Issues with installing Bioconductor packages (eg GEOquery)
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Isabel • 0
@a3b98862
Last seen 7 days ago
United Kingdom

Hello, I am an R newbie and was following the instructions from the Sheffield Bioinformatics Core tutorial to download and analyse GEO data (https://sbc.shef.ac.uk/geo_tutorial/tutorial.nb.html).

I have the latest R version (4.4) and the latest Bioconductor version (3.19), with BiocManager installed, but I cannot install other packages, such as GEOquery. The message says there are version compatibility issues (see below).

Any ideas, or is there something obvious I am missing? Thank you!

> BiocManager::install("GEOquery")
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0 (2024-04-24)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'GEOquery'
GEOquery Bioconductor • 196 views
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@sean-davis-490
Last seen 3 days ago
United States

The GEOquery package is installed, but you still need to load the library. You can check what packages are installed with:

installed.packages()

An installed package still needs to be loaded into your R session. The typical way to do that for a package is to use (for GEOquery as an example):

library(GEOquery)

Then, you should be able to use getGEO() since the package has been loaded.

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Got it now, thank you!

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ATpoint ★ 4.2k
@atpoint-13662
Last seen 10 hours ago
Germany

Read the warning. The package is already installed. It's fine.

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Thank you, but when I try to use the getGEO function as per the tutorial I get the error below - not sure I am doing this right.

gse <- getGEO(my_id) Error in getGEO(my_id) : could not find function "getGEO"

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You need to library() the package first. Please consider to take a basic R course first before diving into analysis.

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