[R-SIG-Mac] udunits and RNetCDF ... simple or hard to get Mac version?

Mon Jan 18 01:25:42 CET 2010

David emailed me the beta of the R package for udunits-2.0, which compiles/installs without problems. With that new package installed, the recompiled RNetCDF and ncdf both seem to work fine now.

Everything will be in the cessoftxxxxxxxx.tgz file (with xxxxxxxx > 20100117) in http://public.me.com/jdeleeuw/software. NB: that file is now close to 4GB and is used
to replace all of /usr/local on our computers. It has the same stuff as localxxxxxxxx.tgz mentioned below, and much more, but it now uses the default gcc-4.2.1 and
Simon's corresponding gfortran.

On Jan 14, 2010, at 17:08 , 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).
> 
> 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.
> 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
> 
> 
> 
> 

===
Jan de Leeuw; Distinguished Professor and Chair, UCLA Department of Statistics;
Director: UCLA Center for Environmental Statistics (CES);
Editor: Journal of Multivariate Analysis, Journal of Statistical Software;
US mail: 8125 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550;  fax (310)-206-5658;  email: deleeuw at stat.ucla.edu
.mac: jdeleeuw ++++++  aim: deleeuwjan ++++++ skype: j_deleeuw
homepages: http://gifi.stat.ucla.edu ++++++ http://www.cuddyvalley.org
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