sf 1.0-17 fails to install with GDAL < 3.4: gdal.cpp:713:16: error: ‘ret’ was not declared in this scope #2436

HenrikBengtsson · 2024-09-11T04:57:01Z

Issue

> install.packages("sf")
Installing package into '/wynton/home/cbi/hb/R/rocky8-x86_64-pc-linux-gnu-library/4.4-CBI-gcc13'
(as 'lib' is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/sf_1.0-17.tar.gz'
Content type 'application/x-gzip' length 3802276 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

* installing *source* package ‘sf’ ...
** package ‘sf’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++17
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.0.4
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /usr/share/gdal/pcs.csv readable... no
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available for running:... yes
configure: GDAL: 3.0.4
configure: pkg-config proj exists, will use it
configure: using proj.h.
configure: PROJ: 6.3.2
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: 3.7.2
checking GEOS version >= 3.4.0... yes
checking for geos_c.h... yes
checking geos: linking with -L/usr/lib64 -lgeos_c... yes
configure: Package CPP flags:   -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include
configure: Package LIBS: -lproj    -L/usr/lib64 -lgdal -L/usr/lib64 -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (GCC) 13.2.1 20231205 (Red Hat 13.2.1-6)’
g++ -std=gnu++17 -I"/wynton/home/cbi/shared/software/CBI/_rocky8/R-4.4.1-gcc13/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/wynton/home/cbi/hb/R/rocky8-x86_64-pc-linux-gnu-library/4.4-CBI-gcc13/Rcpp/include' -I/usr/local/include    -fpic
 -g -O2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/wynton/home/cbi/shared/software/CBI/_rocky8/R-4.4.1-gcc13/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/wynton/home/cbi/hb/R/rocky8-x86_64-pc-linux-gnu-library/4.4-CBI-gcc13/Rcpp/include' -I/usr/local/include    -fpic
 -g -O2   -c bbox.cpp -o bbox.o
g++ -std=gnu++17 -I"/wynton/home/cbi/shared/software/CBI/_rocky8/R-4.4.1-gcc13/lib64/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/wynton/home/cbi/hb/R/rocky8-x86_64-pc-linux-gnu-library/4.4-CBI-gcc13/Rcpp/include' -I/usr/local/include    -fpic
 -g -O2   -c gdal.cpp -o gdal.o
gdal.cpp: In function ‘Rcpp::NumericVector CPL_transform_bounds(Rcpp::NumericVector, Rcpp::List, int)’:
gdal.cpp:713:16: error: ‘ret’ was not declared in this scope
  713 |         return ret;
      |                ^~~
make: *** [/wynton/home/cbi/shared/software/CBI/_rocky8/R-4.4.1-gcc13/lib64/R/etc/Makeconf:204: gdal.o] Error 1
ERROR: compilation failed for package ‘sf’
* removing ‘/wynton/home/cbi/hb/R/rocky8-x86_64-pc-linux-gnu-library/4.4-CBI-gcc13/sf’

This is because ret in:

sf/src/gdal.cpp

Line 713 in 061196e

return ret;

is never refined for GDAL_VERSION_NUM < 3040000.

The text was updated successfully, but these errors were encountered:

weathermiya · 2024-09-11T05:44:55Z

my gdal version is 3.3.0
also has same question.

gdal.cpp: In function ‘Rcpp::NumericVector CPL_transform_bounds(Rcpp::NumericVector, Rcpp::List, int)’:
gdal.cpp:713:16: error: ‘ret’ was not declared in this scope
713 | return ret;
| ^~~
make: *** [/usr/lib64/R/etc/Makeconf:200: gdal.o] Error 1

rsbivand · 2024-09-11T07:06:14Z

@edzer is cycling to Prague: https://mastodon.social/@edzer/113114291930092331. I'll try to put up a PR. IIUC @HenrikBengtsson has GDAL 3.0.4, @weathermiya GDAL 3.3.0, so I need not go further back than 3.0.4; as you point out, the problem is obvious. In rgdal days, we used belt and braces (both checking the external software version in R and compiled code), but here line 696 needs moving to before the conditional compile block.

pat-s · 2024-09-11T07:18:49Z

3.0.4 is the version shipped in RHEL8, which is still widely in use, even though RHEL9 is out for a while already. I also encountered the issue there just now.

