[R] various ordinations

Prof Brian D Ripley ripley at stats.ox.ac.uk
Tue Aug 22 20:27:43 CEST 2000

On Mon, 21 Aug 2000, Michael Camann wrote:

> Colleagues,
> I'm developing a library of functions for community ecology analyses and
> have a couple of questions that I've not been able to answer via faqs or
> docs.

Not the actual shipped docs, though!

> 1) Are there existing functions for:
>     a) Bray-Curtis (polar) ordination?
>     b) non-metric multidimensional scaling (NMDS)?

sammon and isoMDS in package MASS

>     c) canonical correlation analyses (CCA and DCA)?

cancor in package mva

>     d) TWINSPAN (doubtful...)?
> 2) If not, does anyone have these functions already?
> 3) I'm having difficulty figuring out how to dyn.load C object files in a
> windows environment, which I admittedly know little about.  I'm using the
> Cygwin/Gnu compiler, no difficulty compiling or (I think) producing
> .dll's, but I always get an error when I try to dyn.load the .dll's that
> says a file is missing.  Sorry, I can't reproduce the exact error mesg
> from this machine, so let me know if it's critical-- nonetheless the mesg
> is something to the effect that an important file is missing.  I'm running
> R 1.0, so if this is a version problem it'll go away when I update, any
> day now....  As the text above suggests, I'm also not entirely certain
> that I'm producing the .dll's correctly and the 1.0.0 win-faq is a bit vague on
> this point.  

Well, how can we anticipate all your (the users') mistakes!  You have not
used the recommended compiler, nor told us anything about how you did this!

The instructions are *not* in the `1.0.0 win-faq'!! Please update to 1.1.1
before doing anything else, as the availability of tools has changed in the
last 6 months.

Messages that important files are missing are critical!  That's why our
toolset provides pedump.exe for you to check dependencies.  You may be able
to solve this just by supplying the missing file.

> Could someone familiar with this please post brief
> instructions or reply directly?  I didn't see anything in the (recent) help archives.

Please read readme.packages which has the most detailed instructions,
then follow them.

If you are really using Cygwin/Gnu, yes an important file cygwin1.dll will
be missing unless you used the -mno-cygwin flag and have one of the rare
downloads in which it actually all works.  That they are rare is why we do
not recommend this combination.

Advice: start again and follow the instructions to the letter. Then there
is some chance we can help you if you can supply a useful problem report.
That means getting version of the mingw32 compiler and the tools
at www.stats.ox.ac.uk/pub/Rtools .... It really is frustrating to spend
time writing the instructions and keeping them up to date in a rapidly
changing scene, and then to receive such a vague report about an old
version (there have been three since).  The FAQ has important information
on preparing a problem report.

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 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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