[Phylobase-devl] phylobase status

François Michonneau francois.michonneau at gmail.com
Tue Nov 13 05:39:31 CET 2012

Hi Ben,

  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.

  -- François

On Mon, Nov 12, 2012 at 10:40 AM, Jombart, Thibaut <t.jombart at imperial.ac.uk
> wrote:

> Hi Ben,
> 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.
> Cheers
> Thibaut
> ________________________________________
> From: phylobase-devl-bounces at lists.r-forge.r-project.org [
> phylobase-devl-bounces at lists.r-forge.r-project.org] on behalf of Ben
> Bolker [bbolker at gmail.com]
> Sent: 12 November 2012 14:42
> To: phylobase-devl at lists.r-forge.r-project.org; Emmanuel Paradis
> Subject: [Phylobase-devl] phylobase status
> Hash: SHA1
>   I spent a little while cleaning up some problems with phylobase (the
> version on CRAN looks broken -- I don't know how long it's been that
> way).  It now passes checks on my machine with a couple of NOTEs, one
> about the size of the 'libs' directory (which we can't really do
> anything about), and one about redirection of output to stdout and
> stderr, which is frowned upon.
> There appear to be 34 instances of this in the C++ code:
> grep  "\(cout\|cerr\)" *.cpp | wc
>      34     563    3761
>   Is someone willing to spend an hour or so figuring out how to
> replace these appropriately?  (section 6.5 of the R-exts manual says
> to use Rprintf and REprintf)  This has gone under the radar so far,
> but I can imagine CRAN (who have been getting stricter and stricter)
> will complain about this when we resubmit.
>   This is with ape 3.0-6; as I said, it otherwise tests clean on my
> machine, we'll see whether R-Forge complains or not.
>   Volunteers?
>    cheers
>      Ben
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