Homebrew Clang does not have correct search path for system include directory on MacOS Catalina #45061

ssbanerje · 2019-10-09T18:22:29Z

Homebrew Clang does not search the correct include directories in MacOS Catalina.

What you were trying to do (and why)

If I try to compile the following C file after installing LLVM+Clang from homebrew

#include <stdio.h>

int main() {
    printf("hi");
}

What happened

I get the error

» which clang                                                                                                                                                                                             1 ↵
/usr/local/opt/llvm/bin/clang
» clang test.c
In file included from test.c:1:
/Library/Developer/CommandLineTools/usr/include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' file not found
#include <stdio.h>
              ^~~~~~~~~
1 error generated.

What you expected to happen

The program to compile correctly.

However, if I alias clang to the system clang, everything works!

» alias clang=/usr/bin/clang                                                                                                                                                                              1 ↵
» clang test.c
» ./a.out
hi%

By default the Homebrew clang has the following search paths

» echo | clang -E -Wp,-v -
clang -cc1 version 9.0.0 based upon LLVM 9.0.0 default target x86_64-apple-darwin19.0.0
ignoring nonexistent directory "/usr/include"
#include "..." search starts here:
#include <...> search starts here:
 /usr/local/include
 /usr/local/Cellar/llvm/9.0.0/lib/clang/9.0.0/include
 /System/Library/Frameworks (framework directory)
 /Library/Frameworks (framework directory)
End of search list.
# 1 "<stdin>"
# 1 "<built-in>" 1
# 1 "<built-in>" 3
# 352 "<built-in>" 3
# 1 "<command line>" 1
# 1 "<built-in>" 2
# 1 "<stdin>" 2

The system clang looks in different folders

» alias clang=/usr/bin/clang
» echo | clang -E -Wp,-v -
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:
 /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.
# 1 "<stdin>"
# 1 "<built-in>" 1
# 1 "<built-in>" 3
# 362 "<built-in>" 3
# 1 "<command line>" 1
# 1 "<built-in>" 2
# 1 "<stdin>" 2

I think the problem is that until recently /usr/include would have the header files that the compiler requires, however, that directory does not exist anymore (since Catalina update).

I can currently work around this by explicitly setting CPATH. But I think this is a bug, not sure if it is a homebrew problem or upstream in LLVM.

Step-by-step reproduction instructions (by running brew commands)

brew install llvm
export PATH="/usr/local/opt/llvm/bin:$PATH"
clang test.c

My homebrew is updated to the latest version and doctor does not report any problems.

» brew -v                                                                                                                                                                                                 1 ↵
Homebrew 2.1.13
Homebrew/homebrew-core (git revision 4d523; last commit 2019-10-09)
Homebrew/homebrew-cask (git revision c4f9d3; last commit 2019-10-09)

» brew doctor
Your system is ready to brew.

» brew config
HOMEBREW_VERSION: 2.1.13
ORIGIN: https://github.com/Homebrew/brew.git
HEAD: aa043c1d678afd26f50156a83417c296cb9d5a4b
Last commit: 24 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 4d5233f01f792cb83661ccc1a6abfb139c168951
Core tap last commit: 4 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_VISUAL: nvim
CPU: quad-core 64-bit broadwell
Homebrew Ruby: 2.6.3 => /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby
Clang: 11.0 build 1100
Git: 2.23.0 => /usr/local/bin/git
Curl: 7.64.1 => /usr/bin/curl
Java: 12.0.1, 1.8.0_131, 1.8.0_40
macOS: 10.15-x86_64
CLT: 11.0.0.0.1.1567737322
Xcode: 11.1
CLT headers: 11.0.0.0.1.1567737322
XQuartz: 2.7.11 => /opt/X11

The text was updated successfully, but these errors were encountered:

jamiesnape · 2019-10-09T21:02:58Z

There is a CMake variable C_INCLUDE_DIRS
https://github.com/llvm/llvm-project/blob/c0da1282fc036908cc721ee74f574fbb99d5e506/clang/CMakeLists.txt#L225-L226
that maybe could be set.

fxcoudert · 2019-10-10T11:31:47Z

I think @mistydemeo was looking at that issue

tschoonj · 2019-10-11T10:32:30Z

What I did to fix this is pass -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk to CPPFLAGS...

sramsay · 2019-10-12T22:17:39Z

@tschoonj After days of trying to figure this out, setting CPPFLAGS finally did it.

