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

Question

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?

Solution 1

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

Solution 2

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.

Solution 3

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).

Solution 4

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

Solution 5

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

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