NB: There's usually no other OS being more behind than the "old stable" RHEL due to the long RHEL lifecycles, so keeping compatibility for those might solve the issue for all others, also for future occasions.

rsbivand · 2024-09-11T07:31:20Z

Rebuilding 3.3.0 on current Fedora 40 with g++ 14.2.1 fails with:

cpl_xml_validate.cpp: In function ‘void CPLLibXMLWarningErrorCallback(void*, const char*, ...)’:
cpl_xml_validate.cpp:923:48: error: invalid conversion from ‘const xmlError*’ {aka ‘const _xmlError*’} to ‘xmlErrorPtr’ {aka ‘_xmlError*’} [-fpermissive]
  923 |         xmlErrorPtr pErrorPtr = xmlGetLastError();
      |                                 ~~~~~~~~~~~~~~~^~
      |                                                |
      |                                                const xmlError* {aka const _xmlError*}

Which incantation of CXXFLAGS might persuade current g++ to behave as was expected in May 2021?

rsbivand · 2024-09-11T07:54:40Z

This is a source package tarball:
sf_1.0-18.tar.gz, as yet not pushed to my fork. Could someone please check on a system with GDAL < 3.4.0?

weathermiya · 2024-09-11T08:06:05Z

This is a source package tarball: sf_1.0-18.tar.gz, as yet not pushed to my fork. Could someone please check on a system with GDAL < 3.4.0?

gdal3.3.0 install successfully
thanks!

rsbivand · 2024-09-11T08:26:10Z

#2437 created.

pat-s · 2024-09-11T08:38:45Z

Work on RHEL8 with GDAL 3.0.4.

rsbivand · 2024-09-11T09:10:12Z

Over then to @edzer. Should I link to this draft source package on the R-sig-geo mailing list in case others are looking for a fix?

address #2436

rsbivand · 2024-09-11T19:17:13Z

Following the merge, could someone with GDAL < 3.4.0 try remotes::install_github("r-spatial/sf") ?

stevenolen · 2024-09-11T20:01:10Z

worked for me with GDAL 3.0.4 on ubuntu focal 20.04, thank you for the quick fix!

> remotes::install_github(repo = "r-spatial/sf")
Downloading GitHub repo r-spatial/sf@HEAD
Running `R CMD build`...
* checking for file ‘/tmp/RtmpMNsu0s/remotes10c4f632fb6/r-spatial-sf-a07adc6/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_1.0-18.tar.gz’
Installing package into ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.4’
(as ‘lib’ is unspecified)
* installing *source* package ‘sf’ ...
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++17
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.0.4
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /usr/share/gdal/pcs.csv readable... no
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available for running:... yes
configure: GDAL: 3.0.4
configure: pkg-config proj exists, will use it
configure: using proj.h.
configure: PROJ: 6.3.1
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: 3.8.0
checking GEOS version >= 3.4.0... yes
checking for geos_c.h... yes
checking geos: linking with -L/usr/lib/x86_64-linux-gnu -lgeos_c... yes
configure: Package CPP flags:   -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include
configure: Package LIBS: -lproj   -L/usr/lib -lgdal -L/usr/lib/x86_64-linux-gnu -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c bbox.cpp -o bbox.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c gdal.cpp -o gdal.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c gdal_geom.cpp -o gdal_geom.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c gdal_read.cpp -o gdal_read.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c gdal_read_stream.cpp -o gdal_read_stream.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c gdal_utils.cpp -o gdal_utils.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c gdal_write.cpp -o gdal_write.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c geos.cpp -o geos.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c hex.cpp -o hex.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c mdim.cpp -o mdim.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c ops.cpp -o ops.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c polygonize.cpp -o polygonize.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c proj.cpp -o proj.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c proj_info.cpp -o proj_info.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c raster2sf.cpp -o raster2sf.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c sfc-sfg.cpp -o sfc-sfg.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c signed_area.cpp -o signed_area.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c stars.cpp -o stars.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c wkb.cpp -o wkb.o
g++ -std=gnu++17 -I"/opt/R/4.4.1/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/include/gdal -I/usr/include -I'/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c zm_range.cpp -o zm_range.o
g++ -std=gnu++17 -shared -L/opt/R/4.4.1/lib/R/lib -L/usr/local/lib -o sf.so RcppExports.o bbox.o gdal.o gdal_geom.o gdal_read.o gdal_read_stream.o gdal_utils.o gdal_write.o geos.o hex.o mdim.o ops.o polygonize.o proj.o proj_info.o raster2sf.o sfc-sfg.o signed_area.o stars.o wkb.o zm_range.o -lproj -L/usr/lib -lgdal -L/usr/lib/x86_64-linux-gnu -lgeos_c -L/opt/R/4.4.1/lib/R/lib -lR
installing to /cloud/lib/x86_64-pc-linux-gnu-library/4.4/00LOCK-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)

