UNIX 'diff' returns improperly when called using popen in main.c - diff

Question

I have a series of tests for a school project that involves building an assembler.
The tests use popen to catch the output of "make" and "./assembler" -- this is just so the output of these commands don't crowd the output of the test suite.
The problem is that the call to popen that executes "diff" returns a string inside the automated test suite, but not when I call it manually.
Here's the test suite code:
char buf1[256];
FILE* make;
FILE* assemble;
FILE *diff;
make = popen("make", "r");
assemble = popen("./assembler input/simple.s inter.txt out.txt", "r");
diff = popen("diff inter.txt out/ref/simple_ref.int", "r");
fgets(buf1, sizeof(buf1), diff);
printf("\nafter fgets simple -- strlen(buf) is %d\t buf is %s\n", strlen(buf1), buf1);
Here's the segment of the test suite output that corresponds with the above code:
after fgets simple -- strlen(buf) is 8 buf is 1,7c1,6
Here's the series of commands when called manually:
aweeeezy  ⋯  make
rm -f *.o assembler test-assembler core
gcc -g -std=gnu99 -Wall -o assembler assembler.c src/utils.c src/tables.c src/translate_utils.c src/translate.c
aweeeezy  ⋯  ./assembler input/simple.s inter.txt out.txt
Running pass one: input/simple.s -> inter.txt
Running pass two: inter.txt -> out.txt
Assembly operation completed successfully.
aweeeezy  ⋯  diff inter.txt out/ref/simple_ref.int
aweeeezy  ⋯  

Answer 1

When you use popen(), you're launching subprocesses which run at the same time as your program. In the code fragment you showed, the subprocesses will all be running around the same time without coordination.
To replicate the command line behavior, you want to wait until each subprocess is done; which is to say, call pclose() before moving to the next stages of your process. For examples, check something like "Pipes the easy way!" at http://www.tldp.org/LDP/lpg/node12.html