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

2021-08-20 Thread Michal Ben-Nun 
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 
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 
> 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
> > ")
> >
> > 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...

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

2021-08-19 Thread 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
")

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

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

2021-08-19 Thread Simon Urbanek 


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  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
> ")
> 
> 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

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

2021-08-19 Thread Michal Ben-Nun 
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
")

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.

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

2020-11-19 Thread Roy Mendelssohn - NOAA Federal via R-SIG-Mac 
Ditto on the thanks.  Will also remind people that there were warnings that 
folks might want to hold off on upgrading to Big Sur because there might be 
hiccups, and to wait till it looked like most things were resolved.  

I imagine this is a huge amount of work.  Graeful to all who are working on it.

-Roy


> On Nov 19, 2020, at 4:07 PM, Milani Chaloupka  wrote:
> 
> Thank you Simon.
> 
> That worked exactly as you said for macOS Big Sur with rgdal, sf etc.
> 
> Simple. Sensible. No fuss. No nonsense.
> 
> I can also verify that after reinstall that cmdstanr and the Stan ecosystem 
> work as well on Big Sur including using sf for maps results,
> 
> So grateful for the work you do here.
> 
> Milani
> 
> 
> 
> 
> 
> 
> 
> 
>> On 20 Nov 2020, at 6:06 am, Simon Urbanek  
>> wrote:
>> 
>> Just for posterity, please do NOT follow those instructions unless you 
>> really want to build packages from sources and maintain them. Building GDAL 
>> can be tricky since the feature set depends on the libraries you have 
>> available, so use at your own risk.
>> 
>> CRAN libraries have been updated to be compatible with Big Sur which removed 
>> some system libraries, so just re-install rgdal and sf from CRAN (thanks to 
>> Jeroen). To make sure you get the latest versions use
>> install.packages(c("rgdal","sf"),,"https://mac.R-project.org;)
>> 
>> Cheers,
>> Simon
>> 
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

**
"The contents of this message do not reflect any position of the U.S. 
Government or NOAA."
**
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
110 McAllister Way
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

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

2020-11-19 Thread Milani Chaloupka 
Thank you Simon.

That worked exactly as you said for macOS Big Sur with rgdal, sf etc.

Simple. Sensible. No fuss. No nonsense.

I can also verify that after reinstall that cmdstanr and the Stan ecosystem 
work as well on Big Sur including using sf for maps results,

So grateful for the work you do here.

Milani








> On 20 Nov 2020, at 6:06 am, Simon Urbanek  wrote:
> 
> Just for posterity, please do NOT follow those instructions unless you really 
> want to build packages from sources and maintain them. Building GDAL can be 
> tricky since the feature set depends on the libraries you have available, so 
> use at your own risk.
> 
> CRAN libraries have been updated to be compatible with Big Sur which removed 
> some system libraries, so just re-install rgdal and sf from CRAN (thanks to 
> Jeroen). To make sure you get the latest versions use
> install.packages(c("rgdal","sf"),,"https://mac.R-project.org;)
> 
> Cheers,
> Simon
> 

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

2020-11-19 Thread Balamuta, James Joseph 
Simon,

Okay, thanks for the note!

Would you be okay if I add a line to the READMEs on https://github.com/R-macos 
projects about how issues should be raised?
I think there was confusion as to how to best raise an issue. 

Best,

JJB

On 11/19/20, 2:14 PM, "Simon Urbanek"  wrote:

JJB,

FWIW if you have an issue that is related to macOS R please report it here. 
GH is fine for PRs, but I am only batch-processing GH notifications once in a 
while (with close to 100 repos it's not possible to do it continuously), so I 
only act on things flagged here as important.

