Cannot install on mac

[tylermanning]

What versions does this package work with? I've tried 3.3, 3.6, different ways to install. Nothing is working.

[AnthonyEbert]

It should work with both those R versions. How did you try to install it? What error messages did you get?

FYI It's not yet available on CRAN, you need to install the devtools library and then run devtools::install_github("AnthonyEbert/EasyMMD")

[tylermanning]

this is the stack trace, everytime i solve one issue and new one pops up

`

devtools::install_github("AnthonyEbert/EasyMMD")
Downloading GitHub repo AnthonyEbert/EasyMMD@master
✔ checking for file ‘/private/var/folders/w6/r7lqmtbs6lqfs1x9nvtl5q400000gn/T/RtmpcRJMzT/remotes11b403cdb13f4/AnthonyEbert-EasyMMD-a81a8a8/DESCRIPTION’ ...
─ preparing ‘EasyMMD’:
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Removed empty directory ‘EasyMMD/other’
─ building ‘EasyMMD_0.5.3.tar.gz’

• installing source package ‘EasyMMD’ ...
  ** using staged installation
  ** libs
  clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c MMD_full_loop.cpp -o MMD_full_loop.o
  clang: error: unsupported option '-fopenmp'
  make: *** [MMD_full_loop.o] Error 1
  ERROR: compilation failed for package ‘EasyMMD’
• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/EasyMMD’
  Error: Failed to install 'EasyMMD' from GitHub:
  (converted from warning) installation of package ‘/var/folders/w6/r7lqmtbs6lqfs1x9nvtl5q400000gn/T//RtmpcRJMzT/file11b4062bc4d7d/EasyMMD_0.5.3.tar.gz’ had non-zero exit status
  `

[AnthonyEbert]

Strange... could you try

install.packages("RcppArmadillo")

[tylermanning]

That installed no problem it seems:

`

install.packages("RcppArmadillo")
Warning in install.packages :
cannot open URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/PACKAGES.rds': HTTP status was '404 Not Found'
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.6/RcppArmadillo_0.9.700.2.0.tgz'
Content type 'application/x-gzip' length 1740941 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

The downloaded binary packages are in
/var/folders/w6/r7lqmtbs6lqfs1x9nvtl5q400000gn/T//RtmpMNGhuz/downloaded_packages
Warning message:
R graphics engine version 12 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed.
`

[AnthonyEbert]

I don't know... I'll test it out on mac.

[AnthonyEbert]

I tried to install on mac and had your same error

* installing *source* package ‘EasyMMD’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Users/userlJYTh4an/R/Rcpp/include" -I"/Users/userlJYTh4an/R/RcppArmadillo/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp  -fPIC  -Wall -g -O2  -c MMD_full_loop.cpp -o MMD_full_loop.o
clang: error: unsupported option '-fopenmp'
make: *** [MMD_full_loop.o] Error 1
ERROR: compilation failed for package ‘EasyMMD’
* removing ‘/Users/userlJYTh4an/R/EasyMMD’

I don't know how to fix it at the moment. Maybe there is some useful information here
velocyto-team/velocyto.R#2

[tylermanning]

thanks for the help, im gonna give up for now and go back to python

[tylermanning]

I got it working on Linux. Does the quadratic MMD work with matrices? Can you provide a toy test case cause I've tried several combinations and it keeps throwing a mat mult error.

[AnthonyEbert]

I have only implemented the exponential kernel (radial basis function) in EasyMMD.

Here is the example you asked for.

This code is now included in the help file for the MMD function:

library(mvtnorm)

x <- rmvnorm(100, c(0,0), diag(c(2,2)))
sigma <- matrix(c(2,1.5,1.5,2), ncol=2)
y <- rmvnorm(100, c(0,0), sigma = sigma)

MMD(y, x, var = diag(c(0.5, 0.5)), bias = TRUE)