Recently, back in February of 2018, I updated Xcode and installed the macOS High Sierra Supplemental Update as well. I was quite unhappy to find out that, following these updates, compiling software written in C/C++ using gcc (which was up to date!) seemed to be failing with a “stdio.h” file not found error, as follows:
...fatal error: stdio.h: No such file or directory
#import<stdio.h>;
^
1 error generated.
...
The missing file was the same in multiple cases, for multiple software programs that I think included both the species tree inference software SVDquartets and the popgen/selection forward-time simulation program SFS_CODE. The “.h” extension indicates that the compiler could not find an important header file, a kind of file that provides declarations and macros for the main source code of C/C++ software. Luckily, after zooming around online threads, I found the following very straightforward solution here: simply reinstall Xcode Command Line Tools. I did this by typing the following into Terminal and hitting return…
$ xcode-select --install
Next, I clicked “Install” and a window indicated when the install was complete. I then checked the install in Terminal by doing “$ xcode-select -p”…and voila! When I retried make in the software’s distribution or src folder (e.g. the distribution folder in the case of SFS_CODE), I was at last able to get the software to build correctly and produce working executables. I hope this helps someone else who might run across the same or a similar problem.
~J