Cheers,
Simon



> On Nov 20, 2020, at 3:34 AM, Balamuta, James Joseph 
 wrote:
> 
> Prof. Ripley,
> 
> Hope all is well. 
> 
> The issue was raised by Jeroen on GitHub on Oct 30th regarding 
libpq.5.dylib being missing:
> 
> https://github.com/R-macos/recipes/issues/14 
> 
> To date, Simon hasn't responded to it. Not sure re-building with the 
recipe as-is will yield the correct outcome as the pgsql is at: 
/usr/local/pgsql/lib instead of /usr/local/{include,lib}.
> 
> Best,
> 
> JJB
> 
> On 11/19/20, 7:46 AM, "R-SIG-Mac on behalf of Gilberto Camara" 
 wrote:
> 
>Dear Prof Ripley
> 
>There have been reports as follows:
> 
>https://community.rstudio.com/t/rgdal-library-not-loading/88025 

> 
>https://github.com/r-spatial/sf/issues/1542 

> 
>Best
>Gilberto
>===
>Prof Dr Gilberto Camara
>Secretariat Director
>GEO - Group on Earth Observations
>7 bis, Avenue de La Paix
>CH-1211 Geneva - Switzerland
>Tel: +41227308480
>Web: www.earthobservations.org
> 
> 
>> On 19 Nov 2020, at 14:43, Prof Brian Ripley  
wrote:
>> 
>> On 19/11/2020 11:22, GilbertoCamara wrote:
>>> Dear all,
>>> Mac users that have upgraded to Mac OS 11 BigSur have reported having 
problems with “rgdal” and “sf”. The same happened to me when I upgraded my Mac.
>> 
>> What problems are those?  You report nothing, and make reference to no 
reports here nor on R-sig-geo.
>> 
>> I tried the binary package of sf on my Intel 'Big Sur' machine and got
>> 
>>> library(sf)
>> Error: package or namespace load failed for ‘sf’ in dyn.load(file, 
DLLpath = DLLpath, ...):
>> unable to load shared object '/Users/ripley/R/Library/sf/libs/sf.so':
>> dlopen(/Users/ripley/R/Library/sf/libs/sf.so, 6): Library not loaded: 
/usr/lib/libpq.5.dylib
>> Referenced from: /Users/ripley/R/Library/sf/libs/sf.so
>> Reason: image not found
>> 
>> so it seem Apple has removed the PostgreSQL library.
>> 
>>> I managed to get "sf" to run on MacOS 11.0.1 by recompiling most of the 
required packages. Here's the recipe:
>>> 1. Remove all spatial software from brew (if you installed it). Rgdal 
does not like "brewed" stuff (I believe Roger prefers wine). Seriously, it 
appears that rgdal looks for libraries in their default places and not in the 
"Cellar" libraries used by "brew".
>>> 2. Install Xcode 12.3beta (downloaded from Apple Developers). This is 
the latest version of XCode which is compatible with MacOS BigSur.
>>> 3. Install "wget" using brew:
>>> "brew install wget".
>>> 4. Download the libraries below from their sources:
>>> (a) sqlite-autoconf-333.tar.gz from 
"https://www.sqlite.org/download.html ".
>>> (b) tiff-4.1.0.tar.gz from "https://download.osgeo.org/libtiff/ 
"
>>> (c) proj-7.2.0.tar.gz from 
"https://proj.org/download.html#current-release 
"
>>> (d) libgeotiff-1.6.0.tar.gz from 
"https://download.osgeo.org/geotiff/libgeotiff/ 
"
>>> (e) geos-3.8.1.tar.bz2 from "https://trac.osgeo.org/geos 
"
>>> (f) gdal-3.2.0.tar.gz from "https://gdal.org/download.html 
"
>> 
>> At the bottom of https://mac.r-project.org/libs-4/ 
 you will see a reference to 'recipes': you 
could simply have followed those to rebuild for macOS 11, probably only gdal.  
You probably want to ensure that the libpq that libgdal links against is the 
one in the libpq recipe (or build without PostgreSQL support).  Please ask 
Simon to rebuild his gdal accordingly.
>> 
>>> 5. In the order given above, unpack each library and then execute the 
following commands:
>>> % ./configure
>>> % make
>>> % sudo make install
>>> 6. Now you are ready to compile "rgdal" and "sf" from source. Using the 
R console,do:
 install.packages("rgdal", type = "source”)

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

2020-11-19 Thread Simon Urbanek 
JJB,

FWIW if you have an issue that is related to macOS R please report it here. GH 
is fine for PRs, but I am only batch-processing GH notifications once in a 
while (with close to 100 repos it's not possible to do it continuously), so I 
only act on things flagged here as important.

