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

Thu Aug 19 08:19:59 CEST 2021

Michal,

those instructions work for released CRAN R. Apparently, that's not what you are using - if you want to compile sf and gdal from sources, that is more challenging and you have to install all its dependencies first. In the output below you're missing at the very least the PROJ4/6 library - it may not be the only thing you're missing, so make sure you read the errors and install all necessary dependencies.

Cheers,
Simon

> On Aug 19, 2021, at 10:52 AM, Michal Ben-Nun <mbennun using predsci.com> wrote:
> 
> Hi,
> 
> I installed R 4.10 on my Mac OS 11.3.1
> 
> 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
> 
>> 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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