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

Thu Aug 19 18:32:29 CEST 2021

I was able to install the packages after setting the environment
variable PKG_CONFIG_PATH to the location of proj.pc

On Wed, Aug 18, 2021 at 11:20 PM Simon Urbanek <simon.urbanek using r-project.org>
wrote:

> 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
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac using r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
>
>

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