Hi Prof. Ripley- You mention unpacking the sources and trying to install. I am not sure exactly how to get this to work. I am able to download and unpack the ncdf4_1.10.tar.gz. Then I can cd into the ncdf4 directory and run the configure script (./configure). This creates the the src/Makevars file, and I was able to copy (or just edit) the src/Makevars.in file so that my PKG_LIBS line reflects the location of my netcdf install. But I am unclear how to continue the build, and install? I don't have a Makefile, so the commands "make" and "make install" fail. Is there another step or command to generate the Makefile? Is there another step I am missing? Or some gross misunderstanding of how this make/build process works? Thanks, Tobey
Date: Wed, 20 Nov 2013 21:25:20 +0000 > From: Prof Brian Ripley <[email protected]> > To: [email protected] > Subject: Re: [R-SIG-Mac] Problem installing ncdf4, in Homebrew R > Message-ID: <[email protected]> > Content-Type: text/plain; charset=windows-1252; format=flowed > > 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 > > > > [[alternative HTML version deleted]] > > > > > > > > _______________________________________________ > > R-SIG-Mac mailing list > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > > > -- > Brian D. Ripley, [email protected] > 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 > > > [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