farhadsalimi · 2024-09-12T00:34:22Z

Following the merge, could someone with GDAL < 3.4.0 try remotes::install_github("r-spatial/sf") ?

remotes::install_github("r-spatial/sf")
Downloading GitHub repo r-spatial/sf@HEAD
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/RtmplznSaA/remotesd7422586a3d25/r-spatial-sf-a07adc6/DESCRIPTION’ (341ms)
─ preparing ‘sf’:
✔ checking DESCRIPTION meta-information
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘sf_1.0-18.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'

Installing package into ‘/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)

installing source package ‘sf’ ...
** using staged installation
ERROR: 'configure' exists but is not executable -- see the 'R Installation and Administration Manual'
removing ‘/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/sf’
Warning message:
In i.p(...) :
installation of package ‘/tmp/RtmplznSaA/filed7422760f7c25/sf_1.0-18.tar.gz’ had non-zero exit status

dir.create(paste0("/home/", Sys.getenv("LOGNAME"), "/tmp/"))
Warning message:
In dir.create(paste0("/home/", Sys.getenv("LOGNAME"), "/tmp/")) :
'/home/fa079944/tmp' already exists
Sys.setenv(TMPDIR = paste0("/home/", Sys.getenv("LOGNAME"), "/tmp/"))
remotes::install_github("r-spatial/sf")
Downloading GitHub repo r-spatial/sf@HEAD
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/RtmplznSaA/remotesd742249633317/r-spatial-sf-a07adc6/DESCRIPTION’ ...
─ preparing ‘sf’:
✔ checking DESCRIPTION meta-information ...
─ 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_1.0-18.tar.gz’
Warning: file 'sf/cleanup' did not have execute permissions: corrected
Warning: file 'sf/configure' did not have execute permissions: corrected
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'

Installing package into ‘/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)

