[R-sig-Geo] Installing rgdal with gdal 2.0 on Mac using homebrew

[Roger Bivand]

I don't know the OSX incantation, but if gdal 1 is found first, you'd need to put gdal 2 on the path before it.

Roger Bivand
Norwegian School of Economics
Bergen, Norway

Fra: Rainer M Krug
Sendt: mandag 18. juli, 14.40
Emne: Re: Installing rgdal with gdal 2.0 on Mac using homebrew
Til: Roger Bivand
Kopi: r-sig-geo at r-project.org

Roger Bivand writes: > Sounds like an LDPATH issue, where the gdal 1 dylib is found before gdal 2. Hm. Shouldn't, if I supply LDFLAGS, these libraries be used when running (loading) rgdal, or am I missing something here? LDPATH as well as LD_LIBRARY_PATH are not set in bash ,---- | > Sys.getenv("LDPATH") | [1] "" | > Sys.getenv("LD_LIBRARY_PATH") | [1] "" | > `---- Rainer > > Roger Bivand > Norwegian School of Economics > Bergen, Norway > > > > On Mon, Jul 18, 2016 at 10:18 AM +0200, "Rainer M Krug" > wrote: > > Hi > > I want to install rgdal for using gdal 2.0. The standard gdal package in > homebrew provides gdal 1.11.3, and gdal-20 is installed by using the > osgeo/osgeo4mac/gdal-20 formula, so gdal 2.1.0 is installed in > > /usr/local/opt/gdal-20/ > > If I simply say > > ,---- > | install.packages("rgdal, type="source") > `---- > > rgdal is installed without problems, but using gdal 1.11.3. > > But I want to use gdal 2.1.0 > > > The info from the gdal-20 formula says: > > ,---- > | If you build your > | own software and it requires this formula, you'll need to add to your > | build variables: > | > | LDFLAGS: -L/usr/local/opt/gdal-20/lib > | CPPFLAGS: -I/usr/local/opt/gdal-20/include > `---- > > So I did the following to install rgdal: > > ,---- > | > install.packages("rgdal", type = "source", configure.args = > | > "--with-gdal-config=/usr/local/opt/gdal-20/bin/gdal-config;LDFLAGS=-L/usr/local/opt/gdal-20/lib;CPPFLAGS=-I/usr/local/opt/gdal-20/include") > | Installing package into ‘/usr/local/lib/R/3.3/site-library’ > | (as ‘lib’ is unspecified) > | trying URL 'https://cran.rstudio.com/src/contrib/rgdal_1.1-10.tar.gz' > | Content type 'application/x-gzip' length 1653393 bytes (1.6 MB) > | ================================================== > | downloaded 1.6 MB > | > | * installing *source* package ‘rgdal’ ... > | ** package ‘rgdal’ successfully unpacked and MD5 sums checked > | configure: CC: clang > | configure: CXX: clang++ > | configure: rgdal: 1.1-10 > | checking for /usr/bin/svnversion... yes > | configure: svn revision: 622 > | configure: gdal-config set to /usr/local/opt/gdal-20/bin/gdal-config > | checking gdal-config exists... yes > | checking gdal-config executable... yes > | checking gdal-config usability... yes > | configure: GDAL: 2.1.0 > | checking GDAL version >= 1.6.3... yes > | configure: experimental conditional use of GDAL2 > | checking for gcc... clang > | checking whether the C compiler works... yes > | checking for C compiler default output file name... a.out > | checking for suffix of executables... > | checking whether we are cross compiling... no > | checking for suffix of object files... o > | checking whether we are using the GNU C compiler... yes > | checking whether clang accepts -g... yes > | checking for clang option to accept ISO C89... none needed > | checking how to run the C preprocessor... clang -E > | checking for grep that handles long lines and -e... /usr/bin/grep > | checking for egrep... /usr/bin/grep -E > | checking for ANSI C header files... > | rm: conftest.dSYM: is a directory > | rm: conftest.dSYM: is a directory > | yes > | checking for sys/types.h... yes > | checking for sys/stat.h... yes > | checking for stdlib.h... yes > | checking for string.h... yes > | checking for memory.h... yes > | checking for strings.h... yes > | checking for inttypes.h... yes > | checking for stdint.h... yes > | checking for unistd.h... yes > | checking gdal.h usability... yes > | checking gdal.h presence... yes > | checking for gdal.h... yes > | checking gdal: linking with --libs only... yes > | checking GDAL: /usr/local/Cellar/gdal-20/2.1.0/share/gdal/pcs.csv readable... yes > | checking proj_api.h usability... yes > | checking proj_api.h presence... yes > | checking for proj_api.h... yes > | checking for pj_init_plus in -lproj... yes > | configure: PROJ.4 version: > 4.8.0 > | checking PROJ.4: epsg found and readable... yes > | checking PROJ.4: conus found and readable... yes > | configure: Package CPP flags: -I/usr/local/Cellar/gdal-20/2.1.0/include > | configure: Package LIBS: -L/usr/local/Cellar/gdal-20/2.1.0/lib -lgdal -lproj > | configure: creating ./config.status > | config.status: creating src/Makevars > | ** libs > | clang++ -I/usr/local/Cellar/r/3.3.1/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/gdal-20/2.1.0/include -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -I"/usr/local/lib/R/3.3/site-library/sp/include" -fPIC -g -O2 -c OGR_write.cpp -o OGR_write.o > | clang++ -I/usr/local/Cellar/r/3.3.1/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/gdal-20/2.1.0/include -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -I"/usr/local/lib/R/3.3/site-library/sp/include" -fPIC -g -O2 -c gdal-bindings.cpp -o gdal-bindings.o > | clang -I/usr/local/Cellar/r/3.3.1/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/gdal-20/2.1.0/include -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -I"/usr/local/lib/R/3.3/site-library/sp/include" -fPIC -g -O2 -c init.c -o init.o > | clang -I/usr/local/Cellar/r/3.3.1/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/gdal-20/2.1.0/include -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -I"/usr/local/lib/R/3.3/site-library/sp/include" -fPIC -g -O2 -c inverser.c -o inverser.o > | clang -I/usr/local/Cellar/r/3.3.1/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/gdal-20/2.1.0/include -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -I"/usr/local/lib/R/3.3/site-library/sp/include" -fPIC -g -O2 -c local_stubs.c -o local_stubs.o > | clang++ -I/usr/local/Cellar/r/3.3.1/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/gdal-20/2.1.0/include -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -I"/usr/local/lib/R/3.3/site-library/sp/include" -fPIC -g -O2 -c ogr_geom.cpp -o ogr_geom.o > | clang -I/usr/local/Cellar/r/3.3.1/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/gdal-20/2.1.0/include -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -I"/usr/local/lib/R/3.3/site-library/sp/include" -fPIC -g -O2 -c ogr_polygons.c -o ogr_polygons.o > | clang++ -I/usr/local/Cellar/r/3.3.1/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/gdal-20/2.1.0/include -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -I"/usr/local/lib/R/3.3/site-library/sp/include" -fPIC -g -O2 -c ogr_proj.cpp -o ogr_proj.o > | clang++ -I/usr/local/Cellar/r/3.3.1/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/gdal-20/2.1.0/include -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -I"/usr/local/lib/R/3.3/site-library/sp/include" -fPIC -g -O2 -c ogrdrivers.cpp -o ogrdrivers.o > | clang++ -I/usr/local/Cellar/r/3.3.1/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/gdal-20/2.1.0/include -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -I"/usr/local/lib/R/3.3/site-library/sp/include" -fPIC -g -O2 -c ogrsource.cpp -o ogrsource.o > | clang++ -I/usr/local/Cellar/r/3.3.1/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/gdal-20/2.1.0/include -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include -I"/usr/local/lib/R/3.3/site-library/sp/include" -fPIC -g -O2 -c projectit.cpp -o projectit.o > | clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/openssl/lib -L/usr/local/lib -L/usr/local/Cellar/r/3.3.1/R.framework/Resources/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/openssl/lib -L/usr/local/lib -o rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o projectit.o -L/usr/local/Cellar/gdal-20/2.1.0/lib -lgdal -lproj -F/usr/local/Cellar/r/3.3.1/R.framework/.. -framework R -lintl -Wl,-framework -Wl,CoreFoundation > | installing to /usr/local/lib/R/3.3/site-library/rgdal/libs > | ** R > | ** data > | ** inst > | ** preparing package for lazy loading > | ** help > | *** installing help indices > | ** building package indices > | ** installing vignettes > | ** testing if installed package can be loaded > | Error in dyn.load(file, DLLpath = DLLpath, ...) : > | unable to load shared object '/usr/local/lib/R/3.3/site-library/rgdal/libs/rgdal.so': > | dlopen(/usr/local/lib/R/3.3/site-library/rgdal/libs/rgdal.so, 6): Symbol not found: _GDALOpenEx > | Referenced from: /usr/local/lib/R/3.3/site-library/rgdal/libs/rgdal.so > | Expected in: flat namespace > | in /usr/local/lib/R/3.3/site-library/rgdal/libs/rgdal.so > | Error: loading failed > | Execution halted > | ERROR: loading failed > | * removing ‘/usr/local/lib/R/3.3/site-library/rgdal’ > | * restoring previous ‘/usr/local/lib/R/3.3/site-library/rgdal’ > | Warning in install.packages : > | installation of package ‘rgdal’ had non-zero exit status > | > | The downloaded source packages are in > | ‘/private/var/folders/50/wcr5bjwn75q595n6x82gxj280000gn/T/RtmpP8byD0/downloaded_packages’ > | > > `---- > > So it is using gdal 2.1.0 during compilation and installation. > > My understanding is now (but I might be wrong), that everything works in the building step, but > when loading, it still tries to use the gdal 1.11.3 installation to run. > > What am I missing here? > > Thanks, > > Rainer > > > > -- > Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) > > Centre of Excellence for Invasion Biology > Stellenbosch University > South Africa > > Tel : +33 - (0)9 53 10 27 44 > Cell: +33 - (0)6 85 62 59 98 > Fax : +33 - (0)9 58 10 27 44 > > Fax (D): +49 - (0)3 21 21 25 22 44 > > email: Rainer at krugs.de > > Skype: RMkrug > > PGP: 0x0F52F982 > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-Geo mailing list > R-sig-Geo at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-geo > -- Rainer M. Krug email: Rainerkrugsde PGP: 0x0F52F982

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