Mac compatibility - other things

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Mac compatibility - other things

Jason Kwan
Hi Joshua,

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
(cluster_inp.c)
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
$dtd -";

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:
/usr/local/projects/test/output_repository/ncbi-blastn/72_default/i1/g1/16S_col2_noNs.ncbi-blastn.bsml.Z:
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
redundant.

Jason



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