Cheers,
Simon



> On Nov 20, 2020, at 3:34 AM, Balamuta, James Joseph  
> wrote:
> 
> Prof. Ripley,
> 
> Hope all is well. 
> 
> The issue was raised by Jeroen on GitHub on Oct 30th regarding libpq.5.dylib 
> being missing:
> 
> https://github.com/R-macos/recipes/issues/14 
> 
> To date, Simon hasn't responded to it. Not sure re-building with the recipe 
> as-is will yield the correct outcome as the pgsql is at: /usr/local/pgsql/lib 
> instead of /usr/local/{include,lib}.
> 
> Best,
> 
> JJB
> 
> On 11/19/20, 7:46 AM, "R-SIG-Mac on behalf of Gilberto Camara" 
>  wrote:
> 
>Dear Prof Ripley
> 
>There have been reports as follows:
> 
>https://community.rstudio.com/t/rgdal-library-not-loading/88025 
> 
> 
>https://github.com/r-spatial/sf/issues/1542 
> 
> 
>Best
>Gilberto
>===
>Prof Dr Gilberto Camara
>Secretariat Director
>GEO - Group on Earth Observations
>7 bis, Avenue de La Paix
>CH-1211 Geneva - Switzerland
>Tel: +41227308480
>Web: www.earthobservations.org
> 
> 
>> On 19 Nov 2020, at 14:43, Prof Brian Ripley  wrote:
>> 
>> On 19/11/2020 11:22, GilbertoCamara wrote:
>>> Dear all,
>>> Mac users that have upgraded to Mac OS 11 BigSur have reported having 
>>> problems with “rgdal” and “sf”. The same happened to me when I upgraded my 
>>> Mac.
>> 
>> What problems are those?  You report nothing, and make reference to no 
>> reports here nor on R-sig-geo.
>> 
>> I tried the binary package of sf on my Intel 'Big Sur' machine and got
>> 
>>> library(sf)
>> Error: package or namespace load failed for ‘sf’ in dyn.load(file, DLLpath = 
>> DLLpath, ...):
>> unable to load shared object '/Users/ripley/R/Library/sf/libs/sf.so':
>> dlopen(/Users/ripley/R/Library/sf/libs/sf.so, 6): Library not loaded: 
>> /usr/lib/libpq.5.dylib
>> Referenced from: /Users/ripley/R/Library/sf/libs/sf.so
>> Reason: image not found
>> 
>> so it seem Apple has removed the PostgreSQL library.
>> 
>>> I managed to get "sf" to run on MacOS 11.0.1 by recompiling most of the 
>>> required packages. Here's the recipe:
>>> 1. Remove all spatial software from brew (if you installed it). Rgdal does 
>>> not like "brewed" stuff (I believe Roger prefers wine). Seriously, it 
>>> appears that rgdal looks for libraries in their default places and not in 
>>> the "Cellar" libraries used by "brew".
>>> 2. Install Xcode 12.3beta (downloaded from Apple Developers). This is the 
>>> latest version of XCode which is compatible with MacOS BigSur.
>>> 3. Install "wget" using brew:
>>> "brew install wget".
>>> 4. Download the libraries below from their sources:
>>> (a) sqlite-autoconf-333.tar.gz from 
>>> "https://www.sqlite.org/download.html 
>>> ".
>>> (b) tiff-4.1.0.tar.gz from "https://download.osgeo.org/libtiff/ 
>>> "
>>> (c) proj-7.2.0.tar.gz from "https://proj.org/download.html#current-release 
>>> "
>>> (d) libgeotiff-1.6.0.tar.gz from 
>>> "https://download.osgeo.org/geotiff/libgeotiff/ 
>>> "
>>> (e) geos-3.8.1.tar.bz2 from "https://trac.osgeo.org/geos 
>>> "
>>> (f) gdal-3.2.0.tar.gz from "https://gdal.org/download.html 
>>> "
>> 
>> At the bottom of https://mac.r-project.org/libs-4/ 
>>  you will see a reference to 'recipes': 
>> you could simply have followed those to rebuild for macOS 11, probably only 
>> gdal.  You probably want to ensure that the libpq that libgdal links against 
>> is the one in the libpq recipe (or build without PostgreSQL support).  
>> Please ask Simon to rebuild his gdal accordingly.
>> 
>>> 5. In the order given above, unpack each library and then execute the 
>>> following commands:
>>> % ./configure
>>> % make
>>> % sudo make install
>>> 6. Now you are ready to compile "rgdal" and "sf" from source. Using the R 
>>> console,do:
 install.packages("rgdal", type = "source”)
 install.packages("sf", type = "source")
>>> 
>>> 7. After those steps, both "rgdal" and "sf" are working on MacOS BigSur.
>>> Hope this helps Mac users.
>>> Best
>>> Gilberto
>>> [[alternative HTML version deleted]]
>> 
>> Please don't send HTML.
>> 
>> -- 
>> Brian D. Ripley,  rip...@stats.ox.ac.uk 
>> 
>> Emeritus Professor of Applied Statistics, University of Oxford
> 
> 
>   [[alternative HTML version deleted]]
> 
>

