without - xcode gcc

Can't compile a C program on a Mac after upgrading to Catalina 10.15 (5)

There's a previous question Can't compile C program on a Mac after upgrade to Mojave , and the answers to that have covered most of the variations on what goes wrong.

Now — as of Monday 2019-10-07 — you can upgrade to macOS Catalina 10.15. Once again, during the upgrade, the /usr/include directory has been blown away by the update, even though XCode 11.0 was installed before upgrading (from Mojave 10.14.6) to Catalina. Consequently, compilers built to expect that there is a /usr/include directory do not work any longer.

The main recommended step for the Mojave issues — using the command:

open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

does not work out of the gate because the directory /Library/Developer/CommandLineTools/Packages/ does not exist (so there's not yet a .pkg file to open).

Is there a good (official) way to create and populate the directory /usr/include ?


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:


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.


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
/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:

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
/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:
 /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).

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:


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


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.

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

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.

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