I would suggest that appending this to the LLVM build would stifle the sound of people crying all over the world.

fxcoudert · 2019-10-13T13:57:33Z

The problem with -isysroot, I think, is that it then excludes some paths from its header search. Like /usr/local/include.

smorimoto · 2019-10-14T01:06:58Z

I opened a PR. and I can't build it in my environment... (don't have enough spec) So if you want to try it, please checkout the branch.

smorimoto · 2019-10-14T03:52:37Z

I was finally able to build it. and it seems to be working correctly.

fxcoudert · 2019-10-14T08:14:03Z

With the compiler from this pull request, can you take a simple C file (one line #include <stdio.h> will do), run clang -v a.c, and paste the output here?

With an unpatched llvm, I get:

ignoring nonexistent directory "/usr/include"
#include "..." search starts here:
#include <...> search starts here:
 /usr/local/include
 /usr/local/Cellar/llvm/9.0.0/lib/clang/9.0.0/include
 /System/Library/Frameworks (framework directory)
 /Library/Frameworks (framework directory)
End of search list.

dulvinw · 2019-10-14T09:23:52Z

The issue is still there? I still get the error after completely uninstalling llvm, updating brew, reinstalling after deleting the install cache.

smorimoto · 2019-10-14T11:54:37Z

@fxcoudert I added comment on #45304.

smorimoto · 2019-10-14T11:56:00Z

@dulvinw Yes.

LeadroyaL · 2019-10-16T07:10:33Z

Since Command-Line-Tools >= 10.14, there is no /usr/include path. And after macOS Catalina, '/' partition is read-only. So I finally fix it by my self.

I diff the /usr/include for 10.13 and /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include for 10.15. The only difference is that:

Most of them are the same.
10.15 has more header files, maybe some new feature.
10.13 has c++ directory, which is /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++ in macOS 10.15.

So do the following things:

add c++ headers
sudo ln -s /Library/Developer/CommandLineTools/usr/include/c++ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++
reboot to recovery and disable SIP
reboot to desktop,

sudo remount -uw /

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

reboot to recovery and enable SIP.
result:

➜  /usr lsa include
lrwxr-xr-x  1 root  wheel    63B 10 16 14:31 include -> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include

➜  /tmp clang -v test.c
clang version 8.0.0 (tags/RELEASE_800/final)
Target: x86_64-apple-darwin19.0.0
Thread model: posix
........
#include "..." search starts here:
#include <...> search starts here:
 /usr/local/include
 /Users/leadroyal/pllvm/r/lib/clang/8.0.0/include
 /usr/include
 /System/Library/Frameworks (framework directory)
 /Library/Frameworks (framework directory)
End of search list.

smorimoto · 2019-10-16T07:23:37Z

Do NOT disable SIP even if it's temporary. and it's not good solution for many people who work for companies. Some not bad solutions are already listed #45304.

sramsay · 2019-10-16T11:23:51Z

Yeah, I think we're looking for a solution that does not involve disabling a major security feature.

smorimoto · 2019-10-29T23:19:50Z

PR Statuses

llvm.rb llvm: add missing flag for macOS Catalina #45304 - Merged
llvm@4.rb llvm@4: fix C++ compilation for Mojave and Catalina #45958 - Closed
llvm@6.rb llvm@6: Fix C++ compilation for Mojave and Catalina #45693 - Merged
llvm@7.rb llvm@7: fix C++ compilation for Mojave and Catalina #45959 - Merged
llvm@8.rb llvm@8: fix C++ compilation for Mojave and Catalina #45960 - Merged

smorimoto · 2019-10-29T23:42:05Z

@ssbanerje Could you try latest llvm package?

smorimoto · 2019-10-29T23:49:07Z

It works on my MacBook Pro now.

ssbanerje · 2019-10-30T05:16:08Z

@imbsky It works with the version from 9/24

wirelessprv-10-194-242-239 :: ~ » brew info llvm
llvm: stable 9.0.0 (bottled), HEAD [keg-only]
Next-gen compiler infrastructure
https://llvm.org/
/usr/local/Cellar/llvm/9.0.0 (6,839 files, 3.7GB)
  Poured from bottle on 2019-09-24 at 02:34:48

smorimoto · 2019-10-30T05:19:15Z

with SDKROOT?

ssbanerje · 2019-10-30T05:33:01Z

I am not entirely sure what you mean.

