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

[HenrikBengtsson]

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:

https://github.com/r-spatial/sf/blob/061196ef88b9406a2cc429c10f459c47e98b86aa/src/gdal.cpp#L713

is never refined for GDAL_VERSION_NUM < 3040000.

[weathermiya]

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]

@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]

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]

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]

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]

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]

2437 created.

[pat-s]

Work on RHEL8 with GDAL 3.0.4.

[rsbivand]

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?

[rsbivand]

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

[stevenolen]

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]

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)