Paul, as Kevin pointed out you have a big mess in /usr/local - I'd recommend renaming /usr/local/include and /usr//local/lib -- then you shouldn't need to set any custom flags at all (at least in R 4.0.0).
Cheers, Simon > On 4/05/2020, at 9:34 AM, Paul Fishwick <metaph...@gmail.com> wrote: > > @Kevin: This worked great. Thanks. I deleted the line in ~/.R/Makevars and > inserted the line > defining CPPFLAGS as you suggested. Rcpp now works in R! I have not yet tried > to compile > a package from source in R but I am guessing (or hoping) that should now work. > > In the mean time, I will read up on the R.framework.......Makeconf file to > understand it. > > I suppose since /usr/local/include is the offending set of headers, I could > just delete > everything from that directory too (after making a backup). I am not doing > any other > development work except for R/Rcpp, so perhaps it will not make a difference. > > However, since your suggested line does work, I'll leave it at this, and see > if I can > build up my knowledge on conflicting include files. > > Thanks again! > > -paul > > > > > On 5/3/20, 2:51 PM, "Kevin Ushey" <kevinus...@gmail.com> wrote: > >> In file included from /usr/local/include/math.h:8: > > The problem here is you have a bunch of headers in /usr/local/include > that are shadowing / overriding the "normal" system header files; > /usr/local/include/math.h being one of these (but I imagine there's > more). > > To work around this, you'll have to explicitly remove the > -I/usr/local/include bit that's part of CPPFLAGS (normally set by > default by an R installation), or clean up your /usr/local/include > directory. For example, in ~/.R/Makevars, you could set: > > CPPFLAGS = -isysroot > /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk > > See the Makeconf file at: > > /Library/Frameworks/R.framework/Resources/etc/Makeconf > > for more information on where the default values for compilation flags > come from. > > Note that setting the above will probably break compilation for other > packages that depend on headers being located in /usr/local/include; > if that is indeed the case your main recourse would be to clean up > /usr/local/include, or find a way to explicitly include your system > headers before /usr/local/include. > > As an aside, the Makevars variables prefixed with PKG_ are normally > reserved for use by package authors (in their own src/Makevars); you > normally shouldn't try to set or override those. See in R-exts: > > https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-Makevars > > for more details. > > Best, > Kevin > > On Sun, May 3, 2020 at 10:17 AM Paul Fishwick <metaph...@gmail.com> wrote: >> >> It was a good suggestion. I went back to installing R 4.0 as you suggested. >> In Rstudio, which I think >> >> uses whatever R happens to be currently installed, I get into >> >> a similar rcpp issue whenever I say “y” to compiling packages from source. >> There seems >> >> to be consistent disconnect of R finding certain files when compilation with >> >> clang is required. >> >> >> >> ………… >> >> >> >> clang -mmacosx-version-min=10.13 >> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG >> -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include >> -I/usr/local/include -fPIC -Wall -g -O2 -c capture.c -o capture.o >> >> In file included from capture.c:1: >> >> In file included from >> /Library/Frameworks/R.framework/Resources/include/Rinternals.h:44: >> >> In file included from >> /Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:41: >> >> In file included from /usr/local/include/math.h:8: >> >> In file included from /usr/local/include/features.h:10: >> >> /usr/local/include/forwards.h:10:10: fatal error: 'config.h' file not found >> >> #include "config.h" >> >> ^~~~~~~~~~ >> >> 1 error generated. >> >> make: *** [capture.o] Error 1 >> >> ERROR: compilation failed for package ‘rlang’ >> >> >> >> …………………. >> >> >> >> From: Carl Ganz <carlg...@gmail.com> >> Date: Sunday, May 3, 2020 at 12:04 PM >> To: Paul Fishwick <metaph...@gmail.com> >> Cc: <rcpp-devel@lists.r-forge.r-project.org> >> Subject: Re: [Rcpp-devel] Cannot run rcpp due to missing include file(s) >> >> >> >> This is probably beyond my understanding at this point, but the solution I >> offered worked for me with R 4.0 and it looks like this example is R 3.6 >> >> >> >> I vaguely remember some issues with interaction between older R version and >> newer Xcode 11.4.1 so moving to R 4 might help >> >> >> >> On Sun, May 3, 2020 at 9:25 AM Paul Fishwick <metaph...