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sf 1.0-6 requires GDAL (>= 3.0.0)? [SOLVED for sf 1.0-7] #1899

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HenrikBengtsson opened this issue Feb 5, 2022 · 17 comments
Closed

sf 1.0-6 requires GDAL (>= 3.0.0)? [SOLVED for sf 1.0-7] #1899

HenrikBengtsson opened this issue Feb 5, 2022 · 17 comments

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@HenrikBengtsson
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HenrikBengtsson commented Feb 5, 2022 •
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WORKAROUND:

Until sf (>= 1.0-7) is on CRAN, you can install the develop version, which also has version 1.0-7, using:

remotes::install_github("r-spatial/sf")

Consider this an FYI for now, as I guess you get more reports on this soon:

In contrast to sf 1.0-5 (2021-12-17), I think the new sf 1.0-6 (2022-02-04) requires something newer than GDAL (>= 2.0.1) that the DESCRIPTION file mentions.

Because, when I install with GDAL 2.4.4, on R 4.1.2, I get an error on:

stars.cpp:771:7: error: ‘class OGRSpatialReference’ has no member named ‘SetAxisMappingStrategy’
  oSRS.SetAxisMappingStrategy(OAMS_TRADITIONAL_GIS_ORDER);
       ^~~~~~~~~~~~~~~~~~~~~~
stars.cpp:771:30: error: ‘OAMS_TRADITIONAL_GIS_ORDER’ was not declared in this scope
  oSRS.SetAxisMappingStrategy(OAMS_TRADITIONAL_GIS_ORDER);
                              ^~~~~~~~~~~~~~~~~~~~~~~~~~

This is on CentOS 7. I get the same error on Ubuntu 18.04, which has GDAL 2.2.3 (Ubuntu package gdal-bin 2.2.3+dfsg-2). sf 1.0-5 installs fine on both of these systems (see below).

I'll see if I can install the next version up from GDAL 2.4.4, i.e. GDAL 3.0.0, and retry with that.

Details for CentOS run

Setup

$ gdalinfo --version
GDAL 2.4.4, released 2020/01/08

$ geos-config --version
3.4.2

$ proj 2>&1 | head -1
Rel. 4.8.0, 6 March 2012

$ g++ --version | head -1
g++ (GCC) 8.3.1 20190311 (Red Hat 8.3.1-3)

$ R --version | head -1
R version 4.1.2 (2021-11-01) -- "Bird Hippie"

sf 1.0.6 (fails to install)

Click to see install log 
> install.packages("sf")
Installing package into ‘/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/sf_1.0-6.tar.gz'
Content type 'application/x-gzip' length 3528078 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

    

  • installing source package ‘sf’ ...
    
** package ‘sf’ successfully unpacked and MD5 sums checked
    
** using staged installation
    
configure: CC: gcc
    
configure: CXX: g++ -std=gnu++11
    
checking for gdal-config... /wynton/home/cbi/shared/software/CBI/gdal-2.4.4/bin/gdal-config
    
checking gdal-config usability... yes
    
configure: GDAL: 2.4.4
    
checking GDAL version >= 2.0.1... yes
    
checking for gcc... gcc
    
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 gcc accepts -g... yes
    
checking for gcc option to accept ISO C89... none needed
    
checking how to run the C preprocessor... gcc -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: /wynton/home/cbi/shared/software/CBI/gdal-2.4.4/share/gdal/pcs.csv readable... yes
    
checking GDAL: checking whether PROJ is available for linking:... yes
    
checking GDAL: checking whether PROJ is available fur running:... yes
    
configure: GDAL: 2.4.4
    
configure: pkg-config proj exists, will use it
    
checking proj_api.h usability... yes
    
checking proj_api.h presence... yes
    
checking for proj_api.h... yes
    
configure: PROJ: 4.8.0
    
checking for pj_init_plus in -lproj... yes
    
checking PROJ: epsg found and readable... yes
    
checking for geos-config... /usr/bin/geos-config
    
checking geos-config usability... yes
    
configure: GEOS: 3.4.2
    
checking GEOS version >= 3.4.0... yes
    
checking geos_c.h usability... yes
    
checking geos_c.h presence... yes
    
checking for geos_c.h... yes
    
checking geos: linking with -L/usr/lib64 -lgeos_c... yes
    
configure: Package CPP flags:    -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include
    
