Can't compile C program on a Mac after upgrade to Mojave

Question

I have used the gcc command on the terminal to compile C programs but all of a sudden, after an update to my Mac's OS (to macOS 10.14 Mojave, and XCode 10.0), I started receiving the message:

test.c:8:10: fatal error: stdio.h: No such file or directory
#include <stdio.h>
         ^~~~~~~~~
compilation terminated.

I already have gcc installed as I can find it in /usr/local/bin and there really is a gcc in there. I tried running the same file on my other iMac and it worked without any issue.

I tried running xcode-select --install and it already was installed, hence it didn't fix the issue I'm having now. I'm guessing that the path is messed up as it doesn't seem like it can find gcc after I started copying and pasting some commands from other resources to solve this issue.

Would like some help on this.

Answer 1

TL;DR

Make sure you have downloaded the latest 'Command Line Tools' package and run this from a terminal (command line):

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

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For some information on Catalina, see Can't compile a C program on a Mac after upgrading to Catalina 10.15.

---

^{Extracting a semi-coherent answer from rather extensive comments…}

Preamble

Very often, xcode-select --install has been the correct solution, but it does not seem to help this time. Have you tried running the main Xcode GUI interface? It may install some extra software for you and clean up. I did that after installing Xcode 10.0, but a week or more ago, long before upgrading to Mojave.

I observe that if your GCC is installed in /usr/local/bin, you probably aren't using the GCC from Xcode; that's normally installed in /usr/bin.

I too have updated to macOS 10.14 Mojave and Xcode 10.0. However, both the system /usr/bin/gcc and system /usr/bin/clang are working for me (Apple LLVM version 10.0.0 (clang-1000.11.45.2) Target: x86_64-apple-darwin18.0.0 for both.) I have a problem with my home-built GCC 8.2.0 not finding headers in /usr/include, which is parallel to your problem with /usr/local/bin/gcc not finding headers either.

I've done a bit of comparison, and my Mojave machine has no /usr/include at all, yet /usr/bin/clang is able to compile OK. A header (_stdio.h, with leading underscore) was in my old /usr/include; it is missing now (hence my problem with GCC 8.2.0). I ran xcode-select --install and it said "xcode-select: note: install requested for command line developer tools" and then ran a GUI installer which showed me a licence which I agreed to, and it downloaded and installed the command line tools — or so it claimed.

I then ran Xcode GUI (command-space, Xcode, return) and it said it needed to install some more software, but still no /usr/include. But I can compile with /usr/bin/clang and /usr/bin/gcc — and the -v option suggests they're using

InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Working solution

Then Maxxx noted:

I've found a way. If we are using Xcode 10, you will notice that if you navigate to the /usr in the Finder, you will not see a folder called 'include' any more, which is why the terminal complains of the absence of the header files which is contained inside the 'include' folder. In the Xcode 10.0 Release Notes, it says there is a package:

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

and you should install that package to have the /usr/include folder installed. Then you should be good to go.

When all else fails, read the manual or, in this case, the release notes. I'm not dreadfully surprised to find Apple wanting to turn their backs on their Unix heritage, but I am disappointed. If they're careful, they could drive me away. Thank you for the information.

Having installed the package using the following command at the command line, I have /usr/include again, and my GCC 8.2.0 works once more.

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

Downloading Command Line Tools

As Vesal points out in a valuable comment, you need to download the Command Line Tools package for Xcode 10.1 on Mojave 10.14, and you can do so from:

• https://developer.apple.com/download/more/

You need to login with an Apple ID to be able to get the download. When you've done the download, install the Command Line Tools package. Then install the headers as described in the section 'Working Solution'.

This worked for me on Mojave 10.14.1. I must have downloaded this before, but I'd forgotten by the time I was answering this question.

Upgrade to Mojave 10.14.4 and Xcode 10.2

On or about 2019-05-17, I updated to Mojave 10.14.4, and the Xcode 10.2 command line tools were also upgraded (or Xcode 10.1 command line tools were upgraded to 10.2). The open command shown above fixed the missing headers. There may still be adventures to come with upgrading the main Xcode to 10.2 and then re-reinstalling the command line tools and the headers package.

