Build error on Mac OS X

[afrubin]

Installation fails on Mac OS X because -fopenmp is not supported:

* installing *source* package ‘malan’ ...
** libs
clang++ -std=gnu++11 -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/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/RcppProgress/include" -I/usr/local/include  -fopenmp  -fPIC  -Wall -g -O2 -c PROTO.cpp -o PROTO.o
clang: error: unsupported option '-fopenmp'
make: *** [PROTO.o] Error 1
ERROR: compilation failed for package ‘malan’

It appears this is a common issue (see discussion and resolution here velocyto-team/velocyto.R#2) and may involve installing another version of llvm via homebrew.

Is it possible to change the build scripts to work around this?

[mikldk]

Thanks for discovering this. I think I just have to disable OpenMP for Armadillo in Makevars, but I'll have to test it first (maybe on Travis). I'll get back :-).

[mikldk]

I was able to reproduce this. Thank you for discovering and reporting it.

It should be fixed by 616bf58 that disables OpenMP. See also Travis where I have now added OSX target: https://travis-ci.org/mikldk/malan.

Can you confirm that it now compiles and works on Mac OS X for you, too?

[afrubin]

Great, this works for me now.

I should add that as a workaround I tried installing into a new conda environment. This worked since conda has its own version of llvm, but for some reason the vignettes were not installed:

> library('malan')
> vignette(package = 'malan')
no vignettes found

I did some google searching and this might be a bug when installing from GitHub, but the vignettes do appear when installing from GitHub in RStudio.

[mikldk]

Good to hear. Closing as this should be resolved.