Problem installing Velocyto

[aelias1]

I have installed the following packages already: pcaMethods hdf5r

However...when I use the code: install_github("velocyto-team/velocyto.R") I receive the error: clang: warning: no such sysroot directory: '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk' [-Wmissing-sysroot] clang: error: unsupported option '-fopenmp' make: *** [RcppExports.o] Error 1 ERROR: compilation failed for package ‘velocyto.R’

• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/velocyto.R’ Error: Failed to install 'velocyto.R' from GitHub: (converted from warning) installation of package ‘/var/folders/dl/6g933l1j7tq59tn5qx_d1q700000gn/T//RtmpZObUxq/file39944ede999a/velocyto.R_0.6.tar.gz’ had non-zero exit status

Please help me resolve this. Thank you!

[ahadkhalilnezhad]

Hello, More probably, this is what to do to resolve it (reference; https://github.com/BUStools/BUSpaRse):

First, download and install the appropriate (latest) version of the Clang compiler from: https://cran.r-project.org/bin/macosx/tools/

Second, in RStudio:

• Use file.exists("~/.R/Makevars") to check if "~/.R/Makevars" exists.
• Use dir.exists("~/.R") to check that if the "~/.R directory" exists. If it does not, then use dir.create("~/.R") to create the directory.
• Use file.create("~/.R/Makevars") to create that file.
• Navigate to that file in the Files pane in RStudio, open that file in RStudio, and edit it. Then, add the following to the ~/.R/Makevars file:

CC=/usr/local/clang6/bin/clang SHLIB_CXXLD=/usr/local/clang6/bin/clang++ CXX= /usr/local/clang6/bin/clang++ -Wall CXX1X= /usr/local/clang6/bin/clang++ CXX98= /usr/local/clang6/bin/clang++ CXX11= /usr/local/clang6/bin/clang++ CXX14= /usr/local/clang6/bin/clang++ CXX17= /usr/local/clang6/bin/clang++ LDFLAGS=-L/usr/local/clang6/lib

This worked nicely for me, I hope it does for you as well.

[Runuply]

https://daijiang.name/en/2017/06/21/fopenmp-option-of-clang-error/

check this

[evanbiederstedt]

There's a solution provided here: https://github.com/kharchenkolab/conos/wiki/Installing-Conos-for-Mac-OS