Upgrade to Xcode 10.3 (for Mojave 10.14.6)

On 2019-07-22, I got notice via the App Store that the upgrade to Xcode 10.3 is available and that it includes SDKs for iOS 12.4, tvOS 12.4, watchOS 5.3 and macOS Mojave 10.14.6. I installed it one of my 10.14.5 machines, and ran it, and installed extra components as it suggested, and it seems to have left /usr/include intact.

Later the same day, I discovered that macOS Mojave 10.14.6 was available too (System Preferences ⟶ Software Update), along with a Command Line Utilities package IIRC (it was downloaded and installed automatically). Installing the o/s update did, once more, wipe out /usr/include, but the open command at the top of the answer reinstated it again. The date I had on the file for the open command was 2019-07-15.

Upgrade to XCode 11.0 (for Catalina 10.15)

The upgrade to XCode 11.0 ("includes Swift 5.1 and SDKs for iOS 13, tvOS 13, watchOS 6 and macOS Catalina 10.15") was released 2019-09-21. I was notified of 'updates available', and downloaded and installed it onto machines running macOS Mojave 10.14.6 via the App Store app (updates tab) without problems, and without having to futz with /usr/include. Immediately after installation (before having run the application itself), I tried a recompilation and was told:

Agreeing to the Xcode/iOS license requires admin privileges, please run “sudo xcodebuild -license” and then retry this command.

Running that (sudo xcodebuild -license) allowed me to run the compiler. Since then, I've run the application to install extra components it needs; still no problem. It remains to be seen what happens when I upgrade to Catalina itself — but my macOS Mojave 10.14.6 machines are both OK at the moment (2019-09-24).

Answer 2

After trying every answer I could find here and online, I was still getting errors for some missing headers. When trying to compile pyRFR, I was getting errors about stdexcept not being found, which apparently was not installed in /usr/include with the other headers. However, I found where it was hiding in Mojave and added this to the end of my ~/.bash_profile file:

export CPATH=/Library/Developer/CommandLineTools/usr/include/c++/v1

Having done that, I can now compile pyRFR and other C/C++ programs. According to echo | gcc -E -Wp,-v -, gcc was looking in the old location for these headers (without the /c++/v1), but not the new location, so adding that to CFLAGS fixed it.

Answer 3

When you

• updated to Mojave 10.14.6
• your /usr/include was deleted again
• the package mentioned in @Jonathan-lefflers answer doesn't exist anymore The file /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg does not exist. and
• Xcode complains that command line tools are already installed xcode-select --install xcode-select: error: command line tools are already installed, use "Software Update" to install updates

Then, what helped me recover the mentioned package, was deleting the whole CommandLineTools folder (sudo) rm -rf /Library/Developer/CommandLineTools and reinstall it xcode-select --install.

Answer 4

The problem is that Xcode, especially Xcode 10.x, has not installed everything, so ensure the command line tools are installed, type this in a terminal shell:

xcode-select --install

also start Xcode and ensure all the required installation is installed ( you should get prompted if it is not.) and since Xcode 10 does not install the full Mac OS SDK, run the installer at

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

as this package is not installed by Xcode 10.

Answer 5

I've found great solution and explanation at this GitHub comment. The trick:

make SDKROOT=`xcrun --show-sdk-path` MACOSX_DEPLOYMENT_TARGET=

Did the job.

Answer 6

ln -s /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk' might help you. It fixed my problem.

Answer 7

NOTE: The following is likely highly contextual and time-limited before the switch/general availability of macos Catalina 10.15. New laptop. I am writing this Oct 1st, 2019.

These specific circumstances are, I believe, what caused build problems for me. They may not apply in most other cases.

Context:

• macos 10.14.6 Mojave, Xcode 11.0, right before the launch of macos Catalina 10.15. Newly purchased Macbook Pro.

• failure on pip install psycopg2, which is, basically, a Python package getting compiled from source.

• I have already carried out a number of the suggested adjustments in the answers given here.

