[R-sig-Geo] rgdal with R > 3.5.x and GDAL > 2.3.x on macOS

[Roger Bivand]

On Mon, 6 Aug 2018, Patrick Schratz wrote:

> 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.

More luck you than me - I haven't repeated trying to test on OSX for 
years - regular users need to find ways of sharing information but volume 
on R-sig-mac is low.

>> Is the issue advice wrong, and CXX should be
>> 'clang++ -std=gnu++11'?
>
> This seems to be the problem. Using your configuration works!

So R CMD config CXX on your system returned 'clang++ -std=gnu++11'? Please 
let me know off-list, and I'll update the sf issue.

> 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 ;)

Volunteers welcome - it would be easiest to maintain if those doing it had 
a CI framework. I think it is also a mindset thing, OSX should be easier 
than Windows, but often isn't, partly because of Apple making changes that 
are not backward-compatible.

> 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).

Life isn't supposed to be easy, unless one believes the sales talk ... 
thanks for contributing the issue anyway, maybe the signal will get a bit 
stronger ...

Roger

> Thanks again!!
> Patrick
>
> On Aug 6 2018, at 11:05 am, Roger Bivand <Roger.Bivand using 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.
>>>
>>> _______________________________________________
>>> R-sig-Geo mailing list
>>> R-sig-Geo using r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>
>> --
>> 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 using nhh.no
>> http://orcid.org/0000-0003-2392-6140
>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>
>
>

-- 
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 using nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en