The dev version of sf does not install on the rocker/geospatial:dev-osgeo container but the CRAN version does #1553

Robinlovelace · 2020-12-08T14:11:19Z

Reprex:

docker run --rm -ti rocker/geospatial:dev-osgeo R
install.packages("sf") # works
remotes::install_github("r-spatial/sf") # fails

Robinlovelace · 2020-12-08T14:23:16Z

> install.packages("sf")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.r-project.org/src/contrib/sf_0.9-6.tar.gz'
Content type 'application/x-gzip' length 4160758 bytes (4.0 MB)
==================================================
downloaded 4.0 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... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.2.0
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: /usr/local/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: 3.2.0
checking proj.h usability... yes
checking proj.h presence... yes
checking for proj.h... yes
checking PROJ: checking whether PROJ and sqlite3 are available for linking:... yes
checking for geos-config... /usr/local/bin/geos-config
checking geos-config usability... yes
configure: GEOS: 3.8.1
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/local/lib -lgeos_c... yes
configure: Package CPP flags:   -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include
configure: Package LIBS:  -L/usr/local/lib -lgdal -lproj  -L/usr/local/lib -lgdal -L/usr/local/lib -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bbox.cpp -o bbox.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdal.cpp -o gdal.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdal_geom.cpp -o gdal_geom.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdal_read.cpp -o gdal_read.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdal_utils.cpp -o gdal_utils.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdal_write.cpp -o gdal_write.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c geos.cpp -o geos.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c hex.cpp -o hex.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ops.cpp -o ops.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c polygonize.cpp -o polygonize.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c proj.cpp -o proj.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c proj_info.cpp -o proj_info.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c raster2sf.cpp -o raster2sf.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sfg.cpp -o sfg.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c signed_area.cpp -o signed_area.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stars.cpp -o stars.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c wkb.cpp -o wkb.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zm_range.cpp -o zm_range.o
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -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 ops.o polygonize.o proj.o proj_info.o raster2sf.o 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/local/lib -lgeos_c -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/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”
** 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)

The downloaded source packages are in
        ‘/tmp/RtmpvhnEtj/downloaded_packages’
> remotes::install_github("r-spatial/sf")
Downloading GitHub repo r-spatial/sf@HEAD
✔  checking for file ‘/tmp/RtmpvhnEtj/remotes14ee8145d/r-spatial-sf-439b4f5/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_0.9-7.tar.gz’
   