installing source package ‘sf’ ...
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++14
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.2.4
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /usr/local/share/gdal/pcs.csv readable... yes
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available for running:... yes
configure: GDAL: 2.2.4
checking for proj.h... no
checking for proj_api.h... yes
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: 3.5.0
checking GEOS version >= 3.4.0... yes
checking for geos_c.h... yes
checking geos: linking with -L/usr/lib64 -lgeos_c... yes
configure: Package CPP flags: -I/usr/local/include -I/usr/include
configure: Package LIBS: -L/usr/local/lib -lgdal -lproj -L/usr/local/lib -lgdal -L/usr/lib64 -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c bbox.cpp -o bbox.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gdal.cpp -o gdal.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gdal_geom.cpp -o gdal_geom.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gdal_read.cpp -o gdal_read.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gdal_read_stream.cpp -o gdal_read_stream.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gdal_utils.cpp -o gdal_utils.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c gdal_write.cpp -o gdal_write.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c geos.cpp -o geos.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c hex.cpp -o hex.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c mdim.cpp -o mdim.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c ops.cpp -o ops.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c polygonize.cpp -o polygonize.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c proj.cpp -o proj.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c proj_info.cpp -o proj_info.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c raster2sf.cpp -o raster2sf.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c sfc-sfg.cpp -o sfc-sfg.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c signed_area.cpp -o signed_area.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c stars.cpp -o stars.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c wkb.cpp -o wkb.o
g++ -std=gnu++14 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/include -I'/home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c zm_range.cpp -o zm_range.o
g++ -std=gnu++14 -shared -L/opt/R/4.2.2/lib/R/lib -L/usr/local/lib -o sf.so RcppExports.o bbox.o gdal.o gdal_geom.o gdal_read.o gdal_read_stream.o gdal_utils.o gdal_write.o geos.o hex.o mdim.o ops.o polygonize.o proj.o proj_info.o raster2sf.o sfc-sfg.o signed_area.o stars.o wkb.o zm_range.o -L/usr/local/lib -lgdal -lproj -L/usr/local/lib -lgdal -L/usr/lib64 -lgeos_c -L/opt/R/4.2.2/lib/R/lib -lR
installing to /home/fa079944/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-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
converting help for package ‘sf’
finding HTML links ... done
Ops html
aggregate.sf html
bind html
coerce-methods html
dbDataType html
dbWriteTable html
db_drivers html
dot-stop_geos html
extension_map html
gdal html
gdal_addo html
gdal_utils html
geos_binary_ops html
geos_binary_pred html
geos_combine html
geos_measures html
geos_query html
geos_unary html
interpolate_aw html
is_driver_available html
is_driver_can html
is_geometry_column html
merge.sf html
nc html
plot html
prefix_map html
proj_tools html
rawToHex html
reexports html
s2 html
sf-defunct html
sf-package html
sf html
sf_extSoftVersion html
sf_project html
sfc html
sgbp html
st html
st_agr html
st_as_binary html
st_as_grob html
st_as_sf html
st_as_sfc html
st_as_text html
st_bbox html
st_break_antimeridian html
st_cast html
st_cast_sfc_default html
st_collection_extract html
st_coordinates html
st_crop html
st_crs html
st_drivers html
st_geometry html
st_geometry_type html
st_graticule html
st_is html
st_is_longlat html
st_jitter html
st_join html
st_layers html
st_line_project_point html
st_line_sample html
st_m_range html
st_make_grid html
st_nearest_feature html
st_nearest_points html
st_normalize html
st_precision html
st_read html
st_relate html
st_sample html
st_shift_longitude html
st_transform html
st_viewport html
st_write html
st_z_range html
st_zm html
stars html
summary.sfc html
tibble html
tidyverse html
transform.sf html
valid html
vctrs html
*** 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 · 2024-09-25T23:01:50Z

Any news on a CRAN submission? HPC users on Rocky 8 are starting to report on this problem (there are ~1500 users on our end).

sacdosse · 2024-09-30T14:36:16Z

Hi,
On RHEL9, with GEOS 3.10.1 (rpm installed), and GDAL 2.4.4 and PROJ 7.2.1 both installed in ~/.local, I get the "gdal.cpp:713:16: error: ‘ret’ was not declared in this scope" error while trying to installed "sf" in command line:

$ export LD_LIBRARY_PATH=~/.local/lib
$ R

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages('sf', repos="http://cran.r-project.org", configure.args=c("--with-proj-lib=/pbs/home/d/dbouvet/.local/lib --with-proj-include=/pbs/home/d/dbouvet/.local/include --with-gdal-config=/pbs/home/d/dbouvet/.local/bin/gdal-config"), lib="/pbs/home/d/dbouvet/products/R/library/sf")
trying URL 'http://cran.r-project.org/src/contrib/sf_1.0-17.tar.gz'
Content type 'application/x-gzip' length 3802276 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

