rgdal with R > 3.5.x and GDAL > 2.3.x on macOS

Hi,

desperately trying to get rgdal installed on R > 3.5.x with GDAL 2.3.0 
on macOS High Sierra. I am aware of the discussion that a suitable 
compiler is needed since GDAL > 2.3.0.

I've set
CC=clang
CXX=clang++
PKG_CXXFLAGS= -stdlib=libc++ -std=c++11

In ~/.R/Makevars as suggested here https://github.com/r-spatial/sf/issues/726

The automated checking during the rgdal installation shows that C++11 
support is available. But still it complains about a lacking C++11 
support.

I've searched the web but could not find anything helpful. If I've 
overlooked something, please just point me to the link.

Everything installed via homebrew (bottles)
R 3.5.1
proj 5.1.0 (osgeo4mac)
gdal 2.3.1 (homebrew core)

macOS 10.13.1 (High Sierra)

install.packages("rgdal")

Installing package into ?/usr/local/lib/R/3.5/site-library?
(as ?lib? is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/rgdal_1.3-4.tar.gz'
Content type 'application/x-gzip' length 1664774 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ?rgdal? ...
** package ?rgdal? successfully unpacked and MD5 sums checked
configure: R_HOME: /usr/local/Cellar/r/3.5.1/lib/R
configure: CC: clang
configure: CXX: clang++
configure: C++11 support available
configure: rgdal: 1.3-4
checking for /usr/bin/svnversion... yes
configure: svn revision: 766
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.3.1
checking C++11 support for GDAL >= 2.3.0... yes
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
In file included from gdal_test.cc:1:
In file included from /usr/local/Cellar/gdal2/2.3.1/include/gdal.h:45:
/usr/local/Cellar/gdal2/2.3.1/include/cpl_port.h:187:6: error: Must have C++11 or newer.
# error Must have C++11 or newer.
^

Is the issue advice wrong, and CXX should be
'clang++ -std=gnu++11'?

See below inline:
On Mon, 6 Aug 2018, Patrick Schratz wrote:

Hi,
desperately trying to get rgdal installed on R > 3.5.x with GDAL 2.3.0
on macOS High Sierra. I am aware of the discussion that a suitable
compiler is needed since GDAL > 2.3.0.

I've set
CC=clang
CXX=clang++
PKG_CXXFLAGS= -stdlib=libc++ -std=c++11

In ~/.R/Makevars as suggested here https://github.com/r-spatial/sf/issues/726

Does anyone actually know that this is a solution or rather the problem?
Check:

$ R CMD config CXX
## clang++ -std=gnu++11
## for me with an R-devel clang build on Fedora 28

Run this and/or ./configure in the unpacked rgdal source tarball and
report the CXX value. Is the issue advice wrong, and CXX should be
'clang++ -std=gnu++11'?

I have no access to OSX (and no wish to have access) - the OSX users need
to do a full bisection and not guess what is happening.

The automated checking during the rgdal installation shows that C++11
support is available. But still it complains about a lacking C++11
support.

No, that is coming from code in GDAL itself, as you can see. You need to
establish which --std= is actually needed.

I've searched the web but could not find anything helpful. If I've
overlooked something, please just point me to the link.

Searching the web only confirms that there is very little signal there -
search the source code instead, and bisection (which settings worked for
which versions, and which changes provoke the issue)? Is for example the
CRAN R binary reporting a different R CMD config CXX from your
homebrew-built R?

Everything installed via homebrew (bottles)
R 3.5.1
proj 5.1.0 (osgeo4mac)
gdal 2.3.1 (homebrew core)

macOS 10.13.1 (High Sierra)

install.packages("rgdal")

Installing package into ?/usr/local/lib/R/3.5/site-library?
(as ?lib? is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/rgdal_1.3-4.tar.gz'
Content type 'application/x-gzip' length 1664774 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ?rgdal? ...
** package ?rgdal? successfully unpacked and MD5 sums checked
configure: R_HOME: /usr/local/Cellar/r/3.5.1/lib/R
configure: CC: clang
configure: CXX: clang++
configure: C++11 support available
configure: rgdal: 1.3-4
checking for /usr/bin/svnversion... yes
configure: svn revision: 766
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.3.1
checking C++11 support for GDAL >= 2.3.0... yes
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
In file included from gdal_test.cc:1:
In file included from /usr/local/Cellar/gdal2/2.3.1/include/gdal.h:45:
/usr/local/Cellar/gdal2/2.3.1/include/cpl_port.h:187:6: error: Must have C++11 or newer.
# error Must have C++11 or newer.
^

From the GDAL 2.3.1 source at the given line number - your __cplusplus
from homebrew's value needs checking:

/* MSVC fails to define a decent value of __cplusplus. Try to target
VS2015*/
/* as a minimum */

#if defined(__cplusplus) && !defined(CPL_SUPRESS_CPLUSPLUS)
# if !(__cplusplus >= 201103L || (defined(_MSC_VER) && _MSC_VER >= 1900))
# error Must have C++11 or newer.
# endif
# if __cplusplus >= 201402L
# define HAVE_CXX14 1
# endif
/* TODO(schwehr): What is the correct test for C++ 17? */
#endif /* __cplusplus */

Fallback is the CRAN OSX binary for rgdal 1.3-4 (with the addition of proj
datum files as posted yesterday, or Kyngchaos (as on R-sig-mac).

