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

Rainer M Krug Rainer at krugs.de
Mon Jul 18 14:40:20 CEST 2016 

Roger Bivand <Roger.Bivand at nhh.no> 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" <Rainer at krugs.de<mailto:Rainer at krugs.de>> 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
>
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-- 
Rainer M. Krug
email: Rainer<at>krugs<dot>de
PGP: 0x0F52F982
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