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.

Lemon

You can check the search paths of gcc using echo "#include <a.h>" | gcc -v -x c - – Firstly

Very often, xocde-select --install is the correct solution. Which o/s did you upgrade to? Mojave 10.14? Which XCode have you got installed? 10.0 or another version? – Minoan

@JonathanLeffler Mojave 10.14, I've installed the latest xcode from the app store version 10.0 – Lemon

OK; me too. However, both the system /usr/bin/gcc and system /usr/bin/clang are working for me. (I seem to have a problem with my home-built GCC 8.2.0, but that's tangential to your problem.) (Version: Apple LLVM version 10.0.0 (clang-1000.11.45.2) Target: x86_64-apple-darwin18.0.0 for both.) But the previous installation of the command line tools and headers seems to be OK. Hmmm…I'm going to have to think. I just finished activating Mojave (it wasn't ready when I first commented; it is now; two different Macs, one upgraded, one not). – Minoan

Have you tried running the main XCode GUI interface? It may install some stuff for you and clean up? I did that after installing XCode 10.0, but a week or more ago, long before upgrading to Mojave. – Minoan

OK; 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 GUI stuff to get licence agreement and it downloaded and installed them — or so it claimed. I then ran XCode GUI (again — command-space, xcode, return) and it said it needed to install some more stuff… – Minoan

…and still no /usr/include. Grrrr! 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. I don't know what's going on here — sorry for the torrent of "as it happens" commentary which isn't getting to an answer. – Minoan

Time passes — I've just had the automatic updater inform me that there's a new version of XCode available and should it install it. I said "Yes". Maybe it fixes this problem. – Minoan

@JonathanLeffler I've found a way. If we are using XCode 10, you will notice that if you navigate to /usr in the Finder, you will not see a folder called 'include' anymore which is why the terminal complains of the absence of the header files which is contained inside the 'include' folder. In this release statement, developer.apple.com/documentation/xcode_release_notes/… (you navigate to /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg and run that package to have the 'include' folder installed). Then you should be good to go. – Lemon

When all else fails, read the manual! Or the release notes. I'm not dreadfully surprised to find Apple wanting to turn their backs on the Unix heritage. I am disappointed. If they're careful, they could drive me away. Thank you for the information; I will experiment with it later (after catching a few hours shut-eye). – Minoan

Having installed the package (open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg at the command line), I have /usr/include again, and my GCC 8.2.0 works once more. Thanks for the pointer; well done on finding it. I suggest you write up the answer as there'll probably be other people running into the problem. – Minoan

Installation CommandLineTools "macOS_SDK_headers_for_macOS_10.14" helps to solve the case for c99 compiler unsupportability during compilations. – Rancorous

What solved the problem for me was reinstalling the command line tools: sudo rm -rf /Library/Developer/CommandLineTools and sudo xcode-select --install . – Ironist

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

---

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).

Minoan

ah thanks for writing this. Much appreciated. Cheers! – Lemon

Solved it for me!!! Thanks so much for taking the time to write this up! – Reardon

It would just be great if Apple could settle with one approach to update the header files instead of coming up with something different every time the OS gets updated. Ideally, the headers should just be installed when they were installed but that is clearly too much to ask... Thank you Jonathan: that solved the problem for me. – Allegory

I can't figure out if Apple is trying to be more like Sun or like Microsoft when they do stuff like this. – Snowslide

GRUMP!!! Things have changed again with the 10.14.1 update — or, at least, they seem to have changed again. For me, it seems that the o/s update blew away /usr/include, and the package listed in the answer above isn't present in /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg and xcode-select --install says that the command line tools currently aren't available. – Minoan

After downloading the command line tools from here: developer.apple.com/download/more (requires login with apple ID), this finally worked for me. – Keating

UnGrump!!! — See the new section in the answer about downloading CLT; thanks, @Vesal, for providing the missing link. Now my Mojave 10.14.1 machine is back in business again — and I'm willing to upgrade my other machine to 10.14.1 too. – Minoan

Fcking Apple. They can't just leave things that work, they have to move things, add steps and create churn. – Bow

In the hope that search engines will find this answer, the above instructions solved a fatal error: bits/ctype_base.h: No such file or directory: #include <bits/ctype_base.h> when compiling GCC 7.4.0 using libstdc++ on Mojave for me – Epicanthus

after installing the command line tools and installing gcc from conda worked for me thanks a ton – Amyloid

This line open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg saved me. I was deep in a rats nest with llvm and readline trying to compile crystal and then having my ruby environment not work, and this brought me back from the edge of extinction. Thank you. – Operable

This worked for me!!! I have been scouring my computer and the internet to find these missing headers!!! Phew. Thanks a ton. – Goneness

Awesome. This should be in more than just this place on the internet. @GouravMahapatra – Abode

@JoshuaPinter where did you find this command? I spent a week searching for this. – Abode

