TL;DR

It appears that Apple considers /usr/include as something that has gone the way of the dodo — it is extinct — or maybe it's like Monty Python's Parrot.

Using the Apple-provided GCC (actually, that's Clang by any other name, as the version information shows) or Clang avoids problems. Both /usr/bin/gcc and /usr/bin/clang will find the system libraries four directory levels below:

/Applications/Xcode.app/Contents/Developer/Platforms/…

If you build your own GCC or other compiler, you will (probably) need to configure it to find the system libraries under the Xcode application directory.

Explorations

Immediately after the upgrade, I ran XCode 11.0. It wanted to install some extra components, so I let it do so. However, that did not reinstate /usr/include or the directory under /Library.

One of the other bits of advice in the previous question was to run:

xcode-select --install

When doing so, it claimed that it downloaded the command line utilities, and it ensured that /usr/bin/gcc and /usr/bin/clang etc were present. That's a useful step (though I didn't definitively check whether they were present before).

$ /usr/bin/gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 11.0.0 (clang-1100.0.33.8)
Target: x86_64-apple-darwin19.0.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
$

Using /usr/bin/gcc, it is now possible to compile programs:

$ make CC=/usr/bin/gcc al
co  RCS/al.c,v al.c
RCS/al.c,v  -->  al.c
revision 1.7
done
/usr/bin/gcc -I/Users/jleffler/inc -g -O3 -std=c11 -pedantic -Wall -Wextra -Werror -Wshadow -Wmissing-prototypes -Wpointer-arith  -Wold-style-definition -Wcast-qual -Wstrict-prototypes -DHAVE_MEMMEM -DHAVE_STRNDUP -DHAVE_STRNLEN  -DHAVE_GETDELIM   -o al al.c -L/Users/jleffler/lib/64  -ljl
$

However, /usr/include is still missing. There is a directory under /Library now:

$ ls /Library/Developer
CommandLineTools  PrivateFrameworks
$ ls /Library/Developer/CommandLineTools
Library SDKs    usr
$ ls /Library/Developer/CommandLineTools/SDKs
MacOSX.sdk      MacOSX10.14.sdk MacOSX10.15.sdk
$ ls /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/
Entitlements.plist SDKSettings.json   System
Library            SDKSettings.plist  usr
$

Neither the System nor the Library directory contain anything very promising.

When all else fails, read the manual

Next step — find and read the release notes:

• Xcode 11 Release Notes
• macOS Catalina 10.15 Release Notes

There's no information in there that relates to this. So, the probability is (AFAICS, after only an hour or two's effort) that Apple no longer support /usr/include — though it does still have a fully-loaded /usr/lib (no /lib though).

Time to check another compilation with GCC option -v added (in the makefile I used, setting UFLAGS adds the option to C compiler command line):

