sf build error on CRAN platform macos-x86_64-clang

[edzer]

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.

[dieza]

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

[edzer]

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?

[dieza]

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]

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

[edzer]

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.

[rsbivand]

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?

[edzer]

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 Building OSX GDAL/PROJ.4/GEOS and ext-deps for GDAL drivers #79