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