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sf build error on CRAN platform macos-x86_64-clang #40

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edzer opened this Issue Oct 29, 2016 · 7 comments

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edzer commented Oct 29, 2016

For CRAN platform r-devel-macos-x86_64-clang I see the following error:

** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Users/ripley/R/packages/tests-devel/sf.Rcheck/sf/libs/sf.so':
  dlopen(/Users/ripley/R/packages/tests-devel/sf.Rcheck/sf/libs/sf.so, 6): Symbol not found: _H5T_NATIVE_DOUBLE_g
  Referenced from: /Users/ripley/R/packages/tests-devel/sf.Rcheck/sf/libs/sf.so
  Expected in: flat namespace
 in /Users/ripley/R/packages/tests-devel/sf.Rcheck/sf/libs/sf.so
Error: loading failed
Execution halted
ERROR: loading failed

BDR mentioned that you have not allowed for static builds (on macOS, where it needs to link to hdf5, at least) , but I don't see how to solve this.

@edzer edzer added the help wanted label Oct 29, 2016

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dieza Nov 6, 2016

Same error?
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Users/agus/Library/R/3.3/library/sf/libs/sf.so':
dlopen(/Users/agus/Library/R/3.3/library/sf/libs/sf.so, 6): Symbol not found: __ZN4geos2io9WKBReader4readERNSt3__113basic_istreamIcNS2_11char_traitsIcEEEE
Referenced from: /Users/agus/Library/R/3.3/library/sf/libs/sf.so
Expected in: flat namespace
in /Users/agus/Library/R/3.3/library/sf/libs/sf.so
Error: loading failed
Ejecución interrumpida
ERROR: loading failed

dieza commented Nov 6, 2016

Same error?
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Users/agus/Library/R/3.3/library/sf/libs/sf.so':
dlopen(/Users/agus/Library/R/3.3/library/sf/libs/sf.so, 6): Symbol not found: __ZN4geos2io9WKBReader4readERNSt3__113basic_istreamIcNS2_11char_traitsIcEEEE
Referenced from: /Users/agus/Library/R/3.3/library/sf/libs/sf.so
Expected in: flat namespace
in /Users/agus/Library/R/3.3/library/sf/libs/sf.so
Error: loading failed
Ejecución interrumpida
ERROR: loading failed

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edzer Nov 6, 2016

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Similar, but pointing to a symbol (WKBReader) in the GEOS library. Did you try installing directly from CRAN? If yes, what was the full output? Have you tried this?

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edzer commented Nov 6, 2016

Similar, but pointing to a symbol (WKBReader) in the GEOS library. Did you try installing directly from CRAN? If yes, what was the full output? Have you tried this?

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dieza Nov 6, 2016

In other machine, I have no brew install, but I�ve tried to repliclate the gdal-config stuff
devtools::install_github('edzer/sfr')
Downloading GitHub repo edzer/sfr@master
from URL https://api.github.com/repos/edzer/sfr/zipball/master
Installing sf
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
--no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/sm/1djysrdj1clbzvn35gv8vqq40000gn/T/Rtmpbx08DG/devtools15add85fb625/edzer-sfr-bae7c24'
--library='/Users/adiez/Library/R/3.3/library' --install-tests

  • installing source package �sf� ...
    checking for gdal-config... /Library/Frameworks/GDAL.framework/Programs/gdal-config
    checking gdal-config usability... yes
    configure: GDAL: 2.1.1
    checking GDAL version >= 2.0.0... yes
    checking geos-config usability... yes
    configure: GEOS: 3.5.0
    checking GEOS version >= 3.3.0... yes
    configure: creating ./config.status
    config.status: creating src/Makevars
    ** libs
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c bbox.cpp -o bbox.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c gdal.cpp -o gdal.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c gdal_geom.cpp -o gdal_geom.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c gdal_read.cpp -o gdal_read.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c gdal_write.cpp -o gdal_write.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c geos.cpp -o geos.o
    In file included from geos.cpp:8:
    In file included from /Library/Frameworks/GEOS.framework/Versions/3/unix/include/geos/geom/Geometry.h:25:
    /Library/Frameworks/GEOS.framework/Versions/3/unix/include/GEOS/platform.h:129:10: warning: 'ISNAN' macro redefined

    define ISNAN(x) __inline_isnand(static_cast(x))

     ^
    

    /Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:70:11: note: previous definition is here

    define ISNAN(x) R_isnancpp(x)