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

2020-11-19 Thread Simon Urbanek 
Just for posterity, please do NOT follow those instructions unless you really 
want to build packages from sources and maintain them. Building GDAL can be 
tricky since the feature set depends on the libraries you have available, so 
use at your own risk.

CRAN libraries have been updated to be compatible with Big Sur which removed 
some system libraries, so just re-install rgdal and sf from CRAN (thanks to 
Jeroen). To make sure you get the latest versions use
install.packages(c("rgdal","sf"),,"https://mac.R-project.org;)

Cheers,
Simon


> On Nov 20, 2020, at 12:22 AM, GilbertoCamara  wrote:
> 
> Dear all, 
> 
> Mac users that have upgraded to Mac OS 11 BigSur have reported having 
> problems with “rgdal” and “sf”. The same happened to me when I upgraded my 
> Mac.
> 
> I managed to get "sf" to run on MacOS 11.0.1 by recompiling most of the 
> required packages. Here's the recipe:
> 
> 1. Remove all spatial software from brew (if you installed it). Rgdal does 
> not like "brewed" stuff (I believe Roger prefers wine). Seriously, it appears 
> that rgdal looks for libraries in their default places and not in the 
> "Cellar" libraries used by "brew".
> 
> 2. Install Xcode 12.3beta (downloaded from Apple Developers). This is the 
> latest version of XCode which is compatible with MacOS BigSur.
> 
> 3. Install "wget" using brew:
> 
> "brew install wget".
> 
> 4. Download the libraries below from their sources:
> 
> (a) sqlite-autoconf-333.tar.gz from "https://www.sqlite.org/download.html 
> ".
> (b) tiff-4.1.0.tar.gz from "https://download.osgeo.org/libtiff/ 
> "
> (c) proj-7.2.0.tar.gz from "https://proj.org/download.html#current-release 
> "
> (d) libgeotiff-1.6.0.tar.gz from 
> "https://download.osgeo.org/geotiff/libgeotiff/ 
> "
> (e) geos-3.8.1.tar.bz2 from "https://trac.osgeo.org/geos 
> "
> (f) gdal-3.2.0.tar.gz from "https://gdal.org/download.html 
> "
> 
> 5. In the order given above, unpack each library and then execute the 
> following commands:
> % ./configure
> % make
> % sudo make install
> 
> 6. Now you are ready to compile "rgdal" and "sf" from source. Using the R 
> console,do:
> 
>> install.packages("rgdal", type = "source”)
>> install.packages("sf", type = "source")
>   
> 7. After those steps, both "rgdal" and "sf" are working on MacOS BigSur.
> 
> Hope this helps Mac users.
> 
> Best 
> Gilberto
>   [[alternative HTML version deleted]]
> 
> ___
> R-SIG-Mac mailing list
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Re: [R-SIG-Mac] sf installation problem under Mac OS 11 - Big Sur

2020-11-19 Thread Balamuta, James Joseph 
Prof. Ripley,

Hope all is well. 

The issue was raised by Jeroen on GitHub on Oct 30th regarding libpq.5.dylib 
being missing:

https://github.com/R-macos/recipes/issues/14 

To date, Simon hasn't responded to it. Not sure re-building with the recipe 
as-is will yield the correct outcome as the pgsql is at: /usr/local/pgsql/lib 
instead of /usr/local/{include,lib}.

