Thanks -- the solution I used was to install the Simon-Urbanek-modified distribution clang 8.0 from the page noted in my reply.
On Wed, Dec 4, 2019 at 3:10 PM Bunis, Daniel <daniel.bu...@ucsf.edu> wrote: > I was running into the `clang: *error: *unsupported option '-fopenmp’` > yesterday myself. I’m not on Sierra, but I fixed it with the top answer on > this page: > https://stackoverflow.com/questions/43595457/alternate-compiler-for-installing-r-packages-clang-error-unsupported-option/43943631#43943631?newreg=e3bd1c44b597485f981795398d9432b6. > > > Specifically, I used the solution #3 there to turn of the addition of the > -fopenmp option: > 1) Made a folder in my `~/` called .R > 2) Made a file in ~/.R/Makevars containing: > > SHLIB_OPENMP_CFLAGS= > SHLIB_OPENMP_CXXFLAGS= > > Then I was able to install all the packages for which I’d been getting the > -fopenmp error. > > I hope this solution works for you as well! > -Dan > > On Dec 4, 2019, at 8:07 AM, Kasper Daniel Hansen < > kasperdanielhan...@gmail.com> wrote: > > Are you using the clang 6 (R 3.5) / 7 (R 3.6) / 8 (R 4.0) which Simon > supplies? > > This is for clang 6 with full path > > /usr/local/clang6/bin/clang --version > clang version 6.0.0 (tags/RELEASE_600/final) > Target: x86_64-apple-darwin18.7.0 > Thread model: posix > InstalledDir: /usr/local/clang6/bin > > On Wed, Dec 4, 2019 at 11:03 AM Vincent Carey <st...@channing.harvard.edu> > wrote: > > When installing packages from source, > > I frequently run into this error with > > > %vjcair> clang --version > > Apple LLVM version 9.0.0 (clang-900.0.39.2) > > Target: x86_64-apple-darwin16.7.0 > > Thread model: posix > > InstalledDir: > > > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin > > > I am still running macos Sierra ... is there a solution within this > platform? I have been getting around this by modifying Makevars when > needed > > > > * installing *source* package ‘sitmo’ ... > > ** package ‘sitmo’ successfully unpacked and MD5 sums checked > > ** using staged installation > > ** libs > > clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG > -I../inst/include/ > > > -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' > -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk > -I/usr/local/include -fopenmp -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 ‘sitmo’ > > -- > The information in this e-mail is intended only for th...{{dropped:15}} > > > _______________________________________________ > Bioc-devel@r-project.org mailing list > > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=iORugZls2LlYyCAZRB3XLg&r=basuzE7-VlMupNUhjOlOjq3Z71OZ7WVlqjvCai9jtug&m=8ndw52WAHTohPcPQItPQQDlzi2GSSFsa48rBNYORZzQ&s=3Bk4CmiTOaGnnX2gf7KvkUvv3pW8P1ek4otRy5jvrPE&e= > > > -- The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel