<br>Hi Ben,<br><br> I'm currently in the field and won't have a chance to look into it until early December. As I recall most (if not all) of these stdout/stderr are actually remnants of the initial hack of NCL. The phylobase interface was developed based on some example code provided with NCL that was a basic command line parser of NEXUS files. From what I remember, most of these stdout/stderr lines are not used by phylobase at all and could possibly be removed without affecting the rest of the code.<br>
<br> Cheers,<br> -- François<br><br><div class="gmail_quote">On Mon, Nov 12, 2012 at 10:40 AM, Jombart, Thibaut <span dir="ltr"><<a href="mailto:t.jombart@imperial.ac.uk" target="_blank">t.jombart@imperial.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Ben,<br>
<br>
thanks for looking into this. About the printf/Rprintf thing, I've had to make the changes on other packages recently. If it's remained unnoticed thus far I'm afraid there's a good chance the CRAN maintainer will pick up on this soon. Sorry, I don't do C++ so can't make the changes.<br>
<br>
Cheers<br>
<br>
Thibaut<br>
<br>
<br>
________________________________________<br>
From: <a href="mailto:phylobase-devl-bounces@lists.r-forge.r-project.org">phylobase-devl-bounces@lists.r-forge.r-project.org</a> [<a href="mailto:phylobase-devl-bounces@lists.r-forge.r-project.org">phylobase-devl-bounces@lists.r-forge.r-project.org</a>] on behalf of Ben Bolker [<a href="mailto:bbolker@gmail.com">bbolker@gmail.com</a>]<br>
Sent: 12 November 2012 14:42<br>
To: <a href="mailto:phylobase-devl@lists.r-forge.r-project.org">phylobase-devl@lists.r-forge.r-project.org</a>; Emmanuel Paradis<br>
Subject: [Phylobase-devl] phylobase status<br>
<div class="HOEnZb"><div class="h5"><br>
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<br>
I spent a little while cleaning up some problems with phylobase (the<br>
version on CRAN looks broken -- I don't know how long it's been that<br>
way). It now passes checks on my machine with a couple of NOTEs, one<br>
about the size of the 'libs' directory (which we can't really do<br>
anything about), and one about redirection of output to stdout and<br>
stderr, which is frowned upon.<br>
<br>
There appear to be 34 instances of this in the C++ code:<br>
<br>
grep "\(cout\|cerr\)" *.cpp | wc<br>
34 563 3761<br>
<br>
Is someone willing to spend an hour or so figuring out how to<br>
replace these appropriately? (section 6.5 of the R-exts manual says<br>
to use Rprintf and REprintf) This has gone under the radar so far,<br>
but I can imagine CRAN (who have been getting stricter and stricter)<br>
will complain about this when we resubmit.<br>
<br>
This is with ape 3.0-6; as I said, it otherwise tests clean on my<br>
machine, we'll see whether R-Forge complains or not.<br>
<br>
Volunteers?<br>
<br>
cheers<br>
Ben<br>
<br>
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