Message-ID: <048c9bd2-445f-3dee-324b-11c1a6ac27a0@stats.ox.ac.uk>
Date: 2021-08-19T06:28:40Z
From: Brian Ripley
Subject: sf installation problem under Mac OS 11 - Big Sur
In-Reply-To: <CAMY0nH5vH6LEfP3FF56BTHbjkNTXtbKqK2308jTw2CZ+DEUy=w@mail.gmail.com>
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 at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford