install RNetCDF_1.8-1.tar.gz failed
On 16/02/2016 19:50, Marc Girondot wrote:
Dear experts... I try to install the lastest version of RNetCDF (1.8-1.tar.gz) on MacosX (El Capitan) but without success. I send you the precise procedure I have used and some tests: 1/ I have installed MacPort as described here: https://guide.macports.org And it seems to be ok: Marc-Girondot-MBA:~ marc$ port version Version: 2.3.4 2/ I install the ports for udunits, udunits2, hdf5 and netcdf: sudo port install udunits sudo port install udunits sudo port install hdf5 sudo port install netcdf They seem to be well installed, for example (other ports are ok also): Marc-Girondot-MBA:~ marc$ port installed hdf5 The following ports are currently installed: hdf5 @1.8.15-patch1_0+cxx hdf5 @1.8.16_1+cxx+hl (active) 3/ I modify .profile adding the lines: export LD_LIBRARY_PATH=/opt/local/lib:$LD_LIBRARY_PATH export DYLD_LIBRARY_PATH=/opt/local/lib:$DYLD_LIBRARY_PATH export PATH="/opt/local/bin:/opt/local/sbin:$PATH" 4/ I verify that nc-config gave expected results: Marc-Girondot-MBA:lib marc$ nc-config --libs -L/opt/local/lib -lnetcdf Marc-Girondot-MBA:lib marc$ nc-config --includedir /opt/local/include 5/ I run the command to install the package (it is loaded on the desktop): Marc-Girondot-MBA:~ marc$ R CMD INSTALL $HOME/desktop/RNetCDF_1.8-1.tar.gz And it failed at this command: clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DPACKAGE_NAME=\"RNetCDF\" -DPACKAGE_TARNAME=\"rnetcdf\" -DPACKAGE_VERSION=\"1.8-1\" -DPACKAGE_STRING=\"RNetCDF\ 1.8-1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_UDUNITS2_UDUNITS_H=1 -DHAVE_LIBUDUNITS2=1 -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c RNetCDF.c -o RNetCDF.o RNetCDF.c:75:12: fatal error: 'udunits2/udunits.h' file not found #include <udunits2/udunits.h> What surprised me is that I don't see -l/opt/local/lib in the list of locations as I expected because udunits and udunits2 are there. As someone being able to install this package ?
Hmm, if you use MacPorts you are on your own as it is unsupported. However, there is a version of udunits2 (and netcdf and hdf5) at https://r.research.att.com/libs/ which used to work with RNetCDF 1.7-3: 1.8-1 is recent and broken, as you can see at https://cran.r-project.org/web/checks/check_results_RNetCDF.html . (The maintainer has been informed, and not responded ....)
Brian D. Ripley, ripley at stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford