There were also a few other things I had to do to get compile to work on
Mac. A lot of them seem to be differences in how c includes work, but
I'm don't really know anything about c and only really arrived at these
things by trial and error and lots of internet surfing!
1. #include <malloc.h> give errors, but #include <malloc/malloc.h> works
2. I had to change chado_record_uniq.cpp a bit (see attached). I put in
a few more includes (as I said earlier I'm not a c or cpp expert so I
can't guarantee every one is necessary, but in the current state it
works). I had to add a definition of the getline and related functions
that I found on the internet as for some reason this is not in the
version of cpp that Mac OS X has as standard.
3. I had to add #include <libgen.h> to SnpClustererMain.cpp
There is also a problem in dtdValid.pl for Macs with this line, toward
the end of the file:
my $status = system "zcat -f $file | xmllint --noout --nonet --dtdvalid
The version of zcat that is in Snow Leopard is kind of weird and you get
error messages like:
Error executing script exit value: 1zcat:
No such file or directory
Simply changing "zcat" to "gzcat" fixes this!
Hopefully, if I have somehow introduced horrible errors that will haunt
me down the line someone can set me straight. Also, maybe some of it is