Org-babel. :flags in C code blocks dont work correctly anymore

Question

I'm trying to run current code block

#+HEADERS: :includes <math.h> <stdio.h> :flags -lm
#+HEADERS: :var x=1.0 :var y=4.0 :var z=10.0 
#+begin_src C  :tangle trying
double pi = 4*atan(1);
double r, theta, phi;
r = sqrt(x*x+y*y+z*z);
theta = acos(z/r) * 180.0/pi;
phi = atan2(y,x) * 180.0/pi;
printf("%f %f %f", r, theta, phi);
#+end_src

And when I try to execute this code, I got an error:

/tmp/ccPySR8b.o: In function 'main':
C-src-uM2yPq.c:(.text+0x5a): undefined reference to 'sqrt'
C-src-uM2yPq.c:(.text+0x75): undefined reference to 'acos'
C-src-uM2yPq.c:(.text+0xb0): undefined reference to 'atan2'
collect2: error: ld returned 1 exit status

I guess, this happened, because babel put the flag before filename gcc -lm code.c, instead gcc code.c -lm. I don't know how to fix it.

Org mode version 9.1.4
GNU Emacs 27.0.50

In fact, I tested this code block on different PCs, and this case have 100% reproducibility.

UPDATE

-lm must be used with :libs option, not :flags, thx @NickD

Answer 1

I think this problem is caused by an old version of gcc. I tangled your code to create a source file named trying.c. It compiles just fine with the -lm flag before or after the filename with a recent gcc:

gcc -lm trying.c # compiles without error
gcc trying.c -lm # compiles without error
gcc -v # -> gcc version 8.2.0 (Debian 8.2.0-3) 

When I try to run the same code on an older Ubuntu distribution, it fails as you describe:

gcc -lm trying.c
/tmp/cc7tRgsC.o: In function `main':
trying.c:(.text+0x5b): undefined reference to `sqrt'
trying.c:(.text+0x7a): undefined reference to `acos'
trying.c:(.text+0xb5): undefined reference to `atan2'
collect2: error: ld returned 1 exit status

gcc trying.c -lm # compiles without error
gcc -v # -> gcc version 4.8.5 (Ubuntu 4.8.5-4ubuntu8~14.04.2) 

Your original org-mode file compiles just fine on a computer with a recent version of gcc.

As you've discovered, setting the -lm argument using the libs option rather than the flags gets you around the issue. This might be a bug in org-mode, but I'm not familiar enough with C programming to be sure about the difference between libs vs flags.

Answer 2

In org-mode we must pass multiple header files as a list, see code below:

  #+header: :var x=1.0 :var y=4.0 :var z=10.0
  #+BEGIN_SRC C :results output  :flags -lm :includes '(<math.h> <stdio.h>)
  double r=0.0;
  double theta=0.0;
  double phi=0.0;
  double pi = 4.0 * atan(1);
  r = sqrt(x*x + y*y + z*z);
  theta = acos(z/r) *180.0/pi;
  printf("%f %f %f", r, theta, pi);
  #+END_SRC  

  #+RESULTS:
  : 10.816654 22.406871 3.141593