Can you please attach a sample script here which shows this problem?  Somehow I doubt this has anything to do with Apache2..but could you check if compiling a CGI and running the test script with it does the same?

My script:
<?
$command='/sbin/ping -c 1 www.sunet.se';
passthru($command); /* This works */
exec($command); /* This works */
system($command); /* This gives undefined function */
?>
My output:
PING www.sunet.se (192.36.125.18): 56 data bytes 64 bytes from 192.36.125.18: icmp_seq=0 ttl=247 time=14.091 ms --- www.sunet.se ping statistics --- 1 packets transmitted, 1 packets received, 0% packet loss round-trip min/avg/max/stddev = 14.091/14.091/14.091/0.000 ms
Fatal error: Call to undefined function: system() in /usr/local/www/data-dist/test.php on line 8

I just compiled php standalone, it worked, no undefined function.

Can you try compiling a new apache2 module from _clean_ sources (fresh download from www.php.net :) and only include
the minimum amount of configure options. (ie. just the --with-apxs2 one)

+--------------------------------------------------------------------+
|                        *** WARNING ***                             |
|                                                                    |
| In order to build PHP as a Apache2 module on FreeBSD, you have to  |
| add  --with-tsrm-pth to your ./configure line. Therefore you need  |
| to install gnu-pth from /usr/ports/devel/pth.                      |
+--------------------------------------------------------------------+
Should I include this also?

Using --with-apxs2 --with-tsrm-pth

same problem.

Only --with-apxs2 doesn't work, se below:

Syntax error on line 273 of /usr/local/etc/apache2/httpd.conf:
Cannot load /usr/local/libexec/apache2/libphp4.so into server: /usr/local/libexec/apache2/libphp4.so: Undefined symbol "pthread_getspecific"

So it's yet another apache2 problem then.
Could you also try this snapshot:

http://snaps.php.net/php4-latest.tar.gz

./configure --with-apxs2
[loads of suff]
checking for Berkeley DB2 support... no
./configure: 21429: Syntax error: "fi" unexpected (expecting "then")

Trying php4-200209111200:
make install
[a lot of output]
[PEAR] Archive_Tar    - installed: 0.9
[PEAR] Console_Getopt - installed: 0.11
[PEAR] PEAR           - installed: 0.91
Segmentation fault - core dumped
*** Error code 139

Stop in /usr/home/danne/tmp/php4-200209111200.
*** Error code 1

The PHP installation segfaults, but when I compile it against Apache2 I don't get an executable, so how do I debug it?

Yeah, it does that sometimes... just try make install again.

Yes, I've tried daily since Sep 14:th. Same coredump. Would be nice if I could contribute with something useful or work around the problem.

Are you able to successfuly complete the make install if you add --without-pear to your confgure line?

Tried it and it worked well, I've tried a few applications (squirrelmail, gallery) under this build and it works fine.

But the main thing: system() works!

Thanks a lot, case closed!

This bug has been fixed in CVS.

In case this was a PHP problem, snapshots of the sources are packaged
every three hours; this change will be in the next snapshot. You can
grab the snapshot at http://snaps.php.net/.
 
In case this was a documentation problem, the fix will show up soon at
http://www.php.net/manual/.

In case this was a PHP.net website problem, the change will show
up on the PHP.net site and on the mirror sites in short time.
 
Thank you for the report, and for helping us make PHP better.

user reports that problem has been fixed.