* installing *source* package ‘sf’ ...
** package ‘sf’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++17
configure: gdal-config set to /pbs/home/d/dbouvet/.local/bin/gdal-config
checking gdal-config exists... yes
checking gdal-config executable... yes
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /pbs/home/d/dbouvet/.local/share/gdal/pcs.csv readable... yes
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available for running:... yes
configure: GDAL: 2.4.4
checking for proj.h... yes
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: 3.10.1
checking GEOS version >= 3.4.0... yes
checking for geos_c.h... yes
checking geos: linking with -L/usr/lib64 -lgeos_c... yes
configure: Package CPP flags:  -I/pbs/home/d/dbouvet/.local/include -DHAVE_PROJ_H -I/pbs/home/d/dbouvet/.local/include -I/usr/include
configure: Package LIBS: -L/pbs/home/d/dbouvet/.local/lib  -lproj  -L/pbs/home/d/dbouvet/.local/lib -lgdal -L/usr/lib64 -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (GCC) 11.4.1 20231218 (Red Hat 11.4.1-3)’
g++ -std=gnu++17 -I"/pbs/software/redhat-9-x86_64/R/4.3.3/lib64/R/include" -DNDEBUG -I/pbs/home/d/dbouvet/.local/include -DHAVE_PROJ_H -I/pbs/home/d/dbouvet/.local/include -I/usr/include -I'/pbs/software/redhat-9-x86_64/R/4.3.3/lib64/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/pbs/software/redhat-9-x86_64/R/4.3.3/lib64/R/include" -DNDEBUG -I/pbs/home/d/dbouvet/.local/include -DHAVE_PROJ_H -I/pbs/home/d/dbouvet/.local/include -I/usr/include -I'/pbs/software/redhat-9-x86_64/R/4.3.3/lib64/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c bbox.cpp -o bbox.o
g++ -std=gnu++17 -I"/pbs/software/redhat-9-x86_64/R/4.3.3/lib64/R/include" -DNDEBUG -I/pbs/home/d/dbouvet/.local/include -DHAVE_PROJ_H -I/pbs/home/d/dbouvet/.local/include -I/usr/include -I'/pbs/software/redhat-9-x86_64/R/4.3.3/lib64/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c gdal.cpp -o gdal.o
gdal.cpp: In function ‘Rcpp::NumericVector CPL_transform_bounds(Rcpp::NumericVector, Rcpp::List, int)’:
gdal.cpp:713:16: error: ‘ret’ was not declared in this scope
  713 |         return ret;
      |                ^~~
make: *** [/pbs/software/redhat-9-x86_64/R/4.3.3/lib64/R/etc/Makeconf:200: gdal.o] Error 1
ERROR: compilation failed for package ‘sf’
* removing ‘/pbs/home/d/dbouvet/products/R/library/sf/sf’

The downloaded source packages are in
	‘/scratch/users/d/dbouvet/RtmpXo6BX7/downloaded_packages’
Warning message:
In install.packages("sf", repos = "http://cran.r-project.org", configure.args = c("--with-proj-lib=/pbs/home/d/dbouvet/.local/lib --with-proj-include=/pbs/home/d/dbouvet/.local/include --with-gdal-config=/pbs/home/d/dbouvet/.local/bin/gdal-config"),  :
  installation of package ‘sf’ had non-zero exit status
>

Any clue?

edzer · 2024-09-30T15:17:56Z

Yes, please install from github, e.g. with remotes::install_github("r-spatial/sf").

sacdosse · 2024-10-01T08:40:50Z

Thanks @edzer.
I tried the following:

