Re: [R-SIG-Mac] catalina humbug
Roger, check your ~/.R - it looks like you may have custom ~/.R/Makevars which overrides the CRAN R settings. Cheers, Simon > On Oct 15, 2020, at 1:14 AM, Koenker, Roger W wrote: > > Humm… so I have now removed clang7 from /usr/local and I now see: > > /usr/local/clang7/bin/clang > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG > -I/usr/local/clang7/include/c++/v1 -fPIC -Wall -g -O2 -c mcmb.c -o mcmb.o > /bin/sh: /usr/local/clang7/bin/clang: No such file or directory > > But unfortunately I still don’t see where R CMD build is asking for clang7. > I tried reinstalling R > after removing clang7 but this didn’t change the result above. Nothing in my > environment or > in .Rprofile refers to clang > > My ChangeLog reveals that I had a similar problem a couple of years ago, but > unhelpfully it doesn’t reveal > how it was fixed, only that the one C source file of the package was removed > for a while, and then reinstated > after resolving a problem with header files for clang6. > > Roger > > > > >> On Oct 14, 2020, at 12:36 PM, Ken Beath wrote: >> >> clang7 seems to be unnecessary for current R. It isn’t in my system and from >> memory was one of the things I removed to get everything working. This >> involved removing the clang and fortran that had been previously installed. >> I may have needed some other things but my systems will build your package. >> >> Ken >> >>> On 14 Oct 2020, at 10:01 pm, Koenker, Roger W wrote: >>> >>> Simon, >>> >>> Thanks, I still have the same error: >>> >>> In file included from mcmb.c:11: >>> /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' >>> file not found >>> #include_next >>> >>> I didn’t do anything beyond upgrading R and installing fortran 8.2.0, and >>> the CLT 12.2. >>> but I didn’t remove anything, should I have? I now see: >>> >>> yzzy: which clang >>> /usr/bin/clang >>> yzzy: clang --version >>> Apple clang version 12.0.0 (clang-1200.0.32.2) >>> Target: x86_64-apple-darwin19.6.0 >>> Thread model: posix >>> InstalledDir: >>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin >>> >>> >>> The last time I faced this sort of thing James suggested this: >>> https://groups.google.com/g/r-sig-mac/c/rZeYeiyyxtY >>> >>> but the names and locations are somewhat different now, so I’m reluctant to >>> experiment. >>> >>> Roger >>> >>> >>> On Oct 14, 2020, at 11:48 AM, Simon Urbanek wrote: Roger, the error points to an old local clang - did you remove (or move aside) that one? Check your /usr/local - you seem to have some old stuff there that is breaking. That would solve the original issue. You seem to have done a lot after that error, but didn't tell us what happened then… you can't have the same error if you removed it ;) Cheers, Simon > On Oct 14, 2020, at 10:28 PM, Koenker, Roger W > wrote: > > I’ve recently “upgraded” to catalina, and compilation of my quantreg > package failed with: > > In file included from mcmb.c:11: > /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' > file not found > #include_next > > So I’ve tried the following: > > 1. Upgraded R to 4.0.3 > 2. Upgraded the fortran compiler to 8.2.0 as suggested. > 3. Attempted to reinstall command line tools with Xcode-select > —install. This fails with > a popup that says: > > Can’t install the software because it is not currently > available from the Software Update server. > 4. Tried again to reinstall Command line tools 12.2 beta 3 from > https://developer.apple.com/download/more/ > which successfully installed, but my stdio.h error persisted. > 5. Following thread: > http://r-sig-mac.29524.n8.nabble.com/R-SIG-Mac-fatal-error-stdio-h-file-not-found-td889.html > I looked at: > > yzzy: which clang /usr/bin/clang > yzzy: xcode-select -p > /Applications/Xcode.app/Contents/Developer > yzzy: xcrun --show-sdk-path > /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk > > but that didn’t speak to me so further googling led me to: > > https://stackoverflow.com/questions/54557659/r-cant-update-packages-clang-cant-find-head-files > so lurking in: > /Library/Developer/CommandLineTools/usr/include/c++/v1 > is stdio.h, but I’m feeling a bit queasy at this point and > would appreciate some expert advice. > > Roger > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >>>
Re: [R-SIG-Mac] catalina humbug
