On 20/11/2013 20:49, Tobey Carman wrote:
Hi -
I am not sure if this is the right place for this question. I am fairly new
to R and still figuring out how to best manage packages. If this is not the
best venue for this question, please direct me elsewhere.
It will do, but 'the homebrew version of R' is not anything official and
you would probably do better to ask on R-devel since you are treating OS
X as another Unix-alike.
The package has a broken configure, and has been reported to the
so-called maintainer long ago.
You omitted the line with the error. On my (native OS X) system you can
see the log at
http://www.r-project.org/nosvn/R.check/r-devel-macosx-x86_64/ncdf4-00install.html
. Note the link command there:
clang -mtune=native -dynamiclib -Wl,-headerpad_max_install_names
-undefined dynamic_lookup -single_module -multiply_defined suppress
-L/usr/local/lib -o ncdf4.so ncdf.o ncdf2.o ncdf3.o src_ncdf4.o
-Wl,-rpath, -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl
-L/Users/ripley/R/R-devel/lib -lR -dylib_file
libRblas.dylib:/Users/ripley/R/R-devel/lib/libRblas.dylib -Wl,-framework
-Wl,CoreFoundation
The use of -Wl,-rpath, is simply wrong and swallows -lnetcdf. So you
need to correct it.
One way to do so is to unpack the sources, try to install, copy the
PKG_LIBS from src/Makevars to src/Makevars.in, correct it and try again.
I have in src/Makevars.in
PKG_LIBS= -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl
but your mileage may differ (and probably will if you have a dynamic
libndetcdf).
I am trying to install the ncdf4 R package using:
install.packages('ncdf4')
This command, downloads the package, finds nc-config, appears to collect
all the correct settings, and appears to compile ncdf4 with no errors. But
after compiling, and running a few tests, the command fails during a test
to load the just-compiled ncdf4 libraries:
install.packages('ncdf4')
...
skipping lots of output for downloading, nc-config, configuring, compiling,
testing...
...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/usr/local/Cellar/r/3.0.0/R.framework/Versions/3.0/Resources/library/ncdf4/libs/ncdf4.so':
dlopen(/usr/local/Cellar/r/3.0.0/R.framework/Versions/3.0/Resources/library/ncdf4/libs/ncdf4.so,
6): Symbol not found: _nc_close
Referenced from:
/usr/local/Cellar/r/3.0.0/R.framework/Versions/3.0/Resources/library/ncdf4/libs/ncdf4.so
Expected in: flat namespace
in
/usr/local/Cellar/r/3.0.0/R.framework/Versions/3.0/Resources/library/ncdf4/libs/ncdf4.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing
‘/usr/local/Cellar/r/3.0.0/R.framework/Versions/3.0/Resources/library/ncdf4’
Warning in install.packages :
installation of package ‘ncdf4’ had non-zero exit status
I am on a Mac, 10.8.2. I am using Homebrew to manage my packages. I have
the main netcdf library, 4.2.1.1, that is installed via Homebrew and has
been working fine in several other applications. Likewise I am using a
Homebrew version of R.
I am not sure how to keep trouble shooting this. I can provide more output
if necessary.
Thanks,
Tobey Carman
Spatial Ecology Lab,
University of Alaska Fairbanks
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Brian D. Ripley, [email protected]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
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Oxford OX1 3TG, UK Fax: +44 1865 272595
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