[R-SIG-Mac] udunits and RNetCDF ... simple or hard to get Mac version?
Prof Brian Ripley
ripley at stats.ox.ac.uk
Fri Jan 15 16:12:00 CET 2010
On Fri, 15 Jan 2010, Simon Urbanek wrote:
> 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 ...
On Windows I modified udunits to look locally and then shipped the
data file (AFAIK there is only one). But I'd probably not do it
again.
>> 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 Œudunits‚ ...
>> 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 Œudunits‚
>> * removing Œ/Library/Frameworks/R.framework/Versions/2.10/Resources/
>> library/udunits‚
>>
>> The downloaded packages are in
>> Œ/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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>>
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--
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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