configure: Package LIBS: -lproj     -L/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/lib -lgdal -L/usr/lib64 -lgeos_c
    
configure: creating ./config.status
    
config.status: creating src/Makevars
    
** libs
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c bbox.cpp -o bbox.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal.cpp -o gdal.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_geom.cpp -o gdal_geom.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_read.cpp -o gdal_read.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_utils.cpp -o gdal_utils.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_write.cpp -o gdal_write.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c geos.cpp -o geos.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c hex.cpp -o hex.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c mdim.cpp -o mdim.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c ops.cpp -o ops.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c polygonize.cpp -o polygonize.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c proj.cpp -o proj.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c proj_info.cpp -o proj_info.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c raster2sf.cpp -o raster2sf.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c sfg.cpp -o sfg.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c signed_area.cpp -o signed_area.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c stars.cpp -o stars.o
    
stars.cpp: In function ‘void CPL_create(Rcpp::CharacterVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::CharacterVector, Rcpp::NumericVector, Rcpp::NumericVector)’:
    
stars.cpp:771:7: error: ‘class OGRSpatialReference’ has no member named ‘SetAxisMappingStrategy’
    
oSRS.SetAxisMappingStrategy(OAMS_TRADITIONAL_GIS_ORDER);
    
^~~~~~~~~~~~~~~~~~~~~~
    
stars.cpp:771:30: error: ‘OAMS_TRADITIONAL_GIS_ORDER’ was not declared in this scope
    
oSRS.SetAxisMappingStrategy(OAMS_TRADITIONAL_GIS_ORDER);
    
^~~~~~~~~~~~~~~~~~~~~~~~~~
    
make: *** [/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/etc/Makeconf:177: stars.o] Error 1
    
ERROR: compilation failed for package ‘sf’
    • 

  • removing ‘/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/sf’
    • 

  • restoring previous ‘/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/sf’
    • 



The downloaded source packages are in

‘/tmp/Rtmpax2Spi/downloaded_packages’

Warning message:

In install.packages("sf") :

installation of package ‘sf’ had non-zero exit status

sf 1.0.5 (install fine)

Click to see install log 
> install.packages("https://cran.r-project.org/src/contrib/Archive/sf/sf_1.0-5.tar.gz")
Installing package into ‘/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8’
(as ‘lib’ is unspecified)
inferring 'repos = NULL' from 'pkgs'
trying URL 'https://cran.r-project.org/src/contrib/Archive/sf/sf_1.0-5.tar.gz'
Content type 'application/x-gzip' length 3527059 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

    

  • installing source package ‘sf’ ...
    
** package ‘sf’ successfully unpacked and MD5 sums checked
    
** using staged installation
    
configure: CC: gcc
    
configure: CXX: g++ -std=gnu++11
    
checking for gdal-config... /wynton/home/cbi/shared/software/CBI/gdal-2.4.4/bin/gdal-config
    
checking gdal-config usability... yes
    
configure: GDAL: 2.4.4
    
checking GDAL version >= 2.0.1... yes
    
checking for gcc... gcc
    
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 gcc accepts -g... yes
    
checking for gcc option to accept ISO C89... none needed
    
checking how to run the C preprocessor... gcc -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: /wynton/home/cbi/shared/software/CBI/gdal-2.4.4/share/gdal/pcs.csv readable... yes
    
checking GDAL: checking whether PROJ is available for linking:... yes
    
checking GDAL: checking whether PROJ is available fur running:... yes
    
configure: GDAL: 2.4.4
    
configure: pkg-config proj exists, will use it
    
checking proj_api.h usability... yes
    
checking proj_api.h presence... yes
    
checking for proj_api.h... yes
    
configure: PROJ: 4.8.0
    
checking for pj_init_plus in -lproj... yes
    
checking PROJ: epsg found and readable... yes
    
checking for geos-config... /usr/bin/geos-config
    
checking geos-config usability... yes
    
configure: GEOS: 3.4.2
    
checking GEOS version >= 3.4.0... yes
    
checking geos_c.h usability... yes
    
checking geos_c.h presence... yes
    
checking for geos_c.h... yes
    
checking geos: linking with -L/usr/lib64 -lgeos_c... yes
    
configure: Package CPP flags:    -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include
    
configure: Package LIBS: -lproj     -L/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/lib -lgdal -L/usr/lib64 -lgeos_c
    