      ^
    

    1 warning generated.
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c wkb.cpp -o wkb.o
    clang++ -std=c++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 sf.so RcppExports.o bbox.o gdal.o gdal_geom.o gdal_read.o gdal_write.o geos.o wkb.o -framework GDAL -L/Library/Frameworks/GEOS.framework/Versions/3/unix/lib -lgeos -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Users/adiez/Library/R/3.3/library/sf/libs
    ** R
    ** demo
    ** inst
    ** tests
    ** preparing package for lazy loading
    in method for �coerce� with signature �"sf","Spatial"�: no definition for class �Spatial�
    in method for �coerce� with signature �"sfc","Spatial"�: no definition for class �Spatial�
    ** 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 '/Users/adiez/Library/R/3.3/library/sf/libs/sf.so':
    dlopen(/Users/adiez/Library/R/3.3/library/sf/libs/sf.so, 6): Library not loaded: /data/builds/Bob/darwin13.universal.clang51__default/xt_lib_geos/darwin13.universal.clang51/Release/src/geos-2.2.3/../../../../dist/darwin13.universal.clang51/Release/lib/libgeos.2.dylib
    Referenced from: /Users/adiez/Library/R/3.3/library/sf/libs/sf.so
    Reason: image not found
    Error: loading failed
    Execution halted
    ERROR: loading failed

  • removing �/Users/adiez/Library/R/3.3/library/sf�
    Error: Command failed (1)

    devtools::install_github('edzer/sfr')
    Downloading GitHub repo edzer/sfr@master
    from URL https://api.github.com/repos/edzer/sfr/zipball/master
    Installing sf
    '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
    --no-save --no-restore --quiet CMD INSTALL
    '/private/var/folders/sm/1djysrdj1clbzvn35gv8vqq40000gn/T/Rtmpbx08DG/devtools15adda3dd4be/edzer-sfr-bae7c24'
    --library='/Users/adiez/Library/R/3.3/library' --install-tests

  • installing source package �sf� ...
    checking for gdal-config... /Library/Frameworks/GDAL.framework/Programs/gdal-config
    checking gdal-config usability... yes
    configure: GDAL: 2.1.1
    checking GDAL version >= 2.0.0... yes
    checking geos-config usability... yes
    configure: GEOS: 3.5.0
    checking GEOS version >= 3.3.0... yes
    configure: creating ./config.status
    config.status: creating src/Makevars
    ** libs
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c bbox.cpp -o bbox.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c gdal.cpp -o gdal.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c gdal_geom.cpp -o gdal_geom.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c gdal_read.cpp -o gdal_read.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c gdal_write.cpp -o gdal_write.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c geos.cpp -o geos.o
    In file included from geos.cpp:8:
    In file included from /Library/Frameworks/GEOS.framework/Versions/3/unix/include/geos/geom/Geometry.h:25:
    /Library/Frameworks/GEOS.framework/Versions/3/unix/include/GEOS/platform.h:129:10: warning: 'ISNAN' macro redefined

    define ISNAN(x) __inline_isnand(static_cast(x))

     ^
    

    /Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:70:11: note: previous definition is here

    define ISNAN(x) R_isnancpp(x)

      ^
    

    1 warning generated.
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c wkb.cpp -o wkb.o
    clang++ -std=c++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 sf.so RcppExports.o bbox.o gdal.o gdal_geom.o gdal_read.o gdal_write.o geos.o wkb.o -framework GDAL -L/Library/Frameworks/GEOS.framework/Versions/3/unix/lib -lgeos -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Users/adiez/Library/R/3.3/library/sf/libs
    ** R
    ** demo
    ** inst
    ** tests
    ** preparing package for lazy loading
    in method for �coerce� with signature �"sf","Spatial"�: no definition for class �Spatial�
    in method for �coerce� with signature �"sfc","Spatial"�: no definition for class �Spatial�
    ** 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 '/Users/adiez/Library/R/3.3/library/sf/libs/sf.so':
    dlopen(/Users/adiez/Library/R/3.3/library/sf/libs/sf.so, 6): Library not loaded: /data/builds/Bob/darwin13.universal.clang51__default/xt_lib_geos/darwin13.universal.clang51/Release/src/geos-2.2.3/../../../../dist/darwin13.universal.clang51/Release/lib/libgeos.2.dylib
    Referenced from: /Users/adiez/Library/R/3.3/library/sf/libs/sf.so
    Reason: image not found
    Error: loading failed
    Execution halted
    ERROR: loading failed

  • removing �/Users/adiez/Library/R/3.3/library/sf�
    Error: Command failed (1)
    El 6Nov, 2016, a las 2:57 PM, Edzer Pebesma notifications@github.com escribi�:

Similar, but pointing to a symbol (WKBReader) in the GEOS library. Did you try installing directly from CRAN? If yes, what was the full output? Have you tried this?


