Simon. I’ll do that. Thanks. Paul Paul Fishwick, PhD Distinguished University Chair of Arts, Technology, and Emerging Communication Professor of Computer Science Director, Creative Automata Laboratory The University of Texas at Dallas Arts & Technology 800 West Campbell Road, AT10 Richardson, TX 75080-3021 Home: utdallas.edu/atec/fishwick Media: medium.com/@metaphorz Modeling: digest.sigsim.org Twitter: @PaulFishwick
> On May 4, 2020, at 2:39 AM, Simon Urbanek <simon.urba...@r-project.org> wrote: > > 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 >
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