Exactly!!! Thanks very much to all for your patience, and especially for Berend’s suggestion. All now seems well without .R/Makevars > On Oct 14, 2020, at 2:18 PM, Berend Hasselman wrote: > > Do you by any chance have ~/.R/Makevars ? > If yes does it define CC and CXX and LDFLAGS with clang7? > Try removing them. > > Berend > >> On 14 Oct 2020, at 14:14, Koenker, Roger W wrote: >> >> Humm… so I have now removed clang7 from /usr/local and I now see: >> >> /usr/local/clang7/bin/clang >> -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG >> -I/usr/local/clang7/include/c++/v1 -fPIC -Wall -g -O2 -c mcmb.c -o mcmb.o >> /bin/sh: /usr/local/clang7/bin/clang: No such file or directory >> >> But unfortunately I still don’t see where R CMD build is asking for clang7. >> I tried reinstalling R >> after removing clang7 but this didn’t change the result above. Nothing in >> my environment or >> in .Rprofile refers to clang >> >> My ChangeLog reveals that I had a similar problem a couple of years ago, but >> unhelpfully it doesn’t reveal >> how it was fixed, only that the one C source file of the package was removed >> for a while, and then reinstated >> after resolving a problem with header files for clang6. >> >> Roger >> >> >> >> >>> On Oct 14, 2020, at 12:36 PM, Ken Beath wrote: >>> >>> clang7 seems to be unnecessary for current R. It isn’t in my system and >>> from memory was one of the things I removed to get everything working. This >>> involved removing the clang and fortran that had been previously installed. >>> I may have needed some other things but my systems will build your package. >>> >>> Ken >>> On 14 Oct 2020, at 10:01 pm, Koenker, Roger W wrote: Simon, Thanks, I still have the same error: In file included from mcmb.c:11: /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' file not found #include_next I didn’t do anything beyond upgrading R and installing fortran 8.2.0, and the CLT 12.2. but I didn’t remove anything, should I have? I now see: yzzy: which clang /usr/bin/clang yzzy: clang --version Apple clang version 12.0.0 (clang-1200.0.32.2) Target: x86_64-apple-darwin19.6.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin The last time I faced this sort of thing James suggested this: https://groups.google.com/g/r-sig-mac/c/rZeYeiyyxtY but the names and locations are somewhat different now, so I’m reluctant to experiment. Roger > On Oct 14, 2020, at 11:48 AM, Simon Urbanek > wrote: > > Roger, > > the error points to an old local clang - did you remove (or move aside) > that one? Check your /usr/local - you seem to have some old stuff there > that is breaking. That would solve the original issue. You seem to have > done a lot after that error, but didn't tell us what happened then… you > can't have the same error if you removed it ;) > > Cheers, > Simon > > > > >> On Oct 14, 2020, at 10:28 PM, Koenker, Roger W >> wrote: >> >> I’ve recently “upgraded” to catalina, and compilation of my quantreg >> package failed with: >> >> In file included from mcmb.c:11: >> /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' >> file not found >> #include_next >> >> So I’ve tried the following: >> >> 1. Upgraded R to 4.0.3 >> 2. Upgraded the fortran compiler to 8.2.0 as suggested. >> 3. Attempted to reinstall command line tools with Xcode-select >> —install. This fails with >> a popup that says: >> >> Can’t install the software because it is not currently >> available from the Software Update server. >> 4. Tried again to reinstall Command line tools 12.2 beta 3 from >> https://developer.apple.com/download/more/ >> which successfully installed, but my stdio.h error persisted. >> 5. Following thread: >> http://r-sig-mac.29524.n8.nabble.com/R-SIG-Mac-fatal-error-stdio-h-file-not-found-td889.html >> I looked at: >> >> yzzy: which clang /usr/bin/clang >> yzzy: xcode-select -p >> /Applications/Xcode.app/Contents/Developer >> yzzy: xcrun --show-sdk-path >> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk >> >> but that didn’t speak to me so further googling led me to: >> >> https://stackoverflow.com/questions/54557659/r-cant-update-packages-clang-cant-find-head-files >> so lurking in: >> /Library/Developer/CommandLineTools/usr/include/c++/v1 >> is
Re: [R-SIG-Mac] catalina humbug