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dieza commented Nov 6, 2016

In other machine, I have no brew install, but I�ve tried to repliclate the gdal-config stuff
devtools::install_github('edzer/sfr')
Downloading GitHub repo edzer/sfr@master
from URL https://api.github.com/repos/edzer/sfr/zipball/master
Installing sf
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
--no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/sm/1djysrdj1clbzvn35gv8vqq40000gn/T/Rtmpbx08DG/devtools15add85fb625/edzer-sfr-bae7c24'
--library='/Users/adiez/Library/R/3.3/library' --install-tests

  • installing source package �sf� ...
    checking for gdal-config... /Library/Frameworks/GDAL.framework/Programs/gdal-config
    checking gdal-config usability... yes
    configure: GDAL: 2.1.1
    checking GDAL version >= 2.0.0... yes
    checking geos-config usability... yes
    configure: GEOS: 3.5.0
    checking GEOS version >= 3.3.0... yes
    configure: creating ./config.status
    config.status: creating src/Makevars
    ** libs
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c bbox.cpp -o bbox.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c gdal.cpp -o gdal.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c gdal_geom.cpp -o gdal_geom.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c gdal_read.cpp -o gdal_read.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c gdal_write.cpp -o gdal_write.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c geos.cpp -o geos.o
    In file included from geos.cpp:8:
    In file included from /Library/Frameworks/GEOS.framework/Versions/3/unix/include/geos/geom/Geometry.h:25:
    /Library/Frameworks/GEOS.framework/Versions/3/unix/include/GEOS/platform.h:129:10: warning: 'ISNAN' macro redefined

    define ISNAN(x) __inline_isnand(static_cast(x))

     ^
    

    /Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:70:11: note: previous definition is here

    define ISNAN(x) R_isnancpp(x)

      ^
    

    1 warning generated.
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c wkb.cpp -o wkb.o
    clang++ -std=c++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 sf.so RcppExports.o bbox.o gdal.o gdal_geom.o gdal_read.o gdal_write.o geos.o wkb.o -framework GDAL -L/Library/Frameworks/GEOS.framework/Versions/3/unix/lib -lgeos -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Users/adiez/Library/R/3.3/library/sf/libs
    ** R
    ** demo
    ** inst
    ** tests
    ** preparing package for lazy loading
    in method for �coerce� with signature �"sf","Spatial"�: no definition for class �Spatial�
    in method for �coerce� with signature �"sfc","Spatial"�: no definition for class �Spatial�
    ** 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 '/Users/adiez/Library/R/3.3/library/sf/libs/sf.so':
    dlopen(/Users/adiez/Library/R/3.3/library/sf/libs/sf.so, 6): Library not loaded: /data/builds/Bob/darwin13.universal.clang51__default/xt_lib_geos/darwin13.universal.clang51/Release/src/geos-2.2.3/../../../../dist/darwin13.universal.clang51/Release/lib/libgeos.2.dylib
    Referenced from: /Users/adiez/Library/R/3.3/library/sf/libs/sf.so
    Reason: image not found
    Error: loading failed
    Execution halted
    ERROR: loading failed

  • removing �/Users/adiez/Library/R/3.3/library/sf�
    Error: Command failed (1)

    devtools::install_github('edzer/sfr')
    Downloading GitHub repo edzer/sfr@master
    from URL https://api.github.com/repos/edzer/sfr/zipball/master
    Installing sf
    '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
    --no-save --no-restore --quiet CMD INSTALL
    '/private/var/folders/sm/1djysrdj1clbzvn35gv8vqq40000gn/T/Rtmpbx08DG/devtools15adda3dd4be/edzer-sfr-bae7c24'
    --library='/Users/adiez/Library/R/3.3/library' --install-tests

  • installing source package �sf� ...
    checking for gdal-config... /Library/Frameworks/GDAL.framework/Programs/gdal-config
    checking gdal-config usability... yes
    configure: GDAL: 2.1.1
    checking GDAL version >= 2.0.0... yes
    checking geos-config usability... yes
    configure: GEOS: 3.5.0
    checking GEOS version >= 3.3.0... yes
    configure: creating ./config.status
    config.status: creating src/Makevars
    ** libs
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c bbox.cpp -o bbox.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c gdal.cpp -o gdal.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c gdal_geom.cpp -o gdal_geom.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c gdal_read.cpp -o gdal_read.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c gdal_write.cpp -o gdal_write.o
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c geos.cpp -o geos.o
    In file included from geos.cpp:8:
    In file included from /Library/Frameworks/GEOS.framework/Versions/3/unix/include/geos/geom/Geometry.h:25:
    /Library/Frameworks/GEOS.framework/Versions/3/unix/include/GEOS/platform.h:129:10: warning: 'ISNAN' macro redefined

    define ISNAN(x) __inline_isnand(static_cast(x))