Roger

1 error generated.
In file included from gdal_test.cc:1:
In file included from /usr/local/Cellar/gdal2/2.3.1/include/gdal.h:45:
/usr/local/Cellar/gdal2/2.3.1/include/cpl_port.h:187:6: error: Must have C++11 or newer.
# error Must have C++11 or newer.
^
1 error generated.
configure: Install failure: compilation and/or linkage problems.
configure: error: GDALAllRegister not found in libgdal.
ERROR: configuration failed for package ?rgdal?
* removing ?/usr/local/lib/R/3.5/site-library/rgdal?
Warning in install.packages :
installation of package ?rgdal? had non-zero exit status

The downloaded source packages are in
?/private/var/folders/nv/k87rzvfs55l6j6xt_0jwb4wm0000gn/T/Rtmp68hYW1/downloaded_packages?

install.packages("rgdal")

Installing package into ?/usr/local/lib/R/3.5/site-library?
(as ?lib? is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/rgdal_1.3-4.tar.gz'
Content type 'application/x-gzip' length 1664774 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ?rgdal? ...
** package ?rgdal? successfully unpacked and MD5 sums checked
configure: R_HOME: /usr/local/Cellar/r/3.5.1/lib/R
configure: CC: clang
configure: CXX: clang++
configure: C++11 support available
configure: rgdal: 1.3-4
checking for /usr/bin/svnversion... yes
configure: svn revision: 766
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.3.1
checking C++11 support for GDAL >= 2.3.0... yes
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
In file included from gdal_test.cc:1:
In file included from /usr/local/Cellar/gdal/2.3.1_1/include/gdal.h:45:
/usr/local/Cellar/gdal/2.3.1_1/include/cpl_port.h:187:6: error: Must have C++11 or newer.
# error Must have C++11 or newer.
^
1 error generated.
In file included from gdal_test.cc:1:
In file included from /usr/local/Cellar/gdal/2.3.1_1/include/gdal.h:45:
/usr/local/Cellar/gdal/2.3.1_1/include/cpl_port.h:187:6: error: Must have C++11 or newer.
# error Must have C++11 or newer.
^
1 error generated.
configure: Install failure: compilation and/or linkage problems.
configure: error: GDALAllRegister not found in libgdal.
ERROR: configuration failed for package ?rgdal?
* removing ?/usr/local/lib/R/3.5/site-library/rgdal?
Warning in install.packages :
installation of package ?rgdal? had non-zero exit status

The downloaded source packages are in
?/private/var/folders/nv/k87rzvfs55l6j6xt_0jwb4wm0000gn/T/Rtmp68hYW1/downloaded_packages?


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Do not post HTML, only plain text.

--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand at nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

Hi Roger,

thanks for taking the time. To defend myself, I do not use macOS on a 
daily base and just run it in a VM for some package testing.

Is the issue advice wrong, and CXX should be
'clang++ -std=gnu++11'?

This seems to be the problem. Using your configuration works!

I am aware of the small geospatial com on mac and that the osgeo4mac 
repo is not very stable. However I think there is a need for a short 
guide how to either use the kyngchaos frameworks or the osgeo4mac repo 
to have a stable geospatial toolset for R (starting with rgdal to sf and 
so on). Ideally for different R versions if major changes occured. A 
good place would be the README of rgdal if would be hosted on r-spatial 
on Github as most people would look there. As I saw in some issues, 
people sometimes think the cran/rgdal mirror is the place to go. But 
thats all just suggestions ;)

This little issue costed me at least 3h. Its really annyoing to have 
such issues on macOS from time to time (but ofc this is not your or 
anyone else fault).

Thanks again!!
Patrick

On Aug 6 2018, at 11:05 am, Roger Bivand <Roger.Bivand at nhh.no> wrote:

See below inline:
On Mon, 6 Aug 2018, Patrick Schratz wrote:

Hi,
desperately trying to get rgdal installed on R > 3.5.x with GDAL 2.3.0
on macOS High Sierra. I am aware of the discussion that a suitable
compiler is needed since GDAL > 2.3.0.

I've set
CC=clang
CXX=clang++
PKG_CXXFLAGS= -stdlib=libc++ -std=c++11

In ~/.R/Makevars as suggested here https://github.com/r-spatial/sf/issues/726

Does anyone actually know that this is a solution or rather the problem?
Check:

$ R CMD config CXX
## clang++ -std=gnu++11
## for me with an R-devel clang build on Fedora 28

Run this and/or ./configure in the unpacked rgdal source tarball and
report the CXX value. Is the issue advice wrong, and CXX should be
'clang++ -std=gnu++11'?

I have no access to OSX (and no wish to have access) - the OSX users need
to do a full bisection and not guess what is happening.

The automated checking during the rgdal installation shows that C++11
support is available. But still it complains about a lacking C++11
support.