My errors:

pip install psycopg2
Collecting psycopg2
  Using cached https://files.pythonhosted.org/packages/5c/1c/6997288da181277a0c29bc39a5f9143ff20b8c99f2a7d059cfb55163e165/psycopg2-2.8.3.tar.gz
Installing collected packages: psycopg2
  Running setup.py install for psycopg2 ... error
    ERROR: Command errored out with exit status 1:
     command: xxxx/venv/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/bk/_1cwm6dj3h1c0ptrhvr2v7dc0000gs/T/pip-install-z0qca56g/psycopg2/setup.py'"'"'; __file__='"'"'/private/var/folders/bk/_1cwm6dj3h1c0ptrhvr2v7dc0000gs/T/pip-install-z0qca56g/psycopg2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/bk/_1cwm6dj3h1c0ptrhvr2v7dc0000gs/T/pip-record-ef126d8d/install-record.txt --single-version-externally-managed --compile --install-headers xxx/venv/include/site/python3.6/psycopg2


...
/usr/bin/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -pipe -Os -isysroot/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk -DPSYCOPG_VERSION=2.8.3 (dt dec pq3 ext lo64) -DPG_VERSION_NUM=90615 -DHAVE_LO64=1 -I/Users/jluc/kds2/py2/venv/include -I/opt/local/Library/Frameworks/Python.framework/Versions/3.6/include/python3.6m -I. -I/opt/local/include/postgresql96 -I/opt/local/include/postgresql96/server -c psycopg/psycopgmodule.c -o build/temp.macosx-10.14-x86_64-3.6/psycopg/psycopgmodule.o

    clang: warning: no such sysroot directory: 
'/Applications/Xcode.app/Contents/Developer/Platforms
                              ❌the real error❌
/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk' [-Wmissing-sysroot]
    In file included from psycopg/psycopgmodule.c:27:
    In file included from ./psycopg/psycopg.h:34:
    /opt/local/Library/Frameworks/Python.framework/Versions/3.6/include/python3.6m/Python.h:25:10: fatal error: 'stdio.h' file not found
                             ❌ what I thought was the error ❌
    #include <stdio.h>
             ^~~~~~~~~
    1 error generated.

    It appears you are missing some prerequisite to build the package 

What I did so far, without fixing anything:

• xcode-select --install
• installed xcode
• open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg

Still the same error on stdio.h.

which exists in a number of places:

(venv) jluc@bemyerp$ mdfind -name stdio.h
/System/Library/Frameworks/Kernel.framework/Versions/A/Headers/sys/stdio.h
/usr/include/_stdio.h
/usr/include/secure/_stdio.h
/usr/include/stdio.h  ✅  I believe this is the one that's usually missing.
                            but I have it.
/usr/include/sys/stdio.h
/usr/include/xlocale/_stdio.h

So, let's go to that first directory clang is complaining about and look:

(venv) jluc@gotchas$ cd /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs
(venv) jluc@SDKs$ ls -l
total 0
drwxr-xr-x  8 root  wheel  256 Aug 29 23:47 MacOSX.sdk
drwxr-xr-x  4 root  wheel  128 Aug 29 23:47 DriverKit19.0.sdk
drwxr-xr-x  6 root  wheel  192 Sep 11 04:47 ..
lrwxr-xr-x  1 root  wheel   10 Oct  1 13:28 MacOSX10.15.sdk -> MacOSX.sdk  
drwxr-xr-x  5 root  wheel  160 Oct  1 13:34 .

Hah, we have a symlink for MacOSX10.15.sdk, but none for MacOSX10.14.sdk. Here's my first clang error again:

clang: warning: no such sysroot directory: '/Applications/Xcode.app/.../Developer/SDKs/MacOSX10.14.sdk' [-Wmissing-sysroot]

My guess is Apple jumped the gun on their xcode config and are already thinking they're on Catalina. Since it's a new Mac, the old config for 10.14 is not in place.

THE FIX:

Let's symlink 10.14 the same way as 10.15:

ln -s MacOSX.sdk/ MacOSX10.14.sdk

btw, if I go to that sdk directory, I find:

...
./usr/include/sys/stdio.h
./usr/include/stdio.h
....