Best,

JJB

On 11/19/20, 7:46 AM, "R-SIG-Mac on behalf of Gilberto Camara" 
 wrote:

Dear Prof Ripley

There have been reports as follows:

https://community.rstudio.com/t/rgdal-library-not-loading/88025 


https://github.com/r-spatial/sf/issues/1542 


Best
Gilberto
===
Prof Dr Gilberto Camara
Secretariat Director
GEO - Group on Earth Observations
7 bis, Avenue de La Paix
CH-1211 Geneva - Switzerland
Tel: +41227308480
Web: www.earthobservations.org


> On 19 Nov 2020, at 14:43, Prof Brian Ripley  wrote:
> 
> On 19/11/2020 11:22, GilbertoCamara wrote:
>> Dear all,
>> Mac users that have upgraded to Mac OS 11 BigSur have reported having 
problems with “rgdal” and “sf”. The same happened to me when I upgraded my Mac.
> 
> What problems are those?  You report nothing, and make reference to no 
reports here nor on R-sig-geo.
> 
> I tried the binary package of sf on my Intel 'Big Sur' machine and got
> 
> > library(sf)
> Error: package or namespace load failed for ‘sf’ in dyn.load(file, 
DLLpath = DLLpath, ...):
> unable to load shared object '/Users/ripley/R/Library/sf/libs/sf.so':
>  dlopen(/Users/ripley/R/Library/sf/libs/sf.so, 6): Library not loaded: 
/usr/lib/libpq.5.dylib
>  Referenced from: /Users/ripley/R/Library/sf/libs/sf.so
>  Reason: image not found
> 
> so it seem Apple has removed the PostgreSQL library.
> 
>> I managed to get "sf" to run on MacOS 11.0.1 by recompiling most of the 
required packages. Here's the recipe:
>> 1. Remove all spatial software from brew (if you installed it). Rgdal 
does not like "brewed" stuff (I believe Roger prefers wine). Seriously, it 
appears that rgdal looks for libraries in their default places and not in the 
"Cellar" libraries used by "brew".
>> 2. Install Xcode 12.3beta (downloaded from Apple Developers). This is 
the latest version of XCode which is compatible with MacOS BigSur.
>> 3. Install "wget" using brew:
>> "brew install wget".
>> 4. Download the libraries below from their sources:
>> (a) sqlite-autoconf-333.tar.gz from 
"https://www.sqlite.org/download.html ".
>> (b) tiff-4.1.0.tar.gz from "https://download.osgeo.org/libtiff/ 
"
>> (c) proj-7.2.0.tar.gz from 
"https://proj.org/download.html#current-release 
"
>> (d) libgeotiff-1.6.0.tar.gz from 
"https://download.osgeo.org/geotiff/libgeotiff/ 
"
>> (e) geos-3.8.1.tar.bz2 from "https://trac.osgeo.org/geos 
"
>> (f) gdal-3.2.0.tar.gz from "https://gdal.org/download.html 
"
> 
> At the bottom of https://mac.r-project.org/libs-4/ 
 you will see a reference to 'recipes': you 
could simply have followed those to rebuild for macOS 11, probably only gdal.  
You probably want to ensure that the libpq that libgdal links against is the 
one in the libpq recipe (or build without PostgreSQL support).  Please ask 
Simon to rebuild his gdal accordingly.
> 
>> 5. In the order given above, unpack each library and then execute the 
following commands:
>> % ./configure
>> % make
>> % sudo make install
>> 6. Now you are ready to compile "rgdal" and "sf" from source. Using the 
R console,do:
>>> install.packages("rgdal", type = "source”)
>>> install.packages("sf", type = "source")
>>  
>> 7. After those steps, both "rgdal" and "sf" are working on MacOS BigSur.
>> Hope this helps Mac users.
>> Best
>> Gilberto
>>  [[alternative HTML version deleted]]
> 
> Please don't send HTML.
> 
> -- 
> Brian D. Ripley,  rip...@stats.ox.ac.uk 

> Emeritus Professor of Applied Statistics, University of Oxford


[[alternative HTML version deleted]]

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

2020-11-19 Thread Gilberto Camara 
Dear Prof Ripley

There have been reports as follows:

https://community.rstudio.com/t/rgdal-library-not-loading/88025 


https://github.com/r-spatial/sf/issues/1542 


Best
Gilberto
===
Prof Dr Gilberto Camara
Secretariat Director
GEO - Group on Earth Observations
7 bis, Avenue de La Paix
CH-1211 Geneva - Switzerland
Tel: +41227308480
Web: www.earthobservations.org


