I have installed bioconductor, R still asks me to install it
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luhan.ni • 0
@luhanni-22713
Last seen 18 months ago

local({pkg <- select.list(sort(.packages(all.available = TRUE)),graphics=TRUE) + if(nchar(pkg)) library(pkg, character.only=TRUE)}) Bioconductor version 3.10 (BiocManager 1.30.10), ?BiocManager::install for help

source("http://www.bioconductor.org/biocLite.R") Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install

sessionInfo() R version 3.6.2 (2019-12-12) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale: [1] LCCOLLATE=EnglishUnited States.1252 LCCTYPE=EnglishUnited States.1252 LCMONETARY=EnglishUnited States.1252 [4] LCNUMERIC=C LCTIME=English_United States.1252

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] BiocManager_1.30.10

loaded via a namespace (and not attached): [1] compiler3.6.2 tools3.6.2

bioconductor biocLite GEOquery package • 218 views
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@steve-lianoglou-2771
Last seen 18 hours ago
Denali

I don't see a question here, so I'm not sure how best to help you, however you should not be using the older "biocLite"-based installation methods these days.

I see in your post you have source("http://www.bioconductor.org/biocLite.R").

That method is no longer supported to install and manage bioconductor packages.

These days, in order to install and manage your bioconductor packages, you first have to install the BiocManager package from CRAN, then use its BiocManager::install() method to install the packages you want.

Also, it seems you may have a mismash of package versions installed, and it wouldn't hurt to run BiocManager::valid() first to what messages / warnings it generates.

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