Do you by any chance have ~/.R/Makevars ? If yes does it define CC and CXX and LDFLAGS with clang7? Try removing them. Berend > On 14 Oct 2020, at 14:14, Koenker, Roger W wrote: > > Humm… so I have now removed clang7 from /usr/local and I now see: > > /usr/local/clang7/bin/clang > -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG > -I/usr/local/clang7/include/c++/v1 -fPIC -Wall -g -O2 -c mcmb.c -o mcmb.o > /bin/sh: /usr/local/clang7/bin/clang: No such file or directory > > But unfortunately I still don’t see where R CMD build is asking for clang7. > I tried reinstalling R > after removing clang7 but this didn’t change the result above. Nothing in my > environment or > in .Rprofile refers to clang > > My ChangeLog reveals that I had a similar problem a couple of years ago, but > unhelpfully it doesn’t reveal > how it was fixed, only that the one C source file of the package was removed > for a while, and then reinstated > after resolving a problem with header files for clang6. > > Roger > > > > >> On Oct 14, 2020, at 12:36 PM, Ken Beath wrote: >> >> clang7 seems to be unnecessary for current R. It isn’t in my system and from >> memory was one of the things I removed to get everything working. This >> involved removing the clang and fortran that had been previously installed. >> I may have needed some other things but my systems will build your package. >> >> Ken >> >>> On 14 Oct 2020, at 10:01 pm, Koenker, Roger W wrote: >>> >>> Simon, >>> >>> Thanks, I still have the same error: >>> >>> In file included from mcmb.c:11: >>> /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' >>> file not found >>> #include_next >>> >>> I didn’t do anything beyond upgrading R and installing fortran 8.2.0, and >>> the CLT 12.2. >>> but I didn’t remove anything, should I have? I now see: >>> >>> yzzy: which clang >>> /usr/bin/clang >>> yzzy: clang --version >>> Apple clang version 12.0.0 (clang-1200.0.32.2) >>> Target: x86_64-apple-darwin19.6.0 >>> Thread model: posix >>> InstalledDir: >>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin >>> >>> >>> The last time I faced this sort of thing James suggested this: >>> https://groups.google.com/g/r-sig-mac/c/rZeYeiyyxtY >>> >>> but the names and locations are somewhat different now, so I’m reluctant to >>> experiment. >>> >>> Roger >>> >>> >>> On Oct 14, 2020, at 11:48 AM, Simon Urbanek wrote: Roger, the error points to an old local clang - did you remove (or move aside) that one? Check your /usr/local - you seem to have some old stuff there that is breaking. That would solve the original issue. You seem to have done a lot after that error, but didn't tell us what happened then… you can't have the same error if you removed it ;) Cheers, Simon > On Oct 14, 2020, at 10:28 PM, Koenker, Roger W > wrote: > > I’ve recently “upgraded” to catalina, and compilation of my quantreg > package failed with: > > In file included from mcmb.c:11: > /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' > file not found > #include_next > > So I’ve tried the following: > > 1. Upgraded R to 4.0.3 > 2. Upgraded the fortran compiler to 8.2.0 as suggested. > 3. Attempted to reinstall command line tools with Xcode-select > —install. This fails with > a popup that says: > > Can’t install the software because it is not currently > available from the Software Update server. > 4. Tried again to reinstall Command line tools 12.2 beta 3 from > https://developer.apple.com/download/more/ > which successfully installed, but my stdio.h error persisted. > 5. Following thread: > http://r-sig-mac.29524.n8.nabble.com/R-SIG-Mac-fatal-error-stdio-h-file-not-found-td889.html > I looked at: > > yzzy: which clang /usr/bin/clang > yzzy: xcode-select -p > /Applications/Xcode.app/Contents/Developer > yzzy: xcrun --show-sdk-path > /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk > > but that didn’t speak to me so further googling led me to: > > https://stackoverflow.com/questions/54557659/r-cant-update-packages-clang-cant-find-head-files > so lurking in: > /Library/Developer/CommandLineTools/usr/include/c++/v1 > is stdio.h, but I’m feeling a bit queasy at this point and > would appreciate some expert advice. > > Roger > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >>>
Re: [R-SIG-Mac] catalina humbug
Humm… so I have now removed clang7 from /usr/local and I now see: /usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/clang7/include/c++/v1 -fPIC -Wall -g -O2 -c mcmb.c -o mcmb.o /bin/sh: /usr/local/clang7/bin/clang: No such file or directory But unfortunately I still don’t see where R CMD build is asking for clang7. I tried reinstalling R after removing clang7 but this didn’t change the result above. Nothing in my environment or in .Rprofile refers to clang My ChangeLog reveals that I had a similar problem a couple of years ago, but unhelpfully it doesn’t reveal how it was fixed, only that the one C source file of the package was removed for a while, and then reinstated after resolving a problem with header files for clang6. Roger > On Oct 14, 2020, at 12:36 PM, Ken Beath