Package installation errors for Bioconductor and easyRNASeq
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@michaeldhar-9369
Last seen 7.2 years ago

 

Hello,

I am trying to run some Bioconductor and easyRNASeq packages for a biology lab on an HPC system. However, I have been unable to install those R packages. Below are the installation commands, entered from within an R session, and the resulting error messages. Please let me know if you see the resolution to my issue. Thank you

 

1) Bioconductor

Commands:

source("http://bioconductor.org/biocLite.R")

biocLite()

 

 

Error Messages:

Warning message:

installed directory not writable, cannot update packages 'boot', 'class',

  'cluster', 'codetools', 'foreign', 'KernSmooth', 'lattice', 'Matrix', 'mgcv',

  'nlme', 'nnet', 'rpart', 'spatial', 'survival' 

 

2) easyRNASeq

Commands

source("http://bioconductor.org/biocLite.R")

biocLite("easyRNASeq")

 

Errors:

checking for curl-config... no

Cannot find curl-config

ERROR: configuration failed for package ‘RCurl’

* removing ‘/home/mid224/R/x86_64-unknown-linux-gnu-library/3.0/RCurl’

ERROR: dependency ‘RCurl’ is not available for package ‘biomaRt’

* removing ‘/home/mid224/R/x86_64-unknown-linux-gnu-library/3.0/biomaRt’

ERROR: dependency ‘biomaRt’ is not available for package ‘easyRNASeq’

* removing ‘/home/mid224/R/x86_64-unknown-linux-gnu-library/3.0/easyRNASeq’

installation biocinstaller easyrnaseq • 1.3k views
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arfranco ▴ 130
@arfranco-8341
Last seen 19 hours ago
European Union
installed directory not writable

This means you have not permission to write

Run R or RStudio with the sudo option

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@martin-morgan-1513
Last seen 3 days ago
United States

As @arfranco notes, the warning messages (NOT errors) in (1) are because the packages were installed as root, whereas you are running as non-root. There is no requirement for R (and it's base packages) to be installed as root, so the better practice is to install it as a regular user. 

The curl problem is because your system requires the 'dev' version of libcurl, e.g., 

sudo apt-get install libcurl4-openssl-dev

Likely you will also need libxml2-dev.

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