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  lt stdio h gt                     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

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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

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Had similar problems as the OP  Issue     cat hello c    include  lt stdlib h gt  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 gt  amp 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

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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     Install Clang v8 from https   cran r-project org bin macosx tools  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

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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  lt stdio h gt                             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 - gt  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

User · Answer

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

User · Answer

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

User · Answer

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

User · Answer

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

User · Answer

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

User · Answer

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

User · Answer

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

User · Answer

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

User · Answer

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

User · Answer

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

User · Answer

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

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

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