No, that is coming from code in GDAL itself, as you can see. You need to
establish which --std= is actually needed.

I've searched the web but could not find anything helpful. If I've
overlooked something, please just point me to the link.

Searching the web only confirms that there is very little signal there -
search the source code instead, and bisection (which settings worked for
which versions, and which changes provoke the issue)? Is for example the
CRAN R binary reporting a different R CMD config CXX from your
homebrew-built R?

Everything installed via homebrew (bottles)
R 3.5.1
proj 5.1.0 (osgeo4mac)
gdal 2.3.1 (homebrew core)

macOS 10.13.1 (High Sierra)

install.packages("rgdal")

Installing package into ?/usr/local/lib/R/3.5/site-library?
(as ?lib? is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/rgdal_1.3-4.tar.gz'
Content type 'application/x-gzip' length 1664774 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ?rgdal? ...
** package ?rgdal? successfully unpacked and MD5 sums checked
configure: R_HOME: /usr/local/Cellar/r/3.5.1/lib/R
configure: CC: clang
configure: CXX: clang++
configure: C++11 support available
configure: rgdal: 1.3-4
checking for /usr/bin/svnversion... yes
configure: svn revision: 766
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.3.1
checking C++11 support for GDAL >= 2.3.0... yes
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
In file included from gdal_test.cc:1:
In file included from /usr/local/Cellar/gdal2/2.3.1/include/gdal.h:45:
/usr/local/Cellar/gdal2/2.3.1/include/cpl_port.h:187:6: error: Must have C++11 or newer.
# error Must have C++11 or newer.
^

From the GDAL 2.3.1 source at the given line number - your __cplusplus
from homebrew's value needs checking:

/* MSVC fails to define a decent value of __cplusplus. Try to target
VS2015*/
/* as a minimum */

#if defined(__cplusplus) && !defined(CPL_SUPRESS_CPLUSPLUS)
# if !(__cplusplus >= 201103L || (defined(_MSC_VER) && _MSC_VER >= 1900))
# error Must have C++11 or newer.
# endif
# if __cplusplus >= 201402L
# define HAVE_CXX14 1
# endif
/* TODO(schwehr): What is the correct test for C++ 17? */
#endif /* __cplusplus */

Fallback is the CRAN OSX binary for rgdal 1.3-4 (with the addition of proj
datum files as posted yesterday, or Kyngchaos (as on R-sig-mac).

Roger

1 error generated.
In file included from gdal_test.cc:1:
In file included from /usr/local/Cellar/gdal2/2.3.1/include/gdal.h:45:
/usr/local/Cellar/gdal2/2.3.1/include/cpl_port.h:187:6: error: Must have C++11 or newer.
# error Must have C++11 or newer.
^
1 error generated.
configure: Install failure: compilation and/or linkage problems.
configure: error: GDALAllRegister not found in libgdal.
ERROR: configuration failed for package ?rgdal?
* removing ?/usr/local/lib/R/3.5/site-library/rgdal?
Warning in install.packages :
installation of package ?rgdal? had non-zero exit status

The downloaded source packages are in
?/private/var/folders/nv/k87rzvfs55l6j6xt_0jwb4wm0000gn/T/Rtmp68hYW1/downloaded_packages?

install.packages("rgdal")

Installing package into ?/usr/local/lib/R/3.5/site-library?
(as ?lib? is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/rgdal_1.3-4.tar.gz'
Content type 'application/x-gzip' length 1664774 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

* installing *source* package ?rgdal? ...
** package ?rgdal? successfully unpacked and MD5 sums checked
configure: R_HOME: /usr/local/Cellar/r/3.5.1/lib/R
configure: CC: clang
configure: CXX: clang++
configure: C++11 support available
configure: rgdal: 1.3-4
checking for /usr/bin/svnversion... yes
configure: svn revision: 766
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.3.1
checking C++11 support for GDAL >= 2.3.0... yes
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
In file included from gdal_test.cc:1:
In file included from /usr/local/Cellar/gdal/2.3.1_1/include/gdal.h:45:
/usr/local/Cellar/gdal/2.3.1_1/include/cpl_port.h:187:6: error: Must have C++11 or newer.
# error Must have C++11 or newer.
^
1 error generated.
In file included from gdal_test.cc:1:
In file included from /usr/local/Cellar/gdal/2.3.1_1/include/gdal.h:45:
/usr/local/Cellar/gdal/2.3.1_1/include/cpl_port.h:187:6: error: Must have C++11 or newer.
# error Must have C++11 or newer.
^
1 error generated.
configure: Install failure: compilation and/or linkage problems.
configure: error: GDALAllRegister not found in libgdal.
ERROR: configuration failed for package ?rgdal?
* removing ?/usr/local/lib/R/3.5/site-library/rgdal?
Warning in install.packages :
installation of package ?rgdal? had non-zero exit status

The downloaded source packages are in
?/private/var/folders/nv/k87rzvfs55l6j6xt_0jwb4wm0000gn/T/Rtmp68hYW1/downloaded_packages?


[[alternative HTML version deleted]]

Do not post HTML, only plain text.

--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand at nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en