@gmail.com> wrote: >> >> Carl >> >> First, thank you for this quick tip! I had no ~/.R directory and Makevars >> didn’t exist when I searched >> >> for it in Finder. So, I made the directdory ~/.R and then added a new file >> “Makevars” to that directory. >> >> I edited this file to add your PKG_CPPFLAGS: >> >> >> >> (base) <hostname>-5:.R paul$ more Makevars >> >> PKG_CPPFLAGS=-I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include >> >> >> >> Now I get another sequence of compiler errors. I’ll include only the first >> several lines: >> >> >> >> ………. >> >> >> >> In file included from fileb6e52d3a23c3.cpp:1: >> >> In file included from >> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27: >> >> In file included from >> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29: >> >> In file included from >> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67: >> >> In file included from >> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100: >> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:317:9: >> error: no member named 'signbit' in the global namespace >> >> using ::signbit; >> >> ~~^ >> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:318:9: >> error: no member named 'fpclassify' in the global namespace >> >> using ::fpclassify; >> >> ~~^ >> >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:319:9: >> error: no member named 'isfinite' in the global namespace; did you mean >> 'finite'? >> >> using ::isfinite; >> >> ~~^ >> >> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/math.h:749:12: >> note: 'finite' declared here >> >> extern int finite(double) >> >> ^ >> >> >> >> From: Carl Ganz <carlg...@gmail.com> >> Date: Sunday, May 3, 2020 at 11:02 AM >> To: Paul Fishwick <metaph...@gmail.com> >> Cc: <rcpp-devel@lists.r-forge.r-project.org> >> Subject: Re: [Rcpp-devel] Cannot run rcpp due to missing include file(s) >> >> >> >> I experienced similar issues on Mac and was able to fix by adding >> PKG_CPPFLAGS=-I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include >> to my .R/Makevars >> >> >> >> My understanding is that Mac no longer uses the /usr/local/include so you >> need to point it to the usr/include in the Developer SDK folder >> >> >> >> On Sun, May 3, 2020 at 8:59 AM Paul Fishwick <metaph...@gmail.com> wrote: >> >> >> >> >> System: Mac OSX 11 (Catalina), Rstudio with R version 3.6.3 (but have also >> tried 4.0 and 3.3), >> >> Xcode version 11.4.1 >> >> >> >> Went to: http://adv-r.had.co.nz/Rcpp.html#rcpp-intro >> >> >> >> and tried library(rcpp) which worked fine because I previously had installed >> the rcpp package. >> >> >> >> The following yields an error in finding config.h. I did a "find" on >> config.h and sure enough it is not >> >> in the clang++ -I directory references. Here is what I have tried: >> >> >> >> Installing Xcode's command line tools (which were installed using >> xcode-select --install) >> >> Also, downloaded and installed the version of clang8 and gfortran6.1 from: >> >> >> >> https://cran.r-project.org/bin/macosx/tools/ >> >> >> >> The following error occurs when I try this rcpp example from Hadley but it >> also happens whenever >> >> I try to install an R package from source. The compile fails due to not >> finding some include file. >> >> >> >> I would have thought that installing clang8 would have also included the >> proper include (.h) file directories >> >> with their contents needed by R. >> >> >> >> Is there something I am missing below? Thank you. >> >> >> >>> library(Rcpp) >>> cppFunction('int add(int x, int y, int z) { >> + int sum = x + y + z; >> + return sum; >> + }') >> In file included from fileb6e52d3a23c3.cpp:1: >> In file included from >> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp.h:27: >> In file included from >> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/RcppCommon.h:29: >> In file included from >> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/r/headers.h:67: >> In file included from >> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100: >> In file included from >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:304: >> In file included from /usr/local/include/math.h:8: >> In file included from /usr/local/include/features.h:10: >> /usr/local/include/forwards.h:10:10: fatal error: 'config.h' file not found >> #include "config.h" >> ^~~~~~~~~~ >> 1 error generated. >> make: *** [fileb6e52d3a23c3.o] Error 1 >> 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"/private/var/folders/bt/1gd00p5s6n19m_bgh9b04gxc0000gp/T/RtmpRRyaky/sourceCpp-x86_64-apple-darwin15.6.0-1.0.4" >> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk >> -I/usr/local/include -fPIC -Wall -g -O2 -c fileb6e52d3a23c3.cpp -o >> fileb6e52d3a23c3.o >> Error in sourceCpp(code = code, env = env, rebuild = rebuild, cacheDir = >> cacheDir, : >> Error 1 occurred building shared library. >>> >> >> _______________________________________________ >> Rcpp-devel mailing list >> Rcpp-devel@lists.r-forge.r-project.org >> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel >> >> _______________________________________________ >> Rcpp-devel mailing list >> Rcpp-devel@lists.r-forge.r-project.org >> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel > > > _______________________________________________ > Rcpp-devel mailing list > Rcpp-devel@lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel _______________________________________________ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
