udunits and RNetCDF ... simple or hard to get Mac version?

 install.packages('udunits',type='source')

 sessionInfo()

Bob,

On Jan 14, 2010, at 8:08 PM, Robert Chatfield wrote:

 We have been using both ncdf and  RNetCDF
 packages, and often enjoy the general approach
 offered by RNetCDF

 That package has not been available on the Mac for
 some time, it appears, ... but was maybe available
 last year  (see message below).

AFAIR the problem with udunits (the library) is 
that it is not self-contained as it requires 
external files to be present. That means that 
the udunits package will not work properly 
unless you have those files. That is unfortunate 
since it prevents us from shipping packages 
based on it. We have in the past provided 
udunits without those external files thus not 
fully functional (albeit for the tests we did 
have the files installed), but not recently. We 
could do that again if desired but it is not 
very clean ...

 According to the CRAN documentation page and my own
 attempts to acquire RNetCDF,  the problem
 appears to be with the needed package "udunits"

 That package is also useful for atmosphere, oceans,
 and connected sciences.

 With a MacPro 1.1 running 10.5.8 and the indicated R and RGui,
 I get this result

 * installing *source* package ?udunits? ...
 creating cache ./config.cache
 checking how to run the C preprocessor... gcc -arch i386 -std=gnu99 -E
 checking for gcc... gcc -arch i386 -std=gnu99
 checking whether the C compiler (gcc -arch i386 -std=gnu99 -g -O2 ) 
 works... no
 configure: error: installation or configuration problem: C compiler 
 cannot create executables.

As Dave said this is likely a problem in your 
setup. Make sure you have recent Xcode installed 
and check config.log for the exact error (i.e. 
unpack udunits and run R CMD INSTALL udunits -- 
then you'll find config.log inside).

Cheers,
Simon

 > ERROR: configuration failed for package ?udunits?
 > * removing ?/Library/Frameworks/R.framework/Versions/2.10/Resources/
 > library/udunits?
 >
 > The downloaded packages are in
?/private/var/folders/pb/pbT1eFNa2RaEvE+1Yx812U+++TI/-Tmp-/RtmpzhkbgP/
 downloaded_packages?

 sessionInfo()

 R version 2.10.0 (2009-10-26)
 i386-apple-darwin9.8.0

 locale:
 [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

 attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base

 loaded via a namespace (and not attached):
 [1] tools_2.10.0
 Warning message:
 In install.packages(c("udunits"), lib = "/Library/Frameworks/
 R.framework/Resources/library/",  :
   installation of package 'udunits' had non-zero exit status

 ***************
 Is this hard to fix?
 Could there be a RNetCDF without the udunits package?  .... I myself
 use udunits rather rarely.

 Bob Chatfield

 Message: 2
 Date: Sat, 4 Jul 2009 14:35:40 -0700
 From: Jan de Leeuw <deleeuw at stat.ucla.edu>
 Subject: Re: [R-SIG-Mac] Unable to install package RGtk2
 To: "r-sig-mac at stat.math.ethz.ch Mac List"
<r-sig-mac at stat.math.ethz.ch>
 Cc: statcompute <statcompute at mta.stat.ucla.edu>
 Message-ID: <FD535A21-B873-4986-8466-876455B77C1C at stat.ucla.edu>
 Content-Type: text/plain; charset=windows-1252; format=flowed;
delsp=yes

 I have a 2.5 GB file localxxxxxx.tgz, with xxxxxx indicating the 
 date.

 You can get it from afp://gifi.stat.ucla.edu and then
 from my Public directory in /software. Or from a WebDAV connection to
 http://*public.me.com/jdeleeuw/software (it's currently gone from
 me.com, but
 it will be there again soon).

 It contains

 a. 64-bit version of R-devel (a.k.a R-2.10.0) with about 600 
 packages.
 It supports the
   GTK+, tcl/tk, SciViews, etc interfaces.

 b. 64-bit version of grass-trunk (a.k.a. GRASS-7.0).

 c. Support-libraries and executables, all 64-bit, for ImageMagick,
 freetype, GDAL, proj,
   gsl, gmp, mpfr, fftw, mysql, pgsql, hadoop, root, heasoft, hdf4/5,
 netcdf, graphviz,
   ffmpeg, asymptote, expat, cdd, cfitsio, fontconfig, gc, geos,
 geotiff, gd, tiff, jpeg,
   png, svg, gettext, harminv, iconv, intl, jags, jasper, las,
 pixman, qhull, readline,
   sqlite, szip, tcl/tk, udunits, xml2, gtk2, gdk, atk, glib, cairo,
 pango, glade, git,
   wget, gawk, sed, gs, pkg-config, tramo, seats, x12a, yacas, pvm3
 --- probably more.

 d. A 64-bit version of gcc, g++, gfortran 4.2.5 with gomp. 
 Everything,
 including the
   compilers, is compiled with flags "-m64 -O3 -fopenmp -
 mtune=native" -- "native" in
   this context means "nocona", i.e. Intel Core Duo.

 e. texlive-2008

 It is updated one or twice per week with recent cvs, svn or git
 versions. It installs in
 /usr/local. The R is pretty snappy on my machine.

 !!!!!!!!!!!!!!!!!
 Limitations
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

 1. This is for CLI junkies. Normal people will stay away from this.

 2. The quartz device in R works, but many other things are either GTK
 +, tcl/tk, or even
   Athena.

 3. This was compiled on OS X 10.6 (Snow Leopard). Your Leopard 
 mileage
 may vary. No
   universal binaries of any sort, of course.

 4. Basically it creates a separate 64-bit development environment,
 independent of the Apple stuff
   (and independently, if you want, of the "normal" and nice R and
 GRASS framework-builds and GUIs).

 5. This is a large file. After unpacking "du -s /usr/local" says
 14167872 (i.e. 14 GB).

 6. I am not really supporting this for users outside my department.
 That would be unwise.

 Dr. Robert Chatfield
 Earth Sciences, MS 245-5
 NASA Ames Research Center
 Moffett Field, CA 94035    USA

 Ph: 650-604-5490  FAX 650-604-3625

 http://*geo.arc.nasa.gov/sgg/chatfield





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