Trouble Installing

[harpe300]

Hello,

When I try to install your neurosurf package, R errors out because it cannot install the rflann package (which I assume is installed along with neurosurf) (see below for R output; R version 3.6.1). I've tried installing rflann alone, but R cannot install that either.

Any idea on how I can successfully install your package?

Thank you, Jeremy

devtools::install_github("bbuchsbaum/neurosurf") Downloading GitHub repo bbuchsbaum/neurosurf@master These packages have more recent versions available. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: RcppEigen (0.3.3.5.0 -> 0.3.3.7.0) [CRAN] 5: xfun (0.11 -> 0.12 ) [CRAN] 6: callr (3.3.2 -> 3.4.0 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3 Downloading GitHub repo bbuchsbaum/neuroim2@master These packages have more recent versions available. Which would you like to update?

1: All
2: CRAN packages only
3: None
4: RcppEigen (0.3.3.5.0 -> 0.3.3.7.0) [CRAN] 5: xfun (0.11 -> 0.12 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3 Downloading GitHub repo YeeJeremy/rflann@master ─ preparing ‘rflann’:/private/var/folders/zm/7kjqttgj2mxbfqdvkry804d00000gp/T/Rtmpp8uOGx/remotes10bf56d28c132/YeeJeremy-rflann-e0c06e7/DESCRIPTION’ ... checking DESCRIPTION meta-information ...

• installing source package ‘rflann’ ... 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 -I. -I.. -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang: error: unsupported option '-fopenmp' make: *** [RcppExports.o] Error 1 ERROR: compilation failed for package ‘rflann’
• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rflann’ Error: Failed to install 'neurosurf' from GitHub: Failed to install 'neuroim2' from GitHub: Failed to install 'rflann' from GitHub: (converted from warning) installation of package ‘/var/folders/zm/7kjqttgj2mxbfqdvkry804d00000gp/T//Rtmpp8uOGx/file10bf5ea3f19b/rflann_1.5.tar.gz’ had non-zero exit status

  install.packages('rflann')

[bbuchsbaum]

yes, at some point rflann got dropped from CRAN. We can still use it via the github resource: https://github.com/YeeJeremy/rflann

However, it must be compiled from source and that is where you're having a problem.

The key error is:

clang: error: unsupported option '-fopenmp'

Your compiler does not support "openmp". I refer you to this blog for a workaround.

https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/

[harpe300]

Fantastic, this worked. Thank you!

Jeremy

On Jan 16, 2020, at 8:57 PM, bbuchsbaum notifications@github.com wrote:

yes, at some point rflann got dropped from CRAN. We can still use it via the github resource: https://github.com/YeeJeremy/rflann https://github.com/YeeJeremy/rflann However, it must be compiled from source and that is where you're having a problem.

The key error is:

clang: error: unsupported option '-fopenmp'

Your compiler does not support "openmp". I refer you to this blog for a workaround.

https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/ https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/bbuchsbaum/neurosurf/issues/1?email_source=notifications&email_token=ANRKVG2TG3LNUKQJQOFL2PTQ6ENBLA5CNFSM4KHNBUD2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEJGIZFQ#issuecomment-575442070, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANRKVG525GUKTKYFMROCVWLQ6ENBLANCNFSM4KHNBUDQ.