Bioconducter can not be installed on latest RStudio
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@c8321344
Last seen 5 weeks ago
India

Enter the body of text here

Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
ERROR: configuration failed for package ‘xml2’
* removing ‘/home/scis/R/x86_64-pc-linux-gnu-library/4.2/xml2’
ERROR: dependency ‘RCurl’ is not available for package ‘GenomeInfoDb’
* removing ‘/home/scis/R/x86_64-pc-linux-gnu-library/4.2/GenomeInfoDb’
ERROR: dependency ‘curl’ is not available for package ‘httr’
* removing ‘/home/scis/R/x86_64-pc-linux-gnu-library/4.2/httr’
ERROR: dependency ‘GenomeInfoDb’ is not available for package ‘Biostrings’
* removing ‘/home/scis/R/x86_64-pc-linux-gnu-library/4.2/Biostrings’
ERROR: dependencies ‘curl’, ‘httr’ are not available for package ‘BiocFileCache’
* removing ‘/home/scis/R/x86_64-pc-linux-gnu-library/4.2/BiocFileCache’
ERROR: dependencies ‘httr’, ‘Biostrings’ are not available for package ‘KEGGREST’
* removing ‘/home/scis/R/x86_64-pc-linux-gnu-library/4.2/KEGGREST’
ERROR: dependency ‘KEGGREST’ is not available for package ‘AnnotationDbi’
* removing ‘/home/scis/R/x86_64-pc-linux-gnu-library/4.2/AnnotationDbi’
**ERROR: dependencies ‘XML’, ‘AnnotationDbi’, ‘httr’, ‘BiocFileCache’, ‘xml2’ are not available for package ‘biomaRt’**
* removing ‘/home/scis/R/x86_64-pc-linux-gnu-library/4.2/biomaRt’
AnnotationDbi biomaRt Bioconductor • 113 views
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Mike Smith ★ 5.7k
@mike-smith
Last seen 16 hours ago
EMBL Heidelberg / de.NBI

There's very little information to work with here, but my guess is that you're missing some linux system libraries. The xml2 package requires libxml and curl and RCurl require libcurl. There's probably some information on how to install them for your system included in the installation output that is printed to screen, although it's easy to miss in the wall of text.

If you're running Ubuntu I'd suggest trying the following in a terminal:

sudo apt-get install libxml2-dev libcurl4-openssl-dev

Then restart R and try the package installation again. You'll need to do something slightly different if you're using a different Linux distribtution.

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