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Victorian-Bioinformatics-Consortium / degust

Deprecated : Use https://github.com/drpowell/degust
GNU General Public License v3.0
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R packaged limma not found #10

Closed Bjoernsen closed 7 years ago

Bjoernsen commented 10 years ago

Hi,

the back-end analysis did not work for me, because limma was not installed. But this problem was not fixed, after installing limma (and edgeR).

I was able to fix this issue by changing the R library path hard coded in app/backend/r-json.hs

Original line 262:

(_,out,err,pid) <- runInteractiveProcess "Rscript" ["--vanilla",inF] Nothing
                             (Just [("R_LIBS_SITE","/bio/sw/R:")])

New line 262:

(_,out,err,pid) <- runInteractiveProcess "Rscript" ["--vanilla",inF] Nothing
                             (Just [("R_LIBS_SITE","/path/to/my/R/library:")])
drpowell commented 10 years ago

I'd forgotten that. I guess the best solution is to have r-json read a config file of some sort at startup

drpowell commented 7 years ago

Not a problem on the new site : degust.erc.monash.edu