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Question: unable to find Lumi package in R
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gravatar for nayeli0126
21 months ago by
nayeli01260
nayeli01260 wrote:

I am using Bioconductor 3.2, R 3.2.3 and cannot seem to get Lumi to operate. Everytime I try to initaite lumi I get this error

> library(lumi)
Error : .onLoad failed in loadNamespace() for 'rgl', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rgl/libs/rgl.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rgl/libs/rgl.so, 6): Library not loaded: /opt/X11/lib/libGLU.1.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rgl/libs/rgl.so
  Reason: image not found
Error: package or namespace load failed for ‘lumi’

 

 

I have uninstalled and re-installed R and tried installing thorugh package instead of using biocLite. I was only able to get it to work for a short amount of time but I had to use an older version of R which is not compatible with lumiHumanAll.db which I also need.

 

Any help would be appreciated

 

ADD COMMENTlink modified 21 months ago by Steve Lianoglou12k • written 21 months ago by nayeli01260
1
gravatar for Steve Lianoglou
21 months ago by
Genentech
Steve Lianoglou12k wrote:

The error is due to lumi (apparently) trying to load the rgl package, which (in turn) requires that you have a working X11 installed on your system.

According to this stackoverflow thread, you just need to go download XQuartz from macosforge onto your system and you should be good to go.

Install that, then make sure you can load the rgl package (via library(rgl)) then you can proceed from there. Definitely stick with the most current version of R/biocondcutor.

ADD COMMENTlink written 21 months ago by Steve Lianoglou12k

Also note that according to the XQuartz doc, after installing XQuartz, you need to log out of your Mac and log back in before XQuartz will work.

ADD REPLYlink written 21 months ago by Dan Tenenbaum ♦♦ 8.2k
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