OUTCOME:

pip install psycopg2 works.

Note: the actual pip install command made no reference to MacOSX10.14.sdk, that came at a later point, possibly by the Python installation mechanism introspecting the OS version.

Answer 8

Be sure to check Xcode Preferences -> Locations.

The Command Line Tools I had selected was for the previous version of Xcode (8.2.1 instead of 10.1)

Answer 9

Had similar problems as the OP

Issue

cat hello.c

#include <stdlib.h>
int main() { exit(0); }

clang hello.c

/usr/local/include/stdint.h:2:10: error: #include nested too deeply
etc...

Attempted fix

I installed the latest version of XCode, however, release notes indicated the file mentioned in the previous fix, from Jonathan here, was no longer available.

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

Details here https://developer.apple.com/documentation/xcode_release_notes/xcode_10_release_notes , under the New Features section.

---

Solution that worked for me...

Using details in this comment, https://github.com/SOHU-Co/kafka-node/issues/881#issuecomment-396197724

I found that brew doctor reported I had unused includes in my /usr/local/ folder.

So to fix, I used the command provided by user HowCrazy , to find the unused includes and move them to a temporary folder.

Repeated here...

mkdir /tmp/includes
brew doctor 2>&1 | grep "/usr/local/include" | awk '{$1=$1;print}' | xargs -I _ mv _ /tmp/includes

After running the scripts, the include file issue was gone. nb: I commented on this issue here too.

Answer 10

On Big Sur 11.5.2 with XCode 12.5.1 it may help:

sudo ln -s /Library/Developer/CommandLineTools/SDKs/MacOSX11.1.sdk /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk

CMake told me, that /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX11.1.sdk didn't exist, and I decided to make a symlink.

P.S. completely removing CommandLineTools directory, running installation, preforming brew upgrade, etc. didn't help before.

Answer 11

I was having this issue and nothing worked. I ran xcode-select --install and also installed /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg.

BACKGROUND

Since I was having issues with App Store on a new laptop, I was forced to download the Xcode Beta installer from the Apple website to install Xcode outside App Store. So I only had Xcode Beta installed.

SOLUTION

This, (I think), was making clang to not find the SDKROOT directory /Applications/Xcode.app/...., because there is no Beta in the path, or maybe Xcode Beta simply doesn't install it (I don't know). To fix the issue, I had to remove Xcode Beta and resolve the App Store issue to install the release version.

tldr;

If you have Xcode Beta, try cleaning up everything and installing the release version before trying out the solutions that are working for other people.

Answer 12

I tried almost all the posted solutions and nothing worked for me. I use Mojave OS (10.14.6) and what finally worked for me (after removing and re-installing Xcode and CLTs and SDK headers):

1. Install Clang v8 from https://cran.r-project.org/bin/macosx/tools/
2. Modify the following lines from ~/.R/Makevars file

CC=/usr/local/opt/llvm/bin/clang -fopenmp
CXX=/usr/local/opt/llvm/bin/clang++

with

CC=/usr/local/clang8/bin/clang -fopenmp
CXX=/usr/local/clang8/bin/clang++

Now R packages that rely on C compilers install successfully

Answer 13

As Jonathan Leffler points out above, the macOS_SDK_headers.pkg file is no longer there in Xcode 10.1.

What worked for me was to do brew upgrade and the updates of gcc and/or whatever else homebrew did behind the scenes resolved the path problems.

Answer 14

apue.h dependency was still missing in my /usr/local/include after I managed to fix this problem on Mac OS Catalina following the instructions of this answer

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

Answer 15

I had the same issue with Golang (debugging with Goland) after migration. The only (ridiculous) thing that helped is renaming the following folder:

sudo mv /usr/local/include /usr/local/old_include

Apparently it is related to old files that homebrew installed and now broken.

Answer 16

@JL Peyret is right!

if you macos 10.14.6 Mojave, Xcode 11.0+

then

cd /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs

sudo ln -s MacOSX.sdk/ MacOSX10.14.sdk