[Phylobase-devl] New phylobase build approach using static libncl (Was: Rcpp and OS X compiliation)

[Mark Holder]

Hi again,

Mark Holder and then Peter Cowan wrote:
>> I should be able to fix that aspect of things tomorrow.  When I  
>> push those changes to NCL, I'll post to this list so that someone  
>> with write permissions to phylobase's svn repo can copy those  
>> changes into the phylobase.
>
> I'm happy to do this.


At http://people.ku.edu/~mtholder/mth_diff_pkg.tar.gz you'll find a  
tar.gz archive.  If you unpack it, you'll see the contents of  
phylobase's pkg directory with the edits that I had to make to get  
things working. Several files were touched (the archive has all of the  
pkg if I run svn stat I see:

M       pkg/src/NCLInterface.h
M       pkg/src/ReadWithNCL.cpp
M       pkg/src/nxspublicblocks.cpp
M       pkg/src/nxscharactersblock.cpp
M       pkg/src/ncl/nxsreader.h
M       pkg/src/nxsreader.cpp
M       pkg/src/NCLInterface.cpp
M       pkg/inst/nexusfiles/treepluscharV01.nex



Note that pkg/inst/nexusfiles/treepluscharV01.nex  is not a valid  
NEXUS file if you change line 74 from:

	BEGIN CHARACTERS2;
to

	BEGIN CHARACTERS;
then it should work.

Also note that checkTree(object) in  checkdata.R is complaining about  
the data returned from pkg/inst/nexusfiles/co1.nex, but I don't know  
why.  It looks OK to me.  It is possible that I broke something, as  
I'm not too familiar with what was supposed to be returned by NCL (I  
tried to return the same syntax that was originally being returned).





>>> Lastly, is there a way to control the output though Rcpp or  
>>> otherwise, a fair bit of what appears to be stderr gets printed in  
>>> the R console, it'd be nice to control this.
>>
>> The BASICCMDLINE implementation writes lots of status output to the  
>> standard error stream.  When I work with it tomorrow, I can make  
>> its chattiness controllable by an argument.
>
> That would be wonderful!

I'm partially there. For the NCLInterface.cpp code used by phylobase I  
changed it so that it is quiet by default.  It is now be possible to  
send a numeric argument into BASICCMDLINE.Initialize();

Currently (in ReadWithNCL.cpp) it says,
	reader.Initialize(const_cast < char* > (filename.c_str()));

If you change it to
	reader.Initialize(const_cast < char* > (filename.c_str()), 0);

you'll see more messages to stderr.  The numbers 0-7 generate less and  
less output.  8 or higher should be silent (which is the default).


I did not add the hooks in ReadWithNCL.cpp to get a verbosity argument  
from R and pass that along to NCL.






> If you have time, I'd like to have a more in depth conversation of  
> what NCL is capable and how it is organized.  Wrapping NCL is, in my  
> opinion, one of the key features of phylobase.  But, I also get the  
> feeling that there is more functionality we aren't taking advantage  
> of.
>
> Perhaps a GSOC student project could come out of it.  Or at the very  
> least I can expand the developers guide section about NCL so we are  
> better able to maintain it in the future.



The NCL docs are terribly out of date. Completely my fault. Paul Lewis  
is great about documenting his code, but I have not kept up with the  
documenting tasks.  I'm happy to chat.

The main potential problems that I see with the ways that phylobase is  
using NCL now are:
	1. in NCLInterface.cpp there are lots of call to  
RemoveUnderscoresAndSpaces to get rid of spaces and _ in names.  That  
makes names easier to deal with, but at some point will bite you  
(somebody will have dataset with a taxon labelled "AB" and another  
with "A B", after transformation there will be a name clash).

	2. It was not clear to me how different character blocks should  
separated.  I just return the union of all character matrices.  It  
seems like, phylobase will need a richer interaction with NCL if  
phylobase wants to know about whether the data came in under different  
blocks.



all the best,
Mark





Mark Holder

mtholder at ku.edu
http://phylo.bio.ku.edu/mark-holder

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