$ make UFLAGS=-v CC=/usr/bin/gcc ww
co  RCS/ww.c,v ww.c
RCS/ww.c,v  -->  ww.c
revision 4.9
done
/usr/bin/gcc -I/Users/jleffler/inc -g -O3 -std=c11 -pedantic -Wall -Wextra -Werror -Wshadow -Wmissing-prototypes -Wpointer-arith  -Wold-style-definition -Wcast-qual -Wstrict-prototypes -DHAVE_MEMMEM -DHAVE_STRNDUP -DHAVE_STRNLEN  -DHAVE_GETDELIM -v  -o ww ww.c -L/Users/jleffler/lib/64  -ljl
Apple clang version 11.0.0 (clang-1100.0.33.8)
Target: x86_64-apple-darwin19.0.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
 "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.15.0 -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -emit-obj -disable-free -disable-llvm-verifier -discard-value-names -main-file-name ww.c -mrelocation-model pic -pic-level 2 -mthread-model posix -mdisable-fp-elim -fno-strict-return -masm-verbose -munwind-tables -target-sdk-version=10.15 -target-cpu penryn -dwarf-column-info -debug-info-kind=standalone -dwarf-version=4 -debugger-tuning=lldb -ggnu-pubnames -target-linker-version 512.4 -v -resource-dir /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/11.0.0 -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I /Users/jleffler/inc -D HAVE_MEMMEM -D HAVE_STRNDUP -D HAVE_STRNLEN -D HAVE_GETDELIM -I/usr/local/include -O3 -Wall -Wextra -Werror -Wshadow -Wmissing-prototypes -Wpointer-arith -Wold-style-definition -Wcast-qual -Wstrict-prototypes -Wno-framework-include-private-from-public -Wno-atimport-in-framework-header -Wno-extra-semi-stmt -Wno-quoted-include-in-framework-header -pedantic -std=c11 -fdebug-compilation-dir /Users/jleffler/src/cmd -ferror-limit 19 -fmessage-length 110 -stack-protector 1 -fstack-check -mdarwin-stkchk-strong-link -fblocks -fencode-extended-block-signature -fregister-global-dtors-with-atexit -fobjc-runtime=macosx-10.15.0 -fmax-type-align=16 -fdiagnostics-show-option -fcolor-diagnostics -vectorize-loops -vectorize-slp -o /var/folders/77/zx9nk6dn7_dg4xd4stvt42v00000gn/T/ww-4cb85b.o -x c ww.c
clang -cc1 version 11.0.0 (clang-1100.0.33.8) default target x86_64-apple-darwin19.0.0
ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/local/include"
ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/Library/Frameworks"
#include "..." search starts here:
#include <...> search starts here:
 /Users/jleffler/inc
 /usr/local/include
 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/11.0.0/include
 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
 /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include
 /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks (framework directory)
End of search list.
 "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld" -demangle -lto_library /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/libLTO.dylib -dynamic -arch x86_64 -macosx_version_min 10.15.0 -syslibroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -o ww -L/Users/jleffler/lib/64 /var/folders/77/zx9nk6dn7_dg4xd4stvt42v00000gn/T/ww-4cb85b.o -ljl -L/usr/local/lib -lSystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/11.0.0/lib/darwin/libclang_rt.osx.a
 "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/dsymutil" -o ww.dSYM ww
$

The key information in that blizzard of data is:

-isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk

That's effectively the 'root' directory for the compilation, so there should be sub-directories under that for usr and usr/include:

$ ls /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk
Entitlements.plist SDKSettings.json   System
Library            SDKSettings.plist  usr
$ ls /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr
bin     include lib     libexec share
$ ls /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include
AppleTextureEncoder.h  dns_util.h             memory.h               simd
AssertMacros.h         dtrace.h               menu.h                 slapi-plugin.h
Availability.h         editline               miscfs                 spawn.h
AvailabilityInternal.h err.h                  module.modulemap       sqlite3.h
AvailabilityMacros.h   errno.h                monetary.h             sqlite3ext.h
AvailabilityVersions.h eti.h                  monitor.h              stab.h
…lots more lines…
dirent.h               mach-o                 security               xcselect.h
disktab.h              mach_debug             semaphore.h            xlocale
dispatch               machine                servers                xlocale.h
dlfcn.h                malloc                 setjmp.h               xpc
dns.h                  math.h                 sgtty.h                zconf.h
dns_sd.h               membership.h           signal.h               zlib.h
$

This shows that the mile-long and totally unmemorable directory name does contain the standard C and POSIX headers, plus Apple-specific extras.

The previous /usr/local/ directory appears to be intact; the warning about usr/local/include not existing under the -isysrootdir is harmless (and not visible without the -v option).

For me adding the following path to CPATH solved the issue:

export CPATH=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include

Before you proceed, make sure to install xcode command line tools.

xcode-select --install

Actually, you can do it! Actually all the C headers are found here in this folder:

/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/

We just need to create symlink for all the headers file into this folder:

/usr/local/include/

It worked for me! the following command line will take care of all the problems:

sudo ln -s /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/* /usr/local/include/

You will get some warning. Some of the headers already exists, like this:

ln: /usr/local/include//tcl.h: File exists
ln: /usr/local/include//tclDecls.h: File exists
ln: /usr/local/include//tclPlatDecls.h: File exists
ln: /usr/local/include//tclTomMath.h: File exists
ln: /usr/local/include//tclTomMathDecls.h: File exists
ln: /usr/local/include//tk.h: File exists
ln: /usr/local/include//tkDecls.h: File exists
ln: /usr/local/include//tkPlatDecls.h: File exists

totally ok to ignore. that's all.

Set the following implicit Make variables to point to where the headers are now located for Xcode Command Line Tools (Xcode CLI):

export CFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
export CCFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
export CXXFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
export CPPFLAGS+=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

The -isysroot option updates the location of the root files away from the system root directory /.

So, this ensures that the common /usr/* files are found in their new place.