configure: creating ./config.status
    
config.status: creating src/Makevars
    
** libs
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c bbox.cpp -o bbox.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal.cpp -o gdal.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_geom.cpp -o gdal_geom.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_read.cpp -o gdal_read.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_utils.cpp -o gdal_utils.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_write.cpp -o gdal_write.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c geos.cpp -o geos.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c hex.cpp -o hex.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c mdim.cpp -o mdim.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c ops.cpp -o ops.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c polygonize.cpp -o polygonize.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c proj.cpp -o proj.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c proj_info.cpp -o proj_info.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c raster2sf.cpp -o raster2sf.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c sfg.cpp -o sfg.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c signed_area.cpp -o signed_area.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c stars.cpp -o stars.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c wkb.cpp -o wkb.o
    
g++ -std=gnu++11 -I"/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/include -I/usr/include -I'/wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c zm_range.cpp -o zm_range.o
    
g++ -std=gnu++11 -shared -L/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/lib -L/usr/local/lib64 -o sf.so RcppExports.o bbox.o gdal.o gdal_geom.o gdal_read.o gdal_utils.o gdal_write.o geos.o hex.o mdim.o ops.o polygonize.o proj.o proj_info.o raster2sf.o sfg.o signed_area.o stars.o wkb.o zm_range.o -lproj -L/wynton/home/cbi/shared/software/CBI/gdal-2.4.4/lib -lgdal -L/usr/lib64 -lgeos_c -L/wynton/home/cbi/shared/software/CBI/R-4.1.2-gcc8/lib64/R/lib -lR
    
installing to /wynton/home/bengtsson/hb-test/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/00LOCK-sf/00new/sf/libs
    
** R
    
** demo
    
** inst
    
** byte-compile and prepare package for lazy loading
    
in method for ‘dbWriteTable’ with signature ‘"PostgreSQLConnection","character","sf"’: no definition for class “PostgreSQLConnection”
    
in method for ‘dbDataType’ with signature ‘"PostgreSQLConnection","sf"’: no definition for class “PostgreSQLConnection”
    
in method for ‘coerce’ with signature ‘"Spatial","sf"’: no definition for class “Spatial”
    
in method for ‘coerce’ with signature ‘"Spatial","sfc"’: no definition for class “Spatial”
    
in method for ‘coerce’ with signature ‘"sf","Spatial"’: no definition for class “Spatial”
    
in method for ‘coerce’ with signature ‘"sfc","Spatial"’: no definition for class “Spatial”
    
in method for ‘coerce’ with signature ‘"XY","Spatial"’: no definition for class “Spatial”
    
in method for ‘coerce’ with signature ‘"crs","CRS"’: no definition for class “CRS”
    
in method for ‘coerce’ with signature ‘"sgbp","sparseMatrix"’: no definition for class “sparseMatrix”
    
** help
    
*** installing help indices
    
*** copying figures
    
** building package indices
    
** installing vignettes
    
** testing if installed package can be loaded from temporary location
    
** checking absolute paths in shared objects and dynamic libraries
    
** testing if installed package can be loaded from final location
    
** testing if installed package keeps a record of temporary installation path
    • 

  • DONE (sf)
    •
@HenrikBengtsson
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HenrikBengtsson commented Feb 5, 2022 •
edited
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Okay, I've install GDAL 3.0.0, which is the next version after GDAL 2.4.0. GDAL 3.0.0 requires PROJ 6.0.0, so I installed that too. I'm getting closer, but now I get:

proj.cpp:279:14: error: ‘proj_normalize_for_visualization’ was not declared in this scope
   PJ *NewP = proj_normalize_for_visualization(PJ_DEFAULT_CTX, P);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make: *** [/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/etc/Makeconf:177: proj.o] Error 1

This looks like an issue related to PROJ.

Details

$ gdalinfo --version
GDAL 3.0.0, released 2019/05/05

$ geos-config --version
3.4.2

$ proj 2>&1 | head -1
Rel. 6.0.0, March 1st, 2019

$ g++ --version | head -1
g++ (GCC) 8.3.1 20190311 (Red Hat 8.3.1-3)

$ R --version | head -1
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
> install.packages("sf")
Installing package into ‘/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/sf_1.0-6.tar.gz'
Content type 'application/x-gzip' length 3528078 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

