[R-SIG-Mac] sf installation problem under Mac OS 11 - Big Sur

[Prof Brian Ripley]

On 18/08/2021 23:52, Michal Ben-Nun wrote:
> Hi,
> 
> I installed R 4.10 on my Mac OS 11.3.1

Presumably R 4.1.0.
> 
> I am trying to install 'sf' and 'rgdal'
> 
>>From the mailing list I understood that this command should work:
> 
> install.packages(c("rgdal","sf"),,"https://mac.R-project.org
> <https://mac.r-project.org/>")
> 
> However I am still getting an error, see below.
> 
> Any suggestions would be welcome.
> 
> Thanks,
> Michal
> 
> p.s. I am using macports NOT brew

Asking on R-sig-geo would be appropriate as macports/Homebrew are 
generic Unix-alike systems.

Hint: rgdal has

SystemRequirements: PROJ (>= 4.8.0, https://proj.org/download.html) and 
GDAL (>= 1.11.4, https://gdal.org/download.html), with versions either 
(A) PROJ < 6 and GDAL < 3 or (B) PROJ >= 6 and GDAL >= 3.

and it seems you have not installed PROJ



> 
>> install.packages(c("rgdal","sf"),,"https://mac.R-project.org")
> Installing packages into ‘/Users/michal/Library/R/x86_64/4.1/library’
> (as ‘lib’ is unspecified)
> trying URL 'https://mac.R-project.org/src/contrib/rgdal_1.5-23.tar.gz'
> Content type 'application/octet-stream' length 4393536 bytes (4.2 MB)
> ==================================================
> downloaded 4.2 MB
> 
> trying URL 'https://mac.R-project.org/src/contrib/sf_1.0-2.tar.gz'
> Content type 'application/octet-stream' length 3645982 bytes (3.5 MB)
> ==================================================
> downloaded 3.5 MB
> 
> * installing *source* package ‘rgdal’ ...
> ** package ‘rgdal’ successfully unpacked and MD5 sums checked
> ** using staged installation
> configure: R_HOME: /opt/local/Library/Frameworks/R.framework/Resources
> configure: CC: /opt/local/bin/clang-mp-12
> configure: CXX: /opt/local/bin/clang++-mp-12 -std=gnu++14
> configure: CFLAGS: -pipe -Os
> -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk -arch x86_64
> configure: CPPFLAGS: -I/opt/local/include
> -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk
> configure: CXXFLAGS: -pipe -Os -stdlib=libc++
> -isysroot/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk -arch x86_64
> configure: LDFLAGS: -L/opt/local/lib -Wl,-headerpad_max_install_names
> -Wl,-syslibroot,/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk -arch
> x86_64
> configure: LDFLAGS: -L/opt/local/lib -Wl,-headerpad_max_install_names
> -Wl,-syslibroot,/Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk -arch
> x86_64
> configure: CXX11 is: /opt/local/bin/clang++-mp-12, CXX11STD is: -std=gnu++11
> configure: CXX is: /opt/local/bin/clang++-mp-12 -std=gnu++11
> configure: C++11 support available
> configure: rgdal: 1.5-23
> checking for /usr/bin/svnversion... no
> configure: svn revision: 1121
> checking for gdal-config... /opt/local/bin/gdal-config
> checking gdal-config usability... yes
> configure: GDAL: 3.3.0
> 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: /opt/local/share/gdal/stateplane.csv readable... yes
> 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/opt/local/include
> configure: PROJ LIBS:  -lproj
> checking PROJ header API:... yes
> configure: API to be used as yet undetermined, searching ...
> configure: error: API to be used not found
> ERROR: configuration failed for package ‘rgdal’
> * removing ‘/Users/michal/Library/R/x86_64/4.1/library/rgdal’
> * installing *source* package ‘sf’ ...
> ** package ‘sf’ successfully unpacked and MD5 sums checked
> ** using staged installation
> configure: CC: /opt/local/bin/clang-mp-12
> configure: CXX: /opt/local/bin/clang++-mp-12 -std=gnu++11
> checking for gdal-config... /opt/local/bin/gdal-config
> checking gdal-config usability... yes
> configure: GDAL: 3.3.0
> checking GDAL version >= 2.0.1... yes
> checking for gcc... /opt/local/bin/clang-mp-12
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether /opt/local/bin/clang-mp-12 accepts -g... yes
> checking for /opt/local/bin/clang-mp-12 option to accept ISO C89... none
> needed
> checking how to run the C preprocessor... /opt/local/bin/clang-mp-12 -E
> checking for grep that handles long lines and -e... /usr/bin/grep
> checking for egrep... /usr/bin/grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking gdal.h usability... yes
> checking gdal.h presence... yes
> checking for gdal.h... yes
> checking GDAL: linking with --libs only... yes
> checking GDAL: /opt/local/share/gdal/pcs.csv readable... no
> checking GDAL: checking whether PROJ is available for linking:... yes
> checking GDAL: checking whether PROJ is available fur running:... yes
> configure: GDAL: 3.3.0
> checking proj.h usability... no
> checking proj.h presence... no
> checking for proj.h... no
> checking proj_api.h usability... no
> checking proj_api.h presence... no
> checking for proj_api.h... no
> configure: error: proj_api.h not found in standard or given locations.
> ERROR: configuration failed for package ‘sf’
> * removing ‘/Users/michal/Library/R/x86_64/4.1/library/sf’
> 
> The downloaded source packages are in
> ‘/private/var/folders/07/47hs0f_j187393z5drwshbm00000gn/T/RtmpsD9V5a/downloaded_packages’
> Warning messages:
> 1: In install.packages(c("rgdal", "sf"), , "https://mac.R-project.org") :
>    installation of package ‘rgdal’ had non-zero exit status
> 2: In install.packages(c("rgdal", "sf"), , "https://mac.R-project.org") :
>    installation of package ‘sf’ had non-zero exit status
> 
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> 
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-- 
Brian D. Ripley,                  ripley using stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford