Why can't FreeBSD compile anything from source code?
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Perhaps you are doing just that, trying to install source for Linux. Check the programs you are trying to install and check if there is anything about *BSD. If not, the source is probably made for Linux.
To answer your question -- Yes, the BSD's are kind of married to their (ports|pkgsrc). When a package goes into the ports system, the port's build includes patches to make the code work on that particular BSD.
Linux has a lot of stupid little peculiarities that are specific to linux that need to be fixed before they'll work on BSD (or anything else for that matter), and that's what the ports tree is all about.
I think that source from many tarballs check if you are using BSD during the configure script.
For example in the streamtuner configure script, there are 37 lines referencing BSD.
Here are the first five such lines:
echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
echo $ECHO_N "checking for a BSD-compatible install... $ECHO_C" >&6
# (eg FreeBSD returns the mod time of the symlink's containing
# Now try BSD make style include.
_am_result=BSD
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