martin Morgan 25k

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I'm trying to install bioconductor and/or any bioconductor package using the instructions on the install page. When I try to install bioconductor using:

if (!requireNamespace("BiocManager"))
    install.packages("BiocManager")
BiocManager::install()

It says my R version (3.4.1) is incompatible. Because of this I cannot install any package because I don't have BiocManager installed. The package I was originally trying to install was "BioSeqClass".

ADD REPLY • link 6.2 years ago reventropy2003 ▴ 10

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If you want to use an old version of Bioconductor, use the old mechanism for installation

source("https://bioconductor.org/biocLite.R")
biocLite("BioSeqClass")

ADD REPLY • link 6.2 years ago Martin Morgan 25k

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Okay. I was able to reinstall Bioconductor and the packages I needed using biocLite. Why have all of the references to biocLite been removed from the Bioconductor install pages? This change is likely going to cause mass frustration for the majority of users who don't have the newest version of R.

ADD REPLY • link 6.2 years ago reventropy2003 ▴ 10

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I'm in the exact same boat and this is frustrating. I don't have access to the newest version of R, and need this for running important statistics. I'm currently relying on Google's cached version of bioconductor's help pages, and that's no good!

ADD REPLY • link 6.2 years ago ajdude • 0

score 0 · Answer 1 · 2018-11-13

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shepherl 4.1k

@lshep

Last seen 2 days ago

United States

Please note we now have an updated install page that has a section for Legacy and Older versions of R. We still would always recommend updating to the latest version of R and packages but if this is not possible the installation instructions are now available.

ADD COMMENT • link 6.2 years ago shepherl 4.1k