* installing *source* package ‘sf’ ...
** package ‘sf’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++11
checking for gdal-config... /software/c4/cbi/software/gdal-3.0.0/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.0.0
checking GDAL version >= 2.0.1... yes
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -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: /software/c4/cbi/software/gdal-3.0.0/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: 3.0.0
configure: pkg-config proj exists, will use it
configure: using proj.h.
configure: PROJ: 6.0.0
checking PROJ: checking whether PROJ and sqlite3 are available for linking:... yes
checking for geos-config... /usr/bin/geos-config
checking geos-config usability... yes
configure: GEOS: 3.4.2
checking GEOS version >= 3.4.0... yes
checking geos_c.h usability... yes
checking geos_c.h presence... yes
checking for geos_c.h... yes
checking geos: linking with -L/usr/lib64 -lgeos_c... yes
configure: Package CPP flags:  -I/software/c4/cbi/software/proj-6.0.0/include   -DHAVE_PROJ_H -I/software/c4/cbi/software/gdal-3.0.0/include -I/usr/include
configure: Package LIBS: -L/software/c4/cbi/software/proj-6.0.0/lib -lproj     -L/software/c4/cbi/software/gdal-3.0.0/lib -lgdal -L/usr/lib64 -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/proj-6.0.0/include   -DHAVE_PROJ_H -I/software/c4/cbi/software/gdal-3.0.0/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/proj-6.0.0/include   -DHAVE_PROJ_H -I/software/c4/cbi/software/gdal-3.0.0/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c bbox.cpp -o bbox.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/proj-6.0.0/include   -DHAVE_PROJ_H -I/software/c4/cbi/software/gdal-3.0.0/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal.cpp -o gdal.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/proj-6.0.0/include   -DHAVE_PROJ_H -I/software/c4/cbi/software/gdal-3.0.0/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_geom.cpp -o gdal_geom.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/proj-6.0.0/include   -DHAVE_PROJ_H -I/software/c4/cbi/software/gdal-3.0.0/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_read.cpp -o gdal_read.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/proj-6.0.0/include   -DHAVE_PROJ_H -I/software/c4/cbi/software/gdal-3.0.0/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_utils.cpp -o gdal_utils.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/proj-6.0.0/include   -DHAVE_PROJ_H -I/software/c4/cbi/software/gdal-3.0.0/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_write.cpp -o gdal_write.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/proj-6.0.0/include   -DHAVE_PROJ_H -I/software/c4/cbi/software/gdal-3.0.0/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c geos.cpp -o geos.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/proj-6.0.0/include   -DHAVE_PROJ_H -I/software/c4/cbi/software/gdal-3.0.0/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c hex.cpp -o hex.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/proj-6.0.0/include   -DHAVE_PROJ_H -I/software/c4/cbi/software/gdal-3.0.0/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c mdim.cpp -o mdim.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/proj-6.0.0/include   -DHAVE_PROJ_H -I/software/c4/cbi/software/gdal-3.0.0/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c ops.cpp -o ops.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/proj-6.0.0/include   -DHAVE_PROJ_H -I/software/c4/cbi/software/gdal-3.0.0/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c polygonize.cpp -o polygonize.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/proj-6.0.0/include   -DHAVE_PROJ_H -I/software/c4/cbi/software/gdal-3.0.0/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c proj.cpp -o proj.o
proj.cpp: In function ‘Rcpp::NumericMatrix CPL_proj_direct(Rcpp::CharacterVector, Rcpp::NumericMatrix, bool, bool, bool)’:
proj.cpp:279:14: error: ‘proj_normalize_for_visualization’ was not declared in this scope
   PJ *NewP = proj_normalize_for_visualization(PJ_DEFAULT_CTX, P);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make: *** [/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/etc/Makeconf:177: proj.o] Error 1
ERROR: compilation failed for package ‘sf’
* removing ‘/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/sf’
* restoring previous ‘/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/sf’

The downloaded source packages are in
        ‘/scratch/henrik/RtmpSfwGlQ/downloaded_packages’
Warning message:
In install.packages("sf") :
  installation of package ‘sf’ had non-zero exit status

@edzer
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edzer commented Feb 5, 2022

Thanks! The errors you see concerns code that hasn't been touched in a long time; you don't happen to have more than one version of GDAL/PROJ/GEOS installed, do you?

@anirban-mukherjee
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I am getting the same error on a stock debian buster image (Google cloud image). I don't think this machine has multiple versions installed. It should be clean (I did install a few things). I did not get this error when installing on the same image family (the prior version of the image, it has been updated since) about a few days ago. I don't know what has been updated since but there is some chance that something has been automatically updated.

