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

[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
>> 
> 
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**
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**
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NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
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Re: [R-SIG-Mac] sf installation problem under Mac OS 11 - Big Sur

[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

[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

[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

[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]]
> 
> ___
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> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

[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

[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

[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
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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

[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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