wrote: > > clang7 seems to be unnecessary for current R. It isn’t in my system and from > memory was one of the things I removed to get everything working. This > involved removing the clang and fortran that had been previously installed. I > may have needed some other things but my systems will build your package. > > Ken > >> On 14 Oct 2020, at 10:01 pm, Koenker, Roger W wrote: >> >> Simon, >> >> Thanks, I still have the same error: >> >> In file included from mcmb.c:11: >> /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' file >> not found >> #include_next >> >> I didn’t do anything beyond upgrading R and installing fortran 8.2.0, and >> the CLT 12.2. >> but I didn’t remove anything, should I have? I now see: >> >> yzzy: which clang >> /usr/bin/clang >> yzzy: clang --version >> Apple clang version 12.0.0 (clang-1200.0.32.2) >> Target: x86_64-apple-darwin19.6.0 >> Thread model: posix >> InstalledDir: >> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin >> >> >> The last time I faced this sort of thing James suggested this: >> https://groups.google.com/g/r-sig-mac/c/rZeYeiyyxtY >> >> but the names and locations are somewhat different now, so I’m reluctant to >> experiment. >> >> Roger >> >> >> >>> On Oct 14, 2020, at 11:48 AM, Simon Urbanek >>> wrote: >>> >>> Roger, >>> >>> the error points to an old local clang - did you remove (or move aside) >>> that one? Check your /usr/local - you seem to have some old stuff there >>> that is breaking. That would solve the original issue. You seem to have >>> done a lot after that error, but didn't tell us what happened then… you >>> can't have the same error if you removed it ;) >>> >>> Cheers, >>> Simon >>> >>> >>> >>> On Oct 14, 2020, at 10:28 PM, Koenker, Roger W wrote: I’ve recently “upgraded” to catalina, and compilation of my quantreg package failed with: In file included from mcmb.c:11: /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' file not found #include_next So I’ve tried the following: 1. Upgraded R to 4.0.3 2. Upgraded the fortran compiler to 8.2.0 as suggested. 3. Attempted to reinstall command line tools with Xcode-select —install. This fails with a popup that says: Can’t install the software because it is not currently available from the Software Update server. 4. Tried again to reinstall Command line tools 12.2 beta 3 from https://developer.apple.com/download/more/ which successfully installed, but my stdio.h error persisted. 5. Following thread: http://r-sig-mac.29524.n8.nabble.com/R-SIG-Mac-fatal-error-stdio-h-file-not-found-td889.html I looked at: yzzy: which clang /usr/bin/clang yzzy: xcode-select -p /Applications/Xcode.app/Contents/Developer yzzy: xcrun --show-sdk-path /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk but that didn’t speak to me so further googling led me to: https://stackoverflow.com/questions/54557659/r-cant-update-packages-clang-cant-find-head-files so lurking in: /Library/Developer/CommandLineTools/usr/include/c++/v1 is stdio.h, but I’m feeling a bit queasy at this point and would appreciate some expert advice. Roger ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >> >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] catalina humbug
clang7 seems to be unnecessary for current R. It isn’t in my system and from memory was one of the things I removed to get everything working. This involved removing the clang and fortran that had been previously installed. I may have needed some other things but my systems will build your package. Ken > On 14 Oct 2020, at 10:01 pm, Koenker, Roger W wrote: > > Simon, > > Thanks, I still have the same error: > > In file included from mcmb.c:11: > /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' file > not found > #include_next > > I didn’t do anything beyond upgrading R and installing fortran 8.2.0, and the > CLT 12.2. > but I didn’t remove anything, should I have? I now see: > > yzzy: which clang > /usr/bin/clang > yzzy: clang --version > Apple clang version 12.0.0 (clang-1200.0.32.2) > Target: x86_64-apple-darwin19.6.0 > Thread model: posix > InstalledDir: > /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin > > > The last time I faced this sort of thing James suggested this: > https://groups.google.com/g/r-sig-mac/c/rZeYeiyyxtY > > but the names and locations are somewhat different now, so I’m reluctant to > experiment. > > Roger > > > >> On Oct 14, 2020, at 11:48 AM, Simon Urbanek >> wrote: >> >> Roger, >> >> the error points to an old local clang - did you remove (or move aside) that >> one? Check your /usr/local - you seem to have some old stuff there that is >> breaking. That would solve the original issue. You seem to have done a lot >> after that error, but didn't tell us what happened then… you can't have the >> same error if you removed it ;) >> >> Cheers, >> Simon >> >> >> >> >>> On Oct 14, 2020, at 10:28 PM, Koenker, Roger W >>> wrote: >>> >>> I’ve recently “upgraded” to catalina, and compilation of my quantreg >>> package failed with: >>> >>> In file included from mcmb.c:11: >>> /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' >>> file not found >>> #include_next >>> >>> So I’ve tried the following: >>> >>> 1. Upgraded R to 4.0.3 >>> 2. Upgraded the fortran compiler to 8.2.0 as suggested. >>> 3. Attempted to reinstall command line tools with Xcode-select >>> —install. This fails with >>> a popup that says: >>> >>> Can’t install the software because it is not currently >>> available from the Software Update server. >>> 4. Tried again to reinstall Command line tools 12.2 beta 3 from >>> https://developer.apple.com/download/more/ >>> which successfully installed, but my stdio.h error persisted. >>> 5. Following thread: >>> http://r-sig-mac.29524.n8.nabble.com/R-SIG-Mac-fatal-error-stdio-h-file-not-found-td889.html >>> I looked at: >>> >>> yzzy: which clang /usr/bin/clang >>> yzzy: xcode-select -p >>> /Applications/Xcode.app/Contents/Developer >>> yzzy: xcrun --show-sdk-path >>> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk >>> >>> but that didn’t speak to me so further googling led me to: >>> >>> https://stackoverflow.com/questions/54557659/r-cant-update-packages-clang-cant-find-head-files >>> so lurking in: >>> /Library/Developer/CommandLineTools/usr/include/c++/v1 >>> is stdio.h, but I’m feeling a bit queasy at this point and >>> would appreciate some expert advice. >>> >>> Roger >>> >>> ___ >>> R-SIG-Mac mailing list >>> R-SIG-Mac@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] catalina humbug
Simon, Thanks, I still have the same error: In file included from mcmb.c:11: /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' file not found #include_next I didn’t do anything beyond upgrading R and installing fortran 8.2.0, and the CLT 12.2. but I didn’t remove anything, should I have? I now see: yzzy: which clang /usr/bin/clang yzzy: clang --version Apple clang version 12.0.0 (clang-1200.0.32.2) Target: x86_64-apple-darwin19.6.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin The last time I faced this sort of thing James suggested this: https://groups.google.com/g/r-sig-mac/c/rZeYeiyyxtY but the names and locations are somewhat different now, so I’m reluctant to experiment. Roger > On Oct 14, 2020, at 11:48 AM, Simon Urbanek > wrote: > > Roger, > > the error points to an old local clang - did you remove (or move aside) that > one? Check your /usr/local - you seem to have some old stuff there that is > breaking. That would solve the original issue. You seem to have done a lot > after that error, but didn't tell us what happened then… you can't have the > same error if you removed it ;) > > Cheers, > Simon > > > > >> On Oct 14, 2020, at 10:28 PM, Koenker, Roger W wrote: >> >> I’ve recently “upgraded” to catalina, and compilation of my quantreg package >> failed with: >> >> In file included from mcmb.c:11: >> /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' file >> not found >> #include_next >> >> So I’ve tried the following: >> >> 1. Upgraded R to 4.0.3 >> 2. Upgraded the fortran compiler to 8.2.0 as suggested. >> 3. Attempted to reinstall command line tools with Xcode-select >> —install. This fails with >> a popup that says: >> >> Can’t install the software because it is not currently >> available from the Software Update server. >> 4. Tried again to reinstall Command line tools 12.2 beta 3 from >> https://developer.apple.com/download/more/ >> which successfully installed, but my stdio.h error persisted. >> 5. Following thread: >> http://r-sig-mac.29524.n8.nabble.com/R-SIG-Mac-fatal-error-stdio-h-file-not-found-td889.html >> I looked at: >> >> yzzy: which clang /usr/bin/clang >> yzzy: xcode-select -p >> /Applications/Xcode.app/Contents/Developer >> yzzy: xcrun --show-sdk-path >> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk >> >> but that didn’t speak to me so further googling led me to: >> >> https://stackoverflow.com/questions/54557659/r-cant-update-packages-clang-cant-find-head-files >> so lurking in: >> /Library/Developer/CommandLineTools/usr/include/c++/v1 >> is stdio.h, but I’m feeling a bit queasy at this point and >> would appreciate some expert advice. >> >> Roger >> >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] catalina humbug