Any ideas on how best to proceed? Below is exactly what I get:

stars.cpp: In function 'void CPL_create(Rcpp::CharacterVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::CharacterVector, Rcpp::NumericVector, Rcpp::NumericVector)':
stars.cpp:771:7: error: 'class OGRSpatialReference' has no member named 'SetAxisMappingStrategy'
  oSRS.SetAxisMappingStrategy(OAMS_TRADITIONAL_GIS_ORDER);
       ^~~~~~~~~~~~~~~~~~~~~~
stars.cpp:771:30: error: 'OAMS_TRADITIONAL_GIS_ORDER' was not declared in this scope
  oSRS.SetAxisMappingStrategy(OAMS_TRADITIONAL_GIS_ORDER);
                              ^~~~~~~~~~~~~~~~~~~~~~~~~~
make: *** [/usr/lib/R/etc/Makeconf:177: stars.o] Error 1
ERROR: compilation failed for package 'sf'
* removing '/usr/local/lib/R/site-library/sf'

$ gdalinfo --version
GDAL 2.4.0, released 2018/12/14
$ geos-config --version
3.7.1
$ proj 2>&1 | head -1
Rel. 5.2.0, September 15th, 2018
$ g++ --version | head -1
g++ (Debian 8.3.0-6) 8.3.0
$ R --version | head -1
R version 4.1.2 (2021-11-01) -- "Bird Hippie"

@anirban-mukherjee
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I can confirm that sf 1.0-5 installs as expected. I did not change any libraries or update anything else on. I used dev tools to install: install_version("sf", version = "1.0-5", repos = "http://cran.us.r-project.org")

@rsbivand
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rsbivand commented Feb 5, 2022

With hand-installed GDAL: 2.2.4, PROJ: 5.2.0, GEOS: 3.7.3 and sf main HEAD:

g++ -std=gnu++11 -I"/home/rsb/topics/R/R412-share/lib64/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -I/usr/local/include -I'/home/rsb/lib/r_libs/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c stars.cpp -o stars.o
stars.cpp: In function ‘void CPL_create(Rcpp::CharacterVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::CharacterVector, Rcpp::NumericVector, Rcpp::NumericVector)’:
stars.cpp:771:14: error: ‘class OGRSpatialReference’ has no member named ‘SetAxisMappingStrategy’
  771 |         oSRS.SetAxisMappingStrategy(OAMS_TRADITIONAL_GIS_ORDER);
      |              ^~~~~~~~~~~~~~~~~~~~~~
stars.cpp:771:37: error: ‘OAMS_TRADITIONAL_GIS_ORDER’ was not declared in this scope
  771 |         oSRS.SetAxisMappingStrategy(OAMS_TRADITIONAL_GIS_ORDER);
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~
make: *** [/home/rsb/topics/R/R412-share/lib64/R/etc/Makeconf:177: stars.o] Error 1
ERROR: compilation failed for package 'sf'
* removing '/tmp/Rtmpz5a2dN/Rinstc2301fbabdd1/sf'
      -----------------------------------
ERROR: package installation failed

Indeed, OAMS_TRADITIONAL_GIS_ORDER does not seem to be in the GDAL source until 3.0, see the MIGRATION GUIDE:

OSRImportFromEPSG() takes into account official axis order.
Traditional GIS-friendly axis order can be restored with
OGRSpatialReference::SetAxisMappingStrategy(OAMS_TRADITIONAL_GIS_ORDER);

sf_1.0-5 installs cleanly on PROJ 5.2.0 with GDAL 2.2.4, but R CMD check doesn't complete cleanly as terra needed by tmap does not install:

g++ -std=gnu++11 -I"/home/rsb/topics/R/R412-share/lib64/R/include" -DNDEBUG -I/usr/local/include  -I/usr/local/include -I/usr/local/include -I'/home/rsb/lib/r_libs/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c write_ogr.cpp -o write_ogr.o
write_ogr.cpp: In member function ‘GDALDataset* SpatVector::write_ogr(std::string, std::string, std::string, bool, bool, std::vector<std::__cxx11::basic_string<char> >)’:
write_ogr.cpp:126:55: error: ‘invalid_argument’ in namespace ‘std’ does not name a type
  126 |                                         } catch (std::invalid_argument &e)  {
      |                                                       ^~~~~~~~~~~~~~~~
make: *** [/home/rsb/topics/R/R412-share/lib64/R/etc/Makeconf:177: write_ogr.o] Error 1
ERROR: compilation failed for package 'terra'

@rsbivand
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rsbivand commented Feb 5, 2022 •
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@edzer, line 754 in stars.cpp: oSRS.SetAxisMappingStrategy(OAMS_TRADITIONAL_GIS_ORDER);
in add gdal_create() for stars: a6faeb9#diff-37479bf864ddebb7cd25ec6420d4e7bf3eafbfe2629dc18c9789fa5aa0668c81

looks unprotected.

