[R-sig-Geo] install rgdal from source macOS
Edzer Pebesma
edzer@pebe@m@ @end|ng |rom un|-muen@ter@de
Tue Jun 11 19:32:28 CEST 2019
for compiling rgdal from source on OSX against gdal 3 and proj 6.1.0,
please use the dev version on r-forge. See also
https://github.com/r-spatial/sf/issues/1070
On 6/9/19 9:52 PM, Dominik Schneider wrote:
> I'm trying to install rgdal from source on a fresh r 3.6 installation.
> i setup a conda environment to install gdal, proj, geos
>
> install.packages('rgdal', type = "source",
> configure.args=c('--with-proj-include=/Users/dosc3612/Applications/miniconda3/envs/rgdal/include',
> '--with-proj-lib=/Users/dosc3612/Applications/miniconda3/envs/rgdal/lib',
> '--with-gdal-config=/Users/dosc3612/Applications/miniconda3/envs/rgdal/bin/gdal-config'))
>
> The full output is below but the first error I see is:
> ./configure: line 2101: pkg-config: command not found
> configure: pkg-config proj not available
> set PKG_CONFIG_PATH to the directory containing proj.pc
> configure: PROJ version not determined using pkg-config proj
>
> which I don't understand because:
> Sys.getenv('PKG_CONFIG_PATH')
> [1] "/Users/dosc3612/Applications/miniconda3/envs/rgdal/lib/pkgconfig"
>
> and just to confirm:
> (rgdal) Phoenix:~ $ ls `echo $PKG_CONFIG_PATH` | grep proj
> proj.pc
>
> *Is there another way to set PKG_CONFIG_PATH within install.packages?*
>
> There are also some undefined symbols:
> Undefined symbols for architecture x86_64:
> "_pj_ctx_fclose", referenced from:
> _main in proj_conf_test2-9a39dc.o
> "_pj_get_default_ctx", referenced from:
> _main in proj_conf_test2-9a39dc.o
> "_pj_open_lib", referenced from:
> _main in proj_conf_test2-9a39dc.o
> ld: symbol(s) not found for architecture x86_64
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> ./configure: line 2422: ./proj_conf_test2: No such file or directory
>
> I tried with gdal 2.4.1 and gdal 3.0.0 (after seeing
> http://r-sig-geo.2731867.n2.nabble.com/GDAL-3-0-0-and-rgdal-tt7592822.html#a7592834
> )
> proj is 6.1
> geos is 3.7.1
>
> What did I miss? Please advise. Thanks.
>
> FULL OUTPUT:
>> install.packages('rgdal', type = "source",
> configure.args=c('--with-proj-include=/Users/dosc3612/Applications/miniconda3/envs/rgdal/include',
> '--with-proj-lib=/Users/dosc3612/Applications/miniconda3/envs/rgdal/lib',
> '--with-gdal-config=/Users/dosc3612/Applications/miniconda3/envs/rgdal/bin/gdal-config'))
> --- Please select a CRAN mirror for use in this session ---
> trying URL 'https://cloud.r-project.org/src/contrib/rgdal_1.4-4.tar.gz'
> Content type 'application/x-gzip' length 1687518 bytes (1.6 MB)
> ==================================================
> downloaded 1.6 MB
>
> * installing *source* package ‘rgdal’ ...
> ** package ‘rgdal’ successfully unpacked and MD5 sums checked
> ** using staged installation
> configure: R_HOME: /Library/Frameworks/R.framework/Resources
> configure: CC: clang
> configure: CXX: clang++ -std=gnu++11
> configure: C++11 support available
> configure: rgdal: 1.4-4
> checking for /usr/bin/svnversion... yes
> configure: svn revision: 833
> configure: gdal-config set to
> /Users/dosc3612/Applications/miniconda3/envs/rgdal/bin/gdal-config
> checking gdal-config exists... yes
> checking gdal-config executable... yes
> checking gdal-config usability... yes
> configure: GDAL: 2.4.1
> checking C++11 support for GDAL >= 2.3.0... yes
> checking GDAL version >= 1.11.4... yes
> checking GDAL version <= 2.5 or >= 3.0... yes
> checking gdal: linking with --libs only... yes
> checking GDAL: gdal-config data directory readable... yes
> checking GDAL:
> /Users/dosc3612/Applications/miniconda3/envs/rgdal/share/gdal/pcs.csv
> readable... yes
> ./configure: line 2101: pkg-config: command not found
> configure: pkg-config proj not available
> set PKG_CONFIG_PATH to the directory containing proj.pc
> configure: PROJ version not determined using pkg-config proj
> configure: proj CPP flags:
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> checking PROJ header API:... proj_api.h
> checking proj_api.h presence and usability... yes
> checking PROJ version >= 4.8.0... yes
> Undefined symbols for architecture x86_64:
> "_pj_ctx_fclose", referenced from:
> _main in proj_conf_test2-9a39dc.o
> "_pj_get_default_ctx", referenced from:
> _main in proj_conf_test2-9a39dc.o
> "_pj_open_lib", referenced from:
> _main in proj_conf_test2-9a39dc.o
> ld: symbol(s) not found for architecture x86_64
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> ./configure: line 2422: ./proj_conf_test2: No such file or directory
> checking PROJ.4: proj.db found and readable... yes
> Undefined symbols for architecture x86_64:
> "_pj_ctx_fclose", referenced from:
> _main in proj_conf_test3-9f8df7.o
> "_pj_get_default_ctx", referenced from:
> _main in proj_conf_test3-9f8df7.o
> "_pj_open_lib", referenced from:
> _main in proj_conf_test3-9f8df7.o
> ld: symbol(s) not found for architecture x86_64
