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

[HenrikBengtsson]

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]

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]

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]

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]

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]

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]

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

looks unprotected.

[rsbivand]

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]

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]

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

[rsbivand]

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]

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

[HenrikBengtsson]

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]

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