Roger, the error points to an old local clang - did you remove (or move aside) that one? Check your /usr/local - you seem to have some old stuff there that is breaking. That would solve the original issue. You seem to have done a lot after that error, but didn't tell us what happened then… you can't have the same error if you removed it ;) Cheers, Simon > On Oct 14, 2020, at 10:28 PM, Koenker, Roger W wrote: > > I’ve recently “upgraded” to catalina, and compilation of my quantreg package > failed with: > > In file included from mcmb.c:11: > /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' file > not found > #include_next > > So I’ve tried the following: > > 1. Upgraded R to 4.0.3 > 2. Upgraded the fortran compiler to 8.2.0 as suggested. > 3. Attempted to reinstall command line tools with Xcode-select > —install. This fails with > a popup that says: > > Can’t install the software because it is not currently > available from the Software Update server. > 4. Tried again to reinstall Command line tools 12.2 beta 3 from > https://developer.apple.com/download/more/ > which successfully installed, but my stdio.h error persisted. > 5. Following thread: > http://r-sig-mac.29524.n8.nabble.com/R-SIG-Mac-fatal-error-stdio-h-file-not-found-td889.html > I looked at: > > yzzy: which clang /usr/bin/clang > yzzy: xcode-select -p > /Applications/Xcode.app/Contents/Developer > yzzy: xcrun --show-sdk-path > /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk > > but that didn’t speak to me so further googling led me to: > > https://stackoverflow.com/questions/54557659/r-cant-update-packages-clang-cant-find-head-files > so lurking in: > /Library/Developer/CommandLineTools/usr/include/c++/v1 > is stdio.h, but I’m feeling a bit queasy at this point and > would appreciate some expert advice. > > Roger > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] catalina humbug
This is a common error after major macOS upgrades. Install the xcode CLT standalone from Apple and try again. You might also need to install/link to the 10.14 SDK to get certain packages installed from source. On 14. Oct 2020 at 11:39:09 CEST, Dr Eberhard Lisse wrote: Wait a while and try again :-)-O el On 14/10/2020 11:28, Koenker, Roger W wrote: [...] > 3. Attempted to reinstall command line tools with Xcode-select > —install. This fails with > a popup that says: > > Can’t install the software because it is not currently > available from the Software Update server. [...] -- If you want to email me, replace nospam with el ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] catalina humbug
Wait a while and try again :-)-O el On 14/10/2020 11:28, Koenker, Roger W wrote: [...] > 3. Attempted to reinstall command line tools with Xcode-select > —install. This fails with > a popup that says: > > Can’t install the software because it is not currently > available from the Software Update server. [...] -- If you want to email me, replace nospam with el ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] catalina humbug
I’ve recently “upgraded” to catalina, and compilation of my quantreg package failed with: In file included from mcmb.c:11: /usr/local/clang7/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' file not found #include_next So I’ve tried the following: 1. Upgraded R to 4.0.3 2. Upgraded the fortran compiler to 8.2.0 as suggested. 3. Attempted to reinstall command line tools with Xcode-select —install. This fails with a popup that says: Can’t install the software because it is not currently available from the Software Update server. 4. Tried again to reinstall Command line tools 12.2 beta 3 from https://developer.apple.com/download/more/ which successfully installed, but my stdio.h error persisted. 5. Following thread: http://r-sig-mac.29524.n8.nabble.com/R-SIG-Mac-fatal-error-stdio-h-file-not-found-td889.html I looked at: yzzy: which clang /usr/bin/clang yzzy: xcode-select -p /Applications/Xcode.app/Contents/Developer yzzy: xcrun --show-sdk-path /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk but that didn’t speak to me so further googling led me to: https://stackoverflow.com/questions/54557659/r-cant-update-packages-clang-cant-find-head-files so lurking in: /Library/Developer/CommandLineTools/usr/include/c++/v1 is stdio.h, but I’m feeling a bit queasy at this point and would appreciate some expert advice. Roger ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
