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

Jombart, Thibaut t.jombart at imperial.ac.uk
Mon Nov 7 19:18:24 CET 2011

Dear all, 

sorry for not replying sooner, I am just reading these posts now - need to pay more attention to this ML.

The whole situation is very odd. I received only one single automatic notification about adephylo not compiling on windows with R beta, to which I replied the next day. Other than that, I never received any other message about the package - not even in my spambox, assuming a spam filter would dare to tag Brian Ripley's emails as 'spam'. Anyway, I only discovered this morning is that adephylo's been archived, thanks to Ben.

I have submitted a new version this afternoon and adephylo is back on CRAN.

The scary thing is, when I enquired today to BR about what happened, he told me that a package maintainer is not contacted when the package is archived/removed. His reply was one has to check the checks. I'll add that to my checklist.



From: phylobase-devl-bounces at r-forge.wu-wien.ac.at [phylobase-devl-bounces at r-forge.wu-wien.ac.at] on behalf of Ben Bolker [bbolker at gmail.com]
Sent: 05 November 2011 00:35
To: phylobase-devl at r-forge.wu-wien.ac.at
Subject: [Phylobase-devl] Fwd: Re: CRAN packages phylobase and adephylo

  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).


-------- 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 Package adephylo has been archived: it was failing on R 2.14.0 and we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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