[Phylobase-devl] Fwd: Re: CRAN packages phylobase and adephylo

Mark Holder mtholder at gmail.com
Sun Nov 6 18:58:46 CET 2011

	I don't have a Solaris machine to test on either. 

	My guess: 

		If the compiler on Solaris is putting all of the C-functions in C++'s "std"" namespace, then you would see something like this. Changing "sprintf" to "std::sprintf" might fix this (it looks like the std:: namespace decorator will be needed on strcmp, strchr, and memmove at least, probably others). That should not break the builds on other platforms.

	Feel free to direct the Solaris user to me, and I'll try to help diagnose other issues with the NCL build.

all the best,

On Nov 4, 2011, at 7:35 PM, Ben Bolker wrote:

>  Hey guys,
>  Any opinions about this?
>  adephylo is not absolutely necessary to phylobase, but it bothers me
> to spend effort removing it when we might be able to fix it instead.
> Perhaps if Thibaut responds (the fix is fairly trivial) and we then
> grovel to the R Gods/BDR ...
>  It may be necessary for political reasons to make these changes and
> then revert them if/when we get adephylo fixed.
>  We have another issue -- the Solaris build (sigh) is failing, with the
> following error:
> "./ncl/nxsstring.h", line 467: Error: The function "sprintf" must have
> a prototype.
>  Fixing this (by remote control) could be pretty challenging -- R-forge
> doesn't have a Solaris build, so it could involve more grovelling to BDR
> for advice (another reason to temporarily do the adephylo fix, unless we
> can get our act together quickly).
>  cheers
>    Ben
> -------- Original Message --------
> Subject: Re: CRAN packages phylobase and adephylo
> Date: Sun, 6 Nov 2011 16:50:41 +0000 (GMT)
> From: Prof Brian Ripley <ripley at stats.ox.ac.uk>
> To: Ben Bolker <bbolker at gmail.com>
> CC: CRAN at r-project.org
> On Fri, 4 Nov 2011, Ben Bolker wrote:
>> On 11-11-04 04:31 AM, Prof Brian Ripley wrote:
>>> Package adephylo has been archived: it was failing on R 2.14.0 and we
>>> have had no response to several messages to the maintainer.
>>> Package phylobase suggests adephylo, but still passes its checks without
>>> it (and grepping the code suggests that it does not actually use it).
>>> Nevertheless, the documentation needs updating, so can we please have a
>>> revised version of phylobase.
>>> Brian Ripley
>> I think I see the problem with adephylo -- I'm going to try to nag the
>> maintainer (who I know personally) a bit more and see if we can get this
>> resolved from that end.
> It's far too late: adephylo has been archived.  His complete failure
> to respond to messages means we may be reluctant to re-admit it.
> In any case, phylobase needs an update now.
>> thanks
>>   Ben Bolker
> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
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