> remotes::install_github("r-spatial/sf", INSTALL_opts = c("--with-proj-lib=/pbs/home/d/dbouvet/.local/lib --with-proj-include=/pbs/home/d/dbouvet/.local/include --with-gdal-config=/pbs/home/d/dbouvet/.local/bin/gdal-config"), lib="/pbs/home/d/dbouvet/products/R/library/sf")
Downloading GitHub repo r-spatial/sf@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                            
2: CRAN packages only             
3: None                           
4: Rcpp  (1.0.12 -> 1.0.13) [CRAN]
5: wk    (0.9.1  -> 0.9.3 ) [CRAN]
6: e1071 (1.7-14 -> 1.7-16) [CRAN]
7: s2    (1.1.6  -> 1.1.7 ) [CRAN]
8: DBI   (1.2.2  -> 1.2.3 ) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 
Installing 1 packages: units
trying URL 'https://cloud.r-project.org/src/contrib/units_0.8-5.tar.gz'
Content type 'application/x-gzip' length 247974 bytes (242 KB)
==================================================
downloaded 242 KB

Warning: unknown option ‘--with-proj-lib=/pbs/home/d/dbouvet/.local/lib’
Warning: unknown option ‘--with-proj-include=/pbs/home/d/dbouvet/.local/include’
Warning: unknown option ‘--with-gdal-config=/pbs/home/d/dbouvet/.local/bin/gdal-config’
* installing *source* package ‘units’ ...
** package ‘units’ successfully unpacked and MD5 sums checked
** using staged installation
configure: units: 0.8-5
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 the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for _Bool... no
checking for stdbool.h that conforms to C99... yes
checking for error_at_line... yes
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for XML_ParserCreate in -lexpat... yes
checking for udunits2.h... no
checking for udunits2/udunits2.h... yes
checking for ut_read_xml in -ludunits2... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (GCC) 11.4.1 20231218 (Red Hat 11.4.1-3)’
g++ -std=gnu++17 -I"/pbs/software/redhat-9-x86_64/R/4.3.3/lib64/R/include" -DNDEBUG -DUDUNITS2_DIR=1   -I/usr/local/include -I'/pbs/software/redhat-9-x86_64/R/4.3.3/lib64/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/pbs/software/redhat-9-x86_64/R/4.3.3/lib64/R/include" -DNDEBUG -DUDUNITS2_DIR=1   -I/usr/local/include -I'/pbs/software/redhat-9-x86_64/R/4.3.3/lib64/R/library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c udunits.cpp -o udunits.o
g++ -std=gnu++17 -shared -L/pbs/software/redhat-9-x86_64/R/4.3.3/lib64/R/lib -L/usr/local/lib64 -o units.so RcppExports.o udunits.o -lexpat -lexpat -ludunits2 -L/pbs/software/redhat-9-x86_64/R/4.3.3/lib64/R/lib -lR
installing to /pbs/home/d/dbouvet/products/R/library/sf/00LOCK-units/00new/units/libs
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (units)

The downloaded source packages are in
	‘/scratch/users/d/dbouvet/RtmpKGyCeD/downloaded_packages’
── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/scratch/users/d/dbouvet/RtmpKGyCeD/remotes28422a7a6bcef7/r-spatial-sf-39da056/DESCRIPTION’ ...
─  preparing ‘sf’: (1.5s)
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts (980ms)
─  checking for empty or unneeded directories
─  building ‘sf_1.0-18.tar.gz’
   