     ^
    

    /Library/Frameworks/R.framework/Resources/include/R_ext/Arith.h:70:11: note: previous definition is here

    define ISNAN(x) R_isnancpp(x)

      ^
    

    1 warning generated.
    clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/GDAL.framework/Versions/2.1/Headers -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Users/adiez/Library/R/3.3/library/Rcpp/include" -fPIC -Wall -mtune=core2 -g -O2 -c wkb.cpp -o wkb.o
    clang++ -std=c++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 sf.so RcppExports.o bbox.o gdal.o gdal_geom.o gdal_read.o gdal_write.o geos.o wkb.o -framework GDAL -L/Library/Frameworks/GEOS.framework/Versions/3/unix/lib -lgeos -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    installing to /Users/adiez/Library/R/3.3/library/sf/libs
    ** R
    ** demo
    ** inst
    ** tests
    ** preparing package for lazy loading
    in method for �coerce� with signature �"sf","Spatial"�: no definition for class �Spatial�
    in method for �coerce� with signature �"sfc","Spatial"�: no definition for class �Spatial�
    ** 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 '/Users/adiez/Library/R/3.3/library/sf/libs/sf.so':
    dlopen(/Users/adiez/Library/R/3.3/library/sf/libs/sf.so, 6): Library not loaded: /data/builds/Bob/darwin13.universal.clang51__default/xt_lib_geos/darwin13.universal.clang51/Release/src/geos-2.2.3/../../../../dist/darwin13.universal.clang51/Release/lib/libgeos.2.dylib
    Referenced from: /Users/adiez/Library/R/3.3/library/sf/libs/sf.so
    Reason: image not found
    Error: loading failed
    Execution halted
    ERROR: loading failed

  • removing �/Users/adiez/Library/R/3.3/library/sf�
    Error: Command failed (1)
    El 6Nov, 2016, a las 2:57 PM, Edzer Pebesma notifications@github.com escribi�:

Similar, but pointing to a symbol (WKBReader) in the GEOS library. Did you try installing directly from CRAN? If yes, what was the full output? Have you tried this?


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edzer Nov 7, 2016

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Again, this points to a problem with the GEOS library.

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edzer commented Nov 7, 2016

Again, this points to a problem with the GEOS library.

edzer added a commit that referenced this issue Nov 16, 2016

an attempt to solve #40
Signed-off-by: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
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We get a compile on the CRAN macosx machine, but it breaks in runtime on st_union. It might be that checking for geos 3.3.0 in configure is broken, but that would have given a link-time error? @rsbivand . I added #if version > 3.3.0 around GEOSUnion_r() in b1f4841, but suspect the problem is somewhere else.

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edzer commented Nov 25, 2016

We get a compile on the CRAN macosx machine, but it breaks in runtime on st_union. It might be that checking for geos 3.3.0 in configure is broken, but that would have given a link-time error? @rsbivand . I added #if version > 3.3.0 around GEOSUnion_r() in b1f4841, but suspect the problem is somewhere else.

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This suggests that the problem is not that GEOS isn't there, but that GDAL was not built with GEOS. Do we have the config.log of the OSX GDAL build?

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rsbivand commented Nov 25, 2016

This suggests that the problem is not that GEOS isn't there, but that GDAL was not built with GEOS. Do we have the config.log of the OSX GDAL build?

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The issues have now been resolved:

  • the CRAN binaries for MacOSX all work with statically linked libraries, meaning that the dynamic libraries of (binary) R packages only have links to system libraries, and not to anything installed by users
  • GDAL does not allow a static build with GEOS included, meaning that any GEOS operation sf used through the GDAL interface had to be rewritten to directly use GEOS: cc75436
  • GDAL does come with a configure option to statically link to Proj.4, so that can be used through the GDAL interface
  • in addition to that, 0.2-8 will directly link to Proj.4 as this provides stronger error checking on proj4 strings (GDAL will accept nearly anything and then treat it as WGS84)
  • this also resolves #79
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edzer commented Dec 21, 2016

The issues have now been resolved:

  • the CRAN binaries for MacOSX all work with statically linked libraries, meaning that the dynamic libraries of (binary) R packages only have links to system libraries, and not to anything installed by users
  • GDAL does not allow a static build with GEOS included, meaning that any GEOS operation sf used through the GDAL interface had to be rewritten to directly use GEOS: cc75436
  • GDAL does come with a configure option to statically link to Proj.4, so that can be used through the GDAL interface
  • in addition to that, 0.2-8 will directly link to Proj.4 as this provides stronger error checking on proj4 strings (GDAL will accept nearly anything and then treat it as WGS84)
  • this also resolves #79

@edzer edzer closed this Dec 21, 2016

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