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> ./configure: line 2482: ./proj_conf_test3: No such file or directory
> checking PROJ.4: conus found and readable... yes
> configure: Package CPP flags:
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
> configure: Package LIBS:
> -L/Users/dosc3612/Applications/miniconda3/envs/rgdal/lib -lgdal
> -L/Users/dosc3612/Applications/miniconda3/envs/rgdal/lib -lproj
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sp/include"
> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> -I/usr/local/include -fPIC -Wall -g -O2 -c OGR_write.cpp -o OGR_write.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sp/include"
> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> -I/usr/local/include -fPIC -Wall -g -O2 -c gdal-bindings.cpp -o
> gdal-bindings.o
> clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sp/include"
> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
> clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sp/include"
> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> -I/usr/local/include -fPIC -Wall -g -O2 -c inverser.c -o inverser.o
> clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sp/include"
> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> -I/usr/local/include -fPIC -Wall -g -O2 -c local_stubs.c -o local_stubs.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sp/include"
> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> -I/usr/local/include -fPIC -Wall -g -O2 -c ogr_geom.cpp -o ogr_geom.o
> clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sp/include"
> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> -I/usr/local/include -fPIC -Wall -g -O2 -c ogr_polygons.c -o
> ogr_polygons.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sp/include"
> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> -I/usr/local/include -fPIC -Wall -g -O2 -c ogr_proj.cpp -o ogr_proj.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sp/include"
> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> -I/usr/local/include -fPIC -Wall -g -O2 -c ogrdrivers.cpp -o ogrdrivers.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sp/include"
> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> -I/usr/local/include -fPIC -Wall -g -O2 -c ogrsource.cpp -o ogrsource.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sp/include"
> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> -I/usr/local/include -fPIC -Wall -g -O2 -c proj_info6.cpp -o proj_info6.o
> clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include"
> -DNDEBUG -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -I/Users/dosc3612/Applications/miniconda3/envs/rgdal/include
> -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
> -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/sp/include"
> -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> -I/usr/local/include -fPIC -Wall -g -O2 -c projectit.cpp -o projectit.o
> clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names
> -undefined dynamic_lookup -single_module -multiply_defined suppress
> -L/Library/Frameworks/R.framework/Resources/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 proj_info6.o
> projectit.o -L/Users/dosc3612/Applications/miniconda3/envs/rgdal/lib -lgdal
> -L/Users/dosc3612/Applications/miniconda3/envs/rgdal/lib -lproj
> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework
> -Wl,CoreFoundation
> installing to
> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-rgdal/00new/rgdal/libs
> ** R
> ** data
> ** inst
> ** byte-compile and prepare package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded from temporary location
> Error: package or namespace load failed for ‘rgdal’ in dyn.load(file,
> DLLpath = DLLpath, ...):
> unable to load shared object
> '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-rgdal/00new/rgdal/libs/rgdal.so':
>
> dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-rgdal/00new/rgdal/libs/rgdal.so,
> 6): Library not loaded: @rpath/libgdal.20.dylib
> Referenced from:
> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-rgdal/00new/rgdal/libs/rgdal.so
> Reason: image not found
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing
> ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rgdal’
>
> The downloaded source packages are in
> ‘/private/var/folders/bb/13z2kq0j01jg5q_0ypjc76gr0000gn/T/RtmplsyMiu/downloaded_packages’
> Warning message:
> In install.packages("rgdal", type = "source", configure.args =
> c("--with-proj-include=/Users/dosc3612/Applications/miniconda3/envs/rgdal/include",
> :
> installation of package ‘rgdal’ had non-zero exit status
>
> [[alternative HTML version deleted]]
>
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--
Edzer Pebesma
Institute for Geoinformatics
Heisenbergstrasse 2, 48151 Muenster, Germany
Phone: +49 251 8333081
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