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rsbivand commented Feb 5, 2022

A quick fix is to protect that line by:

#if defined(HAVE_PROJ_H) && !defined(ACCEPT_USE_OF_DEPRECATED_PROJ_API_H)
	oSRS.SetAxisMappingStrategy(OAMS_TRADITIONAL_GIS_ORDER);
#endif

but maybe the GDAL version can be queried instead?

@edzer
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edzer commented Feb 5, 2022

Thanks, I used

#if GDAL_VERSION_NUM >= 2050000

similar to https://github.com/r-spatial/sf/blob/main/src/gdal.cpp#L676-L683

This is indeed code that was introduced after sf 1.0-5 was released, in a6faeb9#diff-37479bf864ddebb7cd25ec6420d4e7bf3eafbfe2629dc18c9789fa5aa0668c81 , and not properly tested against older GDAL versions.

edzer added a commit that referenced this issue Feb 5, 2022
@edzer
addresses #1899
df6600c
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edzer commented Feb 5, 2022

This should fix it; would be great if one of you @HenrikBengtsson or @anirban-mukherjee could confirm.

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rsbivand commented Feb 5, 2022

Yes, I can confirm that for my platform the fix removes the problem, but am running hand-installed legacy PROJ+GDAL, so confirmation from the actual cases with binary PROJ+GDAL installs would be very helpful.

@anirban-mukherjee
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Thanks for the super quick fix folks. Confirming that devtools::install_github("r-spatial/sf") compiles and installs as expected on Debian Buster.

@HenrikBengtsson
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Thanks for the quick fix. Confirming it works again on the above CentOS 7.9 and Ubuntu 18.04 setups;

CentOS 7.9:

$ geos-config --version
3.4.2
$ command -v geos-config
/usr/bin/geos-config

$ proj 2>&1 | head -1
Rel. 4.8.0, 6 March 2012
$ command -v proj
/usr/bin/proj

$ gdal-config --version
2.4.4
$ command -v gdal-config
/software/c4/cbi/software/gdal-2.4.4/bin/gdal-config

$ g++ --version | head -1
g++ (GCC) 8.3.1 20190311 (Red Hat 8.3.1-3)
$ command -v gcc
/opt/rh/devtoolset-8/root/usr/bin/gcc

Ubuntu 18.04:

$ geos-config --version
3.6.2
$ command -v geos-config
/usr/bin/geos-config

$ proj 2>&1 | head -1
Rel. 4.9.3, 15 August 2016
$ command -v proj
/usr/bin/proj

$ gdal-config --version
2.2.3
$ command -v gdal-config
/usr/bin/gdal-config

$ g++ --version | head -1
g++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0
$ command -v g++
/usr/bin/g++```

For the records, just so others troubleshooting have something to compare to, here's what it now looks like on the CentOS 7.9 setup:

