Question: Can't install 'lumi'
1
gravatar for stewart999
3.1 years ago by
stewart99910
stewart99910 wrote:

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 • 917 views
ADD COMMENTlink modified 3.1 years ago by Martin Morgan ♦♦ 24k • written 3.1 years ago by stewart99910

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

ADD REPLYlink written 3.1 years ago by James W. MacDonald52k
Answer: Can't install 'lumi'
1
gravatar for Martin Morgan
3.1 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

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

ADD COMMENTlink written 3.1 years ago by Martin Morgan ♦♦ 24k
Answer: Can't install 'lumi'
1
gravatar for smhughes
3.1 years ago by
smhughes10
smhughes10 wrote:

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")

 

ADD COMMENTlink written 3.1 years ago by smhughes10
Answer: Can't install 'lumi'
1
gravatar for Gordon Smyth
3.1 years ago by
Gordon Smyth39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth39k wrote:

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().

ADD COMMENTlink written 3.1 years ago by Gordon Smyth39k
Answer: Can't install 'lumi'
0
gravatar for Martin Morgan
3.1 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

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

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Martin Morgan ♦♦ 24k
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