Can't install 'lumi'
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stewart999 ▴ 10
@stewart999-11769
Last seen 10 months ago
United Kingdom

I've compiled and installed R-3.3.2 but can't install lumi

 

I'm not sure if lumi is still in development or if it's not properly indexed in bioconductor as the release page for lumi (https://www.bioconductor.org/packages/release/bioc/html/lumi.html) has the string "Bioconductor version: Development (3.4)". If I click on the "stable release version" link it takes me back to the same page. Any help appreciated.

 

Cheers, Stewart

lumi • 1.4k views
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How did you try to install lumi? What was the error message? What is the output from sessionInfo()?

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@martin-morgan-1513
Last seen 17 days ago
United States

lumi is failing to build in release and devel, the maintainers have been contacted / harassed, but have not yet responded with an update.

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smhughes ▴ 10
@smhughes-11737
Last seen 3.4 years ago

I had this problem as well, and was able to successfully install the package by installing from source from github. 

# install.packages("devtools") # if you don't have it
devtools::install_github("Bioconductor-mirror/lumi")

 

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@gordon-smyth
Last seen 28 minutes ago
WEHI, Melbourne, Australia

If you can't get lumi, then the limma package also provides excellent functionality for reading and pre-processing Illumina microarrays. See the functions read.idat(), read.ilmn() and neqc().

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@martin-morgan-1513
Last seen 17 days ago
United States

lumi is again available in release (version 2.26.2) and devel, biocLite("lumi").

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