[R-sig-Geo] install rgdal from source macOS
Roger Bivand
Roger@B|v@nd @end|ng |rom nhh@no
Fri Jun 21 11:24:32 CEST 2019
You are making everything unnecessarily complicated. What is happening is
that rgdal is being build against the headers and libraries you specify,
but the GDAL shared object loaded by rgdal.so is not the one used to build
it (so you have multiple copies of at least GDAL installed). These
speculations do seem to match what you report:
** 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.26.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
Further, you probably also have multiple copies of PROJ and GDAL support
files installed for different versions of PROJ and GDAL.
If you read the output carefully, you'll also see that you do not seem to
have the pkg-config program installed, so setting the environment variable
to point to where proj.pc lives will not work; try pkg-config --help at
the command line to check its availability.
./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
Roger
On Fri, 21 Jun 2019, Dominik Schneider wrote:
> I finally got back to this. Unfortunately this did not work.
> It still doesn't like PKG_CONFIG_PATH and now pcs.csv was not readable. It
> did not exist in 'share/gdal' but I found it in miniconda3/pkgs/libgdal* so
> I copied it to share/gdal.
>
>> Sys.getenv('PKG_CONFIG_PATH')
> [1] "/Users/dosc3612/Applications/miniconda3/envs/rgdal/lib/pkgconfig"
>> grep('proj.pc',dir(Sys.getenv('PKG_CONFIG_PATH')))
>
> I'm not sure why it can't find the pkg config
>
>> install.packages('rgdal', repo = 'https://r-forge.r-project.org', 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','--with-proj-share=/Users/dosc3612/Applications/miniconda3/envs/rgdal/share/proj',
> '--with-data-copy=yes'))
> trying URL 'https://r-forge.r-project.org/src/contrib/rgdal_1.4-5.tar.gz'
> Content type 'application/x-gzip' length 1687877 bytes (1.6 MB)
> ==================================================
> downloaded 1.6 MB
>
> * installing *source* package ‘rgdal’ ...
> ** 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
> cat: inst/SVN_VERSION: No such file or directory
> configure: svn revision:
> 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: 3.0.0
> 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
> configure: PROJ_LIB:
> /Users/dosc3612/Applications/miniconda3/envs/rgdal/share/proj
> dyld: Library not loaded: @rpath/libproj.15.dylib
> Referenced from:
> /private/var/folders/bb/13z2kq0j01jg5q_0ypjc76gr0000gn/T/RtmpVtyBCi/R.INSTALL76ca8b2ce2d/rgdal/./proj_conf_test2
> Reason: image not found
> ./configure: line 2451: 30994 Abort trap: 6
> PROJ_LIB="${proj_share_path}" ./proj_conf_test2
> checking PROJ: proj.db found and readable... yes
> configure: Copy data for:
> configure: PROJ.4:
> /Users/dosc3612/Applications/miniconda3/envs/rgdal/share/proj
> configure: GDAL:
> /Users/dosc3612/Applications/miniconda3/envs/rgdal/share/gdal
> 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.26.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/Rtmpqaf8Yh/downloaded_packages’
> Warning message:
> In install.packages("rgdal", repo = "https://r-forge.r-project.org", :
> installation of package ‘rgdal’ had non-zero exit status
>>
>
>
>
>
>
> I also tried passing
> '--with-proj-share=/Users/dosc3612/Applications/miniconda3/envs/rgdal/lib'
> because that is where I found libproj.15.dylib but the installer still says
> it can't find it.
>
>
> *any suggestions?*
>
>
>> install.packages('rgdal', repo = 'https://r-forge.r-project.org', 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','--with-proj-share=/Users/dosc3612/Applications/miniconda3/envs/rgdal/lib',
> '--with-data-copy=yes'))
> trying URL 'https://r-forge.r-project.org/src/contrib/rgdal_1.4-5.tar.gz'
> Content type 'application/x-gzip' length 1687877 bytes (1.6 MB)
> ==================================================
> downloaded 1.6 MB
>
> * installing *source* package ‘rgdal’ ...
> ** 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
> cat: inst/SVN_VERSION: No such file or directory
> configure: svn revision:
> 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: 3.0.0
> 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
> configure: PROJ_LIB: /Users/dosc3612/Applications/miniconda3/envs/rgdal/lib
> dyld: Library not loaded: @rpath/libproj.15.dylib
> Referenced from:
> /private/var/folders/bb/13z2kq0j01jg5q_0ypjc76gr0000gn/T/Rtmpcbzrca/R.INSTALL7a1919c4df31/rgdal/./proj_conf_test2
> Reason: image not found
> ./configure: line 2451: 31841 Abort trap: 6
> PROJ_LIB="${proj_share_path}" ./proj_conf_test2
> checking PROJ: proj.db found and readable... yes
> configure: Copy data for:
> configure: PROJ.4:
> /Users/dosc3612/Applications/miniconda3/envs/rgdal/share/proj
> configure: GDAL:
> /Users/dosc3612/Applications/miniconda3/envs/rgdal/share/gdal
> 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.26.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/Rtmpqaf8Yh/downloaded_packages’
> Warning message:
> In install.packages("rgdal", repo = "https://r-forge.r-project.org", :
> installation of package ‘rgdal’ had non-zero exit status
>>
>
> On Tue, Jun 11, 2019 at 10:32 AM Edzer Pebesma <
> edzer.pebesma using uni-muenster.de> wrote:
>
>> 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]]
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> R-sig-Geo using r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>
>> --
>> Edzer Pebesma
>> Institute for Geoinformatics
>> Heisenbergstrasse 2, 48151 Muenster, Germany
>> Phone: +49 251 8333081
>> _______________________________________________
>> R-sig-Geo mailing list
>> R-sig-Geo using r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-Geo mailing list
> R-sig-Geo using r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
>
--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand using nhh.no
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
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