Installation error on Mac

ksadtle3 commented 6 years ago

Hi, I am trying to work through the FlowJo plugin for SPADE. And currently am having an issue on one of my computers (of course the one with more processing power) where I cannot get the SPADE package to download in R. Apologies if this is an obvious/simple error to fix -- I am not well versed in R. Here is the error I am receiving:

> install_github("nolanlab/Rclusterpp")
Downloading GitHub repo nolanlab/Rclusterpp@master
from URL https://api.github.com/repos/nolanlab/Rclusterpp/zipball/master
Installing Rclusterpp
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save  \
  --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/4r/wqfd9gm11z14vsmt57qy7thc0000gn/T/RtmplAojvg/devtools2b24e66c3d8/nolanlab-Rclusterpp-740cb0b'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests 

* installing *source* package ‘Rclusterpp’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppEigen/include" -I/usr/local/include  -I../inst/include -fopenmp -fPIC  -Wall -g -O2  -c hclust.cpp -o hclust.o
clang: error: unsupported option '-fopenmp'
make: *** [hclust.o] Error 1
ERROR: compilation failed for package ‘Rclusterpp’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rclusterpp’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rclusterpp’
Installation failed: Command failed (1)

lifengt commented 6 years ago

I have a same issue with you. Hope someone can help us.

SamGG commented 6 years ago

Hi, the error states a problem with installing Rclusterpp. I think the best is to post your message to the Rclusterpp Github repository. Robert Bruggner is the maintainer of Rclusterpp and knows everything about compilation on Mac. https://github.com/nolanlab/Rclusterpp

zbjornson commented 6 years ago

Can you try the steps listed here please? https://github.com/velocyto-team/velocyto.R/issues/2#issuecomment-346193485

Sounds like using an older version of R might work also, but that's not a very nice solution.

zbjornson commented 6 years ago

A more direct link to R's instructions: https://cloud.r-project.org/bin/macosx/tools/

nolanlab / spade

Installation error on Mac #137