Hi @JonathanLeffler I just tried your approach to solve the problem, but even with MacOS 10.14.4 and Xcode 10.2.1, it did not worked.! So I took first approach of downloading the CLT package from Apple developer site and installed according to your guidance. Now it says ` /usr/include/Availability.h:497:18: error: missing binary operator before token "(" ` which is I guess issue because of c++17. Can you please help. You can reproduce results by installing cchardet package. – Shupe

On one of my two machines (work and home), when I upgraded to Xcode 10.2.1 (on macOS 10.14.4), I had to rerun open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg because the directory /usr/include was missing after the install. IIRC, on that machine, I kicked off the update manually when something suggested the update was available. On the other machine, I didn't have to start the update manually (it was complete by the time I looked), but I also still had /usr/include left in place. – Minoan

I'm not sure what those observations tell us except that the behaviour is not simple or 100% consistent (which is frustrating for everyone). I was very glad I had my answer to copy the open command from — I'd've upvoted myself if it was allowed (it isn't, so I didn't). I've downloaded the cChardet 2.0.0 source. It doesn't give installation instructions AFAICS, so I've no idea how I'm supposed to compile it. It isn't autoconfigurable — and I don't run setup.py or similar names since I don't know what they do and I therefore don't trust them (and I don't want to read those scripts). – Minoan

I've done some poking around; I see other people have had some problems on macOS 10.14.4. One of the closed issues says "it works" and gives a whole bunch of steps. It looks like you need uchardet as well as cChardet and you may need pyenv or some other Python software around (there was some brew involved). At this stage, I have no clue what's up. You should either add an issue in the cChardet or uchardet projects, or consider asking a question here on SO with appropriate tags. I don't have the context to help, and it isn't clear that this question deals with the problem you face. – Minoan

@HarshPatel: the previous three comments are aimed at you — I forgot to add the @ designation. AFAICS, you're saying that you can run the compiler, but maybe there's a problem with a header file? Have you looked at the Availability.h header around line 497 to see what's up? I see: 497 #if __has_include(<AvailabilityProhibitedInternal.h>). It hasn't yet caused me grief. I note that cChardet 2.1.4 doesn't include build instructions either. I'm sorely tempted to create an issue about "Please add an INSTALL file (or equivalent) that outlines the install process and prerequisites". – Minoan

Installation CommandLineTools "macOS_SDK_headers_for_macOS_10.14" helps to solve the case for c99 compiler unsupportability during compilations – Rancorous

Apple is absolutely ridiculous with those issues; almost every time I upgrade XCode I have to browse the internet to find how to get my good ol' gcc working again! – Hype

As of Xcode 11.1, it appears the /usr/include directory is indeed wiped out, and the macOS_SDK_headers_for_macOS_10.14.pkg file used to regenerate it has been removed (as the Xcode 10.0 release notes warned). Thanks, Apple! sigh – Tiaratibbetts

@Andrew: yes — see the "Catalina" version of this question which I created (and provisionally answered) yesterday. I am downloading XCode 11.1 to my Catalina machine now, but the 11.0 version is similar to what you say for 11.1. – Minoan

On Catalina, I managed to get perl module Text::Levenshtein::XS to compile by setting C_INCLUDE_PATH environment variable to point at XCode 11 header directory $ C_INCLUDE_PATH=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE make – Rodgerrodgers

I was having problems installing git2r in a brand new macOS Mojave 10.14.6 installation. Following the steps in @JonathanLeffler post helped me fix the error: configure: error: cannot run C compiled programs.. I used clang7 and gfortran-6.1 – Ostensorium

@JoshuaPinter "this brought me back from the edge of extinction" was the best and perhaps most personally relevant comment I've seen on SO – Hercules

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.

Halftruth

Nothing worked, but this one did. Thank you very much!! – Exurbia

wickedsickbrothnx – Geophagy

This worked for me too for macOS Big Sur. – Epidemic

Worked for me on MacOS 12.5 – Tabbitha

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.

Gustafsson

Excellent! After your steps, the macOS_SDK_headers_for_macOS_10.14.pkg get available, and the command open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg did what was supposed to do. Thanks a million!! – Kleiman

For me, the following worked: export CPATH=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/include – Nettles

Thank you! I was stuck but this really worked for me with Mojave 10.4.6 and XCode 11.3.1 – Dextrad

Everytime Apple released a system update I have to fix this problem with Clion in different way. – Teddie

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.

Jennings

This saved me. Thanks a lot! – Joshia

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.

Varicolored

This solved my problem on macOS Ventura 13.3.1, thank you – Hopson

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.

Grandmotherly

You're a life saver. Worked for me after updating to XCode 12.2 – Rationality

Yeah, same here! Helped me after upgrading to XCode 12.2! – Allmon

@BilalAhmedYaseen You need to create the directory structure yourself (my own ln does this automatically). – Grandmotherly

Worked in BigSur 11.2.3 – Manysided

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.

Giustino

Which pip are you using? I think that could be the key problem. – Drinker

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)

Episcopalian

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.

Extroversion

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.

Lesh

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.

Verecund

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

Activist

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.

Hurtless

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

Fabiano

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.

Depravity

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

Munguia

Shouldn’t this be a comment? – Drinker