I just "clang test.c" without any other parameters or environment variables.

smorimoto · 2019-10-30T05:37:39Z

Oh, I'm sorry. You can set the SDKROOT variable to work around the issue. I thought you used it. anyway, I'm glad this issue has been solved for you.

smorimoto · 2019-10-30T05:39:20Z

Information for other users: The current latest build containing the fix must be Poured from bottle on 2019-10-30 at 08:34:55.

ssbanerje · 2019-10-30T05:44:19Z

Yeah the latest build works.

I dont know why but brew upgrade did not pull the latest version. So I had to delete it and install it again.

smorimoto · 2019-11-01T02:30:34Z

@ssbanerje Sorry, It's definitely our mistake and has already been fixed in the latest brew!

smorimoto · 2019-11-03T04:25:33Z

Finally, all LLVM versions except llvm@4 have been fixed and now available.

dreampiggy · 2019-12-17T08:59:19Z

Does this issue been fixed ? I still found the search path with clang (actually I use libclang):

Code:

#import <Foundation/Foundation.h>

Compile:

clang -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk

Log:

"/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/CoreFoundation.framework/Headers/CoreFoundation.h:17:10: fatal error: 'stdarg.h' file not found"

The problem maybe this strange include ? Xcode 11 does not have that SDK/usr/local/include, only SDK/usr/include

/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/local/include   <---- This does not exist !
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/include  <---- This exist

jamiesnape · 2019-12-17T14:08:48Z

Setting -isysroot overrides the fix, which was setting a default for the sysroot.

ssbanerje changed the title ~~Homebrew Clang does not have correct search path for system include directory~~ Homebrew Clang does not have correct search path for system include directory on MacOS Catalina Oct 9, 2019

smorimoto mentioned this issue Oct 14, 2019

llvm: add missing flag for macOS Catalina #45304

Closed

jamiesnape mentioned this issue Oct 22, 2019

llvm@6: Fix C++ compilation for Mojave and Catalina #45693

Closed

5 tasks

This was referenced Oct 29, 2019

llvm@4: fix C++ compilation for Mojave and Catalina #45958

Closed

llvm@7: fix C++ compilation for Mojave and Catalina #45959

Closed

llvm@8: fix C++ compilation for Mojave and Catalina #45960

Closed

smorimoto mentioned this issue Oct 30, 2019

Unable to install Ruby 2.6.5 on macOS 10.15 Catalina rbenv/ruby-build#1361

Closed

fxcoudert closed this as completed Oct 30, 2019

lock bot added the outdated PR was locked due to age label Jan 16, 2020

lock bot locked as resolved and limited conversation to collaborators Jan 16, 2020

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Homebrew Clang does not have correct search path for system include directory on MacOS Catalina #45061

Homebrew Clang does not have correct search path for system include directory on MacOS Catalina #45061

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Homebrew Clang does not have correct search path for system include directory on MacOS Catalina #45061

Homebrew Clang does not have correct search path for system include directory on MacOS Catalina #45061

Comments

ssbanerje commented Oct 9, 2019 • edited Loading

What you were trying to do (and why)

What happened

What you expected to happen

Step-by-step reproduction instructions (by running brew commands)

jamiesnape commented Oct 9, 2019

fxcoudert commented Oct 10, 2019

tschoonj commented Oct 11, 2019

sramsay commented Oct 12, 2019

fxcoudert commented Oct 13, 2019

smorimoto commented Oct 14, 2019 • edited Loading

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smorimoto commented Oct 14, 2019

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