That is, the files at /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk are now found. These files are:

Entitlements.plist 
Library
SDKSettings.json
SDKSettings.plist
System
usr

apue.h dependency was still missing in my /usr/local/include after following Komol Nath Roy answer in this question.

I downloaded the dependency manually from git and placed it in /usr/local/include

I am a newbie with C++ compiler for R in OSX and I got the same issue that C++ could not find the header after OS was updated (missing math.h although it was there). I followed instructions from https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/ but nothing changed.

Finally, it worked for me after I reinstalled the Xcode CLI

xcode-select --install

and then change the flags to Var as @Coatless suggested:

export CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
export CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
export CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
export CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

I tried 1) manually linking 2) brew install llvm, but they did not work.

Finally, this worked for me: https://gitmemory.com/issue/pytorch/pytorch/31190/565153503

By setting the following env vars:

export CC=clang
export CXX=clang++
export MACOSX_DEPLOYMENT_TARGET=10.9

In my case I seemed to have llvm and gcc also installed using homebrew. When I removed those, and thus relied fully on the macOS clang, it could find the headers and the compiling worked again.

On MacOS Catalina 10.15.4, with Xcode Version 11.5 (11E608c) I also needed to update the library path in my .zshrc (the MacOSX.sdk paths are new):

export CPATH='/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include:/opt/local/include'
export LIBRARY_PATH='/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib:/opt/local/lib'

Short Answer

/Library/Developer/CommandLineTools/usr/bin/clang++ -o main main.cpp -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk

The Result

Explanation

In current macOS version, the c/c++ headers are searched inside /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/, instead of /usr/include. So you need to 'reset' the root directory using -isysroot option.

Hope this makes sense 🙂.

In my case, i did a millions things but i reckon following steps helped fix ruby installation.

1. xcode-select --install
2. Set these flags

export CFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
export CCFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
export CXXFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
export CPPFLAGS=-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

3. sudo ln -s /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/* /usr/local/include/

4. export SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

5. rbenv install 2.6.3 -v

If you have both the command line tools and XCode installed, make sure the SDK installed by the command line tools is actually being used:

#Check the current sdk

$ xcrun --show-sdk-path

#Change sdk

$ sudo xcode-select -s /Library/Developer/CommandLineTools #Using CommandLineTools SDK

$ sudo xcode-select -s /Applications/Xcode.app/Contents/Developer #Using XCode.app SDK

kudos to https://stackoverflow.com/a/61526989/596599 for this answer.

For me the error was: xcrun[20873:1179298] Failed to open macho file at /Library/Developer/CommandLineTools/usr/bin/clang++ for reading: Too many levels of symbolic links

So I opened my terminal and went to the following folder (as mentioned by the error message): /Library/Developer/CommandLineTools/usr/bin/

Then I deleted the shortcut file named clang++

sudo rm clang++

Next, I made a copy of executable file named clang and renamed the copied file to clang++

sudo cp clang clang++

And finally it works.

If using an external LLVM installation, add these to your ~/.bash_profile

LLVM_PATH="/usr/local/opt/llvm/" # or any other path
LLVM_VERSION="11.0.0"
export PATH="$LLVM_PATH:$PATH"
export SDKROOT=$(xcrun --sdk macosx --show-sdk-path)
export LD_LIBRARY_PATH="$LLVM_PATH/lib/:$LD_LIBRARY_PATH"
export DYLD_LIBRARY_PATH="$LLVM_PATH/lib/:$DYLD_LIBRARY_PATH"
export CPATH="$LLVM_PATH/lib/clang/$LLVM_VERSION/include/"
export LDFLAGS="-L$LLVM_PATH/lib"
export CPPFLAGS="-I$LLVM_PATH/include"
export CC="$LLVM_PATH/bin/clang"
export CXX="$LLVM_PATH/bin/clang++"

(adjust the clang version and the external llvm installation path.)

Then run source ~/.bash_profile

For me, it works well as follow:

1. xcode-select --install

2. sudo ln -s /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/* /usr/local/include/

3. export SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk

The solution was simpler than I thought. Install clang/llvm.

brew install llvm

Then we need to create symlinks ourselves.

for f in /usr/local/Cellar/llvm/9.0.0_1/bin/clang*; do ln -s ${f} /usr/local/bin/"${f##*/}"; done

And

ln -s /usr/local/Cellar/llvm/9.0.0_1/include/c++ /usr/local/include/c++

Depending upon your llvm version, modify the above commands.

Now, you can compile C++ programs without passing any custom flags.

clang++ hello.cpp