$ R
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
...
> remotes::install_github("r-spatial/sf")
Downloading GitHub repo r-spatial/sf@HEAD
Running `R CMD build`...
* checking for file ‘/scratch/henrik/Rtmp22lau6/remotes550f39c8ef64/r-spatial-sf-df6600c/DESCRIPTION’ ... OK
* preparing ‘sf’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘sf_1.0-7.tar.gz’
Installing package into ‘/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8’
(as ‘lib’ is unspecified)
* installing *source* package ‘sf’ ...
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++11
checking for gdal-config... /software/c4/cbi/software/gdal-2.4.4/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.4.4
checking GDAL version >= 2.0.1... yes
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -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 for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /software/c4/cbi/software/gdal-2.4.4/share/gdal/pcs.csv readable... yes
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available fur running:... yes
configure: GDAL: 2.4.4
configure: pkg-config proj exists, will use it
checking proj_api.h usability... yes
checking proj_api.h presence... yes
checking for proj_api.h... yes
configure: PROJ: 4.8.0
checking for pj_init_plus in -lproj... yes
checking PROJ: epsg found and readable... yes
checking for geos-config... /usr/bin/geos-config
checking geos-config usability... yes
configure: GEOS: 3.4.2
checking GEOS version >= 3.4.0... yes
checking geos_c.h usability... yes
checking geos_c.h presence... yes
checking for geos_c.h... yes
checking geos: linking with -L/usr/lib64 -lgeos_c... yes
configure: Package CPP flags:    -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include
configure: Package LIBS: -lproj     -L/software/c4/cbi/software/gdal-2.4.4/lib -lgdal -L/usr/lib64 -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c bbox.cpp -o bbox.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal.cpp -o gdal.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_geom.cpp -o gdal_geom.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_read.cpp -o gdal_read.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_utils.cpp -o gdal_utils.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c gdal_write.cpp -o gdal_write.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c geos.cpp -o geos.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c hex.cpp -o hex.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c mdim.cpp -o mdim.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c ops.cpp -o ops.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c polygonize.cpp -o polygonize.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c proj.cpp -o proj.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c proj_info.cpp -o proj_info.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c raster2sf.cpp -o raster2sf.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c sfg.cpp -o sfg.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c signed_area.cpp -o signed_area.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c stars.cpp -o stars.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c wkb.cpp -o wkb.o
g++ -std=gnu++11 -I"/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/include" -DNDEBUG -I/software/c4/cbi/software/gdal-2.4.4/include -I/usr/include -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -c zm_range.cpp -o zm_range.o
g++ -std=gnu++11 -shared -L/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/lib -L/usr/local/lib64 -o sf.so RcppExports.o bbox.o gdal.o gdal_geom.o gdal_read.o gdal_utils.o gdal_write.o geos.o hex.o mdim.o ops.o polygonize.o proj.o proj_info.o raster2sf.o sfg.o signed_area.o stars.o wkb.o zm_range.o -lproj -L/software/c4/cbi/software/gdal-2.4.4/lib -lgdal -L/usr/lib64 -lgeos_c -L/software/c4/cbi/software/R-4.1.2-gcc8/lib64/R/lib -lR
installing to /c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI-gcc8/00LOCK-sf/00new/sf/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
in method for ‘dbWriteTable’ with signature ‘"PostgreSQLConnection","character","sf"’: no definition for class “PostgreSQLConnection”
in method for ‘dbDataType’ with signature ‘"PostgreSQLConnection","sf"’: no definition for class “PostgreSQLConnection”
in method for ‘coerce’ with signature ‘"Spatial","sf"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"Spatial","sfc"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"sf","Spatial"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"sfc","Spatial"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"XY","Spatial"’: no definition for class “Spatial”
in method for ‘coerce’ with signature ‘"crs","CRS"’: no definition for class “CRS”
in method for ‘coerce’ with signature ‘"sgbp","sparseMatrix"’: no definition for class “sparseMatrix”
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sf)

@HenrikBengtsson
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Looks like this one's solved. I let you guys decided when to close this issue.

@HenrikBengtsson HenrikBengtsson changed the title sf 1.0-6 requires GDAL (>= 3.0.0)? sf 1.0-6 requires GDAL (>= 3.0.0)? [SOLVED for sf 1.0-7] Feb 5, 2022
@HenrikBengtsson
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My only suggestion would be to set up a GitHub Action that runs R CMD check with these older versions.

@jhnwllr jhnwllr mentioned this issue Feb 7, 2022
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@rsbivand rsbivand mentioned this issue Feb 7, 2022
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@stragu
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stragu commented Feb 9, 2022

Also confirming that, after getting the 'class OGRSpatialReference' has no member named 'SetAxisMappingStrategy' error when updating to 1.0-6, devtools::install_github("r-spatial/sf") does not error now, on Ubuntu 18.04.6.
Thanks for the quick fix!

@edzer edzer closed this as completed Feb 15, 2022
@edzer edzer mentioned this issue Feb 15, 2022
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@HenrikBengtsson
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What's an ETA for releasing a fixed version to CRAN?

@yutannihilation yutannihilation mentioned this issue Feb 21, 2022
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@edzer
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edzer commented Mar 7, 2022

Now on CRAN.

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@edzer @HenrikBengtsson @stragu @rsbivand @anirban-mukherjee