Warning: unknown option ‘--with-proj-lib=/pbs/home/d/dbouvet/.local/lib’
Warning: unknown option ‘--with-proj-include=/pbs/home/d/dbouvet/.local/include’
Warning: unknown option ‘--with-gdal-config=/pbs/home/d/dbouvet/.local/bin/gdal-config’
* installing *source* package ‘sf’ ...
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++17
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.4.3
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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for gdal.h... yes
checking GDAL: linking with --libs only... yes
checking GDAL: /usr/share/gdal/pcs.csv readable... no
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available for running:... ERROR 1: PROJ: proj_create_from_database: /pbs/home/d/dbouvet/.local/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 0 whereas a number >= 2 is expected. It comes from another PROJ installation.
ERROR 1: PROJ: proj_create_from_database: /pbs/home/d/dbouvet/.local/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 0 whereas a number >= 2 is expected. It comes from another PROJ installation.
ERROR 1: PROJ: proj_create: unrecognized format / unknown name
ERROR 1: PROJ: proj_create: unrecognized format / unknown name
no
configure: error: OGRCoordinateTransformation() does not return a coord.trans: PROJ not available?
ERROR: configuration failed for package ‘sf’
* removing ‘/pbs/home/d/dbouvet/products/R/library/sf/sf’
Warning message:
In i.p(...) :
  installation of package ‘/scratch/users/d/dbouvet/RtmpKGyCeD/file28422a404dace9/sf_1.0-18.tar.gz’ had non-zero exit status

but it failed because PROJ and GDAL were not found as --with-proj-lib, --with-proj-include and --with-gdal-config are unrecognized options.
What is the correct sentence for these options with remotes::install_github?

edzer · 2024-10-01T08:48:24Z

That error might indicate that you have more than one instance (and version) of PROJ installed on your system; see the README.md.

sacdosse · 2024-10-01T09:22:16Z

PROJ 8.2.0 is installed via rpm with RHEL9. But as "sf" needs pcs.csv, I had to installed PROJ 7.2.1 in ~/.local.

When trying to install with install.packages method, I already got this error on PROJ with the error /usr/share/gdal/pcs.csv readable... no. When pcs.csv was found PROJ was correctly linked.
The error on pcs.csv went away with --with-gdal-config option.
How can I pass this --with-gdal-config option to get ride of pcs.csv readable... no error?

edzer · 2024-10-01T09:42:35Z

You're hijacking this issue to get help for another, known issue; feel free to open a new issue, but I'm afraid that the general advice is to install sf on system without multiple installs of the upstream libs PROJ, GEOS or GDAL.

sacdosse · 2024-10-01T15:03:36Z

Finally manage to installed "sf" by initialising PATH before launching R so gdal-config is found (export PATH=~/.local/bin:$PATH)
This solved both error on pcs.csv and PROJ.

albertus82 · 2024-10-09T05:22:58Z

Hi, v1.0-18 isn't yet available on CRAN, is there anything you can do to speedup the process? Thanks a lot!

kadyb · 2024-10-11T10:32:24Z

@albertus82, version 1.0.18 is already on CRAN 🎉

HenrikBengtsson changed the title ~~sf 1.0-17 fail to install with GDAL < 3.4: gdal.cpp:713:16: error: ‘ret’ was not declared in this scope~~ sf 1.0-17 fails to install with GDAL < 3.4: gdal.cpp:713:16: error: ‘ret’ was not declared in this scope Sep 11, 2024

rsbivand added a commit to rsbivand/sf that referenced this issue Sep 11, 2024

address r-spatial#2436

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rsbivand mentioned this issue Sep 11, 2024

address #2436 #2437

Merged

edzer added a commit that referenced this issue Sep 11, 2024

Merge pull request #2437 from rsbivand/issue2436

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address #2436

edzer closed this as completed Oct 1, 2024

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sf 1.0-17 fails to install with GDAL < 3.4: gdal.cpp:713:16: error: ‘ret’ was not declared in this scope #2436

sf 1.0-17 fails to install with GDAL < 3.4: gdal.cpp:713:16: error: ‘ret’ was not declared in this scope #2436

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sf 1.0-17 fails to install with GDAL < 3.4: gdal.cpp:713:16: error: ‘ret’ was not declared in this scope #2436

sf 1.0-17 fails to install with GDAL < 3.4: gdal.cpp:713:16: error: ‘ret’ was not declared in this scope #2436

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