> On 19 Nov 2020, at 14:43, Prof Brian Ripley  wrote:
> 
> On 19/11/2020 11:22, GilbertoCamara wrote:
>> Dear all,
>> Mac users that have upgraded to Mac OS 11 BigSur have reported having 
>> problems with “rgdal” and “sf”. The same happened to me when I upgraded my 
>> Mac.
> 
> What problems are those?  You report nothing, and make reference to no 
> reports here nor on R-sig-geo.
> 
> I tried the binary package of sf on my Intel 'Big Sur' machine and got
> 
> > library(sf)
> Error: package or namespace load failed for ‘sf’ in dyn.load(file, DLLpath = 
> DLLpath, ...):
> unable to load shared object '/Users/ripley/R/Library/sf/libs/sf.so':
>  dlopen(/Users/ripley/R/Library/sf/libs/sf.so, 6): Library not loaded: 
> /usr/lib/libpq.5.dylib
>  Referenced from: /Users/ripley/R/Library/sf/libs/sf.so
>  Reason: image not found
> 
> so it seem Apple has removed the PostgreSQL library.
> 
>> I managed to get "sf" to run on MacOS 11.0.1 by recompiling most of the 
>> required packages. Here's the recipe:
>> 1. Remove all spatial software from brew (if you installed it). Rgdal does 
>> not like "brewed" stuff (I believe Roger prefers wine). Seriously, it 
>> appears that rgdal looks for libraries in their default places and not in 
>> the "Cellar" libraries used by "brew".
>> 2. Install Xcode 12.3beta (downloaded from Apple Developers). This is the 
>> latest version of XCode which is compatible with MacOS BigSur.
>> 3. Install "wget" using brew:
>> "brew install wget".
>> 4. Download the libraries below from their sources:
>> (a) sqlite-autoconf-333.tar.gz from 
>> "https://www.sqlite.org/download.html 
>> ".
>> (b) tiff-4.1.0.tar.gz from "https://download.osgeo.org/libtiff/ 
>> "
>> (c) proj-7.2.0.tar.gz from "https://proj.org/download.html#current-release 
>> "
>> (d) libgeotiff-1.6.0.tar.gz from 
>> "https://download.osgeo.org/geotiff/libgeotiff/ 
>> "
>> (e) geos-3.8.1.tar.bz2 from "https://trac.osgeo.org/geos 
>> "
>> (f) gdal-3.2.0.tar.gz from "https://gdal.org/download.html 
>> "
> 
> At the bottom of https://mac.r-project.org/libs-4/ 
>  you will see a reference to 'recipes': 
> you could simply have followed those to rebuild for macOS 11, probably only 
> gdal.  You probably want to ensure that the libpq that libgdal links against 
> is the one in the libpq recipe (or build without PostgreSQL support).  Please 
> ask Simon to rebuild his gdal accordingly.
> 
>> 5. In the order given above, unpack each library and then execute the 
>> following commands:
>> % ./configure
>> % make
>> % sudo make install
>> 6. Now you are ready to compile "rgdal" and "sf" from source. Using the R 
>> console,do:
>>> install.packages("rgdal", type = "source”)
>>> install.packages("sf", type = "source")
>>  
>> 7. After those steps, both "rgdal" and "sf" are working on MacOS BigSur.
>> Hope this helps Mac users.
>> Best
>> Gilberto
>>  [[alternative HTML version deleted]]
> 
> Please don't send HTML.
> 
> -- 
> Brian D. Ripley,  rip...@stats.ox.ac.uk 
> 
> Emeritus Professor of Applied Statistics, University of Oxford


[[alternative HTML version deleted]]

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

2020-11-19 Thread Prof Brian Ripley 

On 19/11/2020 11:22, GilbertoCamara wrote:

Dear all,

Mac users that have upgraded to Mac OS 11 BigSur have reported having problems 
with “rgdal” and “sf”. The same happened to me when I upgraded my Mac.


What problems are those?  You report nothing, and make reference to no 
reports here nor on R-sig-geo.


I tried the binary package of sf on my Intel 'Big Sur' machine and got

> library(sf)
Error: package or namespace load failed for ‘sf’ in dyn.load(file, 
DLLpath = DLLpath, ...):

 unable to load shared object '/Users/ripley/R/Library/sf/libs/sf.so':
  dlopen(/Users/ripley/R/Library/sf/libs/sf.so, 6): Library not loaded: 
/usr/lib/libpq.5.dylib

  Referenced from: /Users/ripley/R/Library/sf/libs/sf.so
  Reason: image not found

so it seem Apple has removed the PostgreSQL library.


I managed to get "sf" to run on MacOS 11.0.1 by recompiling most of the 
required packages. Here's the recipe:

1. Remove all spatial software from brew (if you installed it). Rgdal does not like "brewed" stuff 
(I believe Roger prefers wine). Seriously, it appears that rgdal looks for libraries in their default places 
and not in the "Cellar" libraries used by "brew".

2. Install Xcode 12.3beta (downloaded from Apple Developers). This is the 
latest version of XCode which is compatible with MacOS BigSur.

3. Install "wget" using brew:

"brew install wget".

4. Download the libraries below from their sources:

(a) sqlite-autoconf-333.tar.gz from "https://www.sqlite.org/download.html 
".
(b) tiff-4.1.0.tar.gz from "https://download.osgeo.org/libtiff/ 
"
(c) proj-7.2.0.tar.gz from "https://proj.org/download.html#current-release 
"
(d) libgeotiff-1.6.0.tar.gz from "https://download.osgeo.org/geotiff/libgeotiff/ 
"
(e) geos-3.8.1.tar.bz2 from "https://trac.osgeo.org/geos 
"
(f) gdal-3.2.0.tar.gz from "https://gdal.org/download.html 
"


At the bottom of https://mac.r-project.org/libs-4/ you will see a 
reference to 'recipes': you could simply have followed those to rebuild 
for macOS 11, probably only gdal.  You probably want to ensure that the 
libpq that libgdal links against is the one in the libpq recipe (or 
build without PostgreSQL support).  Please ask Simon to rebuild his gdal 
accordingly.



5. In the order given above, unpack each library and then execute the following 
commands:
% ./configure
% make
% sudo make install

6. Now you are ready to compile "rgdal" and "sf" from source. Using the R 
console,do:


install.packages("rgdal", type = "source”)
install.packages("sf", type = "source")


7. After those steps, both "rgdal" and "sf" are working on MacOS BigSur.

Hope this helps Mac users.

Best
Gilberto
[[alternative HTML version deleted]]


Please don't send HTML.

--
Brian D. Ripley,  rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

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

2020-11-19 Thread GilbertoCamara 
Dear all, 

Mac users that have upgraded to Mac OS 11 BigSur have reported having problems 
with “rgdal” and “sf”. The same happened to me when I upgraded my Mac.

I managed to get "sf" to run on MacOS 11.0.1 by recompiling most of the 
required packages. Here's the recipe:

1. Remove all spatial software from brew (if you installed it). Rgdal does not 
like "brewed" stuff (I believe Roger prefers wine). Seriously, it appears that 
rgdal looks for libraries in their default places and not in the "Cellar" 
libraries used by "brew".

2. Install Xcode 12.3beta (downloaded from Apple Developers). This is the 
latest version of XCode which is compatible with MacOS BigSur.

3. Install "wget" using brew:

"brew install wget".

4. Download the libraries below from their sources:

(a) sqlite-autoconf-333.tar.gz from "https://www.sqlite.org/download.html 
".
(b) tiff-4.1.0.tar.gz from "https://download.osgeo.org/libtiff/ 
"
(c) proj-7.2.0.tar.gz from "https://proj.org/download.html#current-release 
"
(d) libgeotiff-1.6.0.tar.gz from 
"https://download.osgeo.org/geotiff/libgeotiff/ 
"
(e) geos-3.8.1.tar.bz2 from "https://trac.osgeo.org/geos 
"
(f) gdal-3.2.0.tar.gz from "https://gdal.org/download.html 
"

5. In the order given above, unpack each library and then execute the following 
commands:
% ./configure
% make
% sudo make install

6. Now you are ready to compile "rgdal" and "sf" from source. Using the R 
console,do:

> install.packages("rgdal", type = "source”)
> install.packages("sf", type = "source")

7. After those steps, both "rgdal" and "sf" are working on MacOS BigSur.

Hope this helps Mac users.

Best 
Gilberto
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