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘sf’ ...
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++11
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.2.0
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: /usr/local/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: 3.2.0
checking proj.h usability... yes
checking proj.h presence... yes
checking for proj.h... yes
checking PROJ: checking whether PROJ and sqlite3 are available for linking:... yes
checking for geos-config... /usr/local/bin/geos-config
checking geos-config usability... yes
configure: GEOS: 3.8.1
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/local/lib -lgeos_c... yes
configure: Package CPP flags:   -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include
configure: Package LIBS:  -L/usr/local/lib -lgdal -lproj  -L/usr/local/lib -lgdal -L/usr/local/lib -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bbox.cpp -o bbox.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdal.cpp -o gdal.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdal_geom.cpp -o gdal_geom.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdal_read.cpp -o gdal_read.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdal_utils.cpp -o gdal_utils.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdal_write.cpp -o gdal_write.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c geos.cpp -o geos.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c hex.cpp -o hex.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ops.cpp -o ops.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c polygonize.cpp -o polygonize.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c proj.cpp -o proj.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c proj_info.cpp -o proj_info.o
proj_info.cpp:144:2: error: #else without #if
  144 | #else
      |  ^~~~
In file included from proj_info.cpp:145:
/usr/local/include/proj_api.h:37:2: error: #error 'To use the proj_api.h you must define the macro ACCEPT_USE_OF_DEPRECATED_PROJ_API_H'
   37 | #error 'To use the proj_api.h you must define the macro ACCEPT_USE_OF_DEPRECATED_PROJ_API_H'
      |  ^~~~~
proj_info.cpp:317:2: error: #endif without #if
  317 | #endif // HAVE_PROJ_H
      |  ^~~~~
proj_info.cpp:153:8: error: redefinition of ‘struct PJ_LIST’
  153 | struct PJ_LIST {
      |        ^~~~~~~
In file included from proj_info.cpp:4:
/usr/local/include/proj.h:223:8: note: previous definition of ‘struct PJ_LIST’
  223 | struct PJ_LIST {
      |        ^~~~~~~
proj_info.cpp:159:8: error: redefinition of ‘struct PJ_ELLPS’
  159 | struct PJ_ELLPS {
      |        ^~~~~~~~
In file included from proj_info.cpp:4:
/usr/local/include/proj.h:231:8: note: previous definition of ‘struct PJ_ELLPS’
  231 | struct PJ_ELLPS {
      |        ^~~~~~~~
proj_info.cpp:173:8: error: redefinition of ‘struct PJ_UNITS’
  173 | struct PJ_UNITS {
      |        ^~~~~~~~
In file included from proj_info.cpp:4:
/usr/local/include/proj.h:239:8: note: previous definition of ‘struct PJ_UNITS’
  239 | struct PJ_UNITS {
      |        ^~~~~~~~
proj_info.cpp:185:12: error: redefinition of ‘Rcpp::List CPL_proj_info(int)’
  185 | Rcpp::List CPL_proj_info(int type) {
      |            ^~~~~~~~~~~~~
proj_info.cpp:7:12: note: ‘Rcpp::List CPL_proj_info(int)’ previously defined here
    7 | Rcpp::List CPL_proj_info(int type) {
      |            ^~~~~~~~~~~~~
make: *** [/usr/local/lib/R/etc/Makeconf:181: proj_info.o] Error 1
ERROR: compilation failed for package ‘sf’
* removing ‘/usr/local/lib/R/site-library/sf’
* restoring previous ‘/usr/local/lib/R/site-library/sf’
Error: Failed to install 'sf' from GitHub:
  (converted from warning) installation of package ‘/tmp/RtmpvhnEtj/file15f44cf40/sf_0.9-7.tar.gz’ had non-zero exit status

edzer · 2020-12-08T14:31:20Z

Thanks!

Robinlovelace · 2020-12-08T14:38:26Z

Confirmed, great work! Logs below for completeness:

remotes::install_github("r-spatial/sf") 
Downloading GitHub repo r-spatial/sf@HEAD
✔  checking for file ‘/tmp/RtmpvhnEtj/remotes1456b6a8a/r-spatial-sf-1ace5ce/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_0.9-7.tar.gz’
   
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘sf’ ...
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++11
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.2.0
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: /usr/local/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: 3.2.0
checking proj.h usability... yes
checking proj.h presence... yes
checking for proj.h... yes
checking PROJ: checking whether PROJ and sqlite3 are available for linking:... yes
checking for geos-config... /usr/local/bin/geos-config
checking geos-config usability... yes
configure: GEOS: 3.8.1
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/local/lib -lgeos_c... yes
configure: Package CPP flags:   -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include
configure: Package LIBS:  -L/usr/local/lib -lgdal -lproj  -L/usr/local/lib -lgdal -L/usr/local/lib -lgeos_c
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bbox.cpp -o bbox.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdal.cpp -o gdal.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdal_geom.cpp -o gdal_geom.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdal_read.cpp -o gdal_read.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdal_utils.cpp -o gdal_utils.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gdal_write.cpp -o gdal_write.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c geos.cpp -o geos.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c hex.cpp -o hex.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ops.cpp -o ops.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c polygonize.cpp -o polygonize.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c proj.cpp -o proj.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c proj_info.cpp -o proj_info.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c raster2sf.cpp -o raster2sf.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sfg.cpp -o sfg.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c signed_area.cpp -o signed_area.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c stars.cpp -o stars.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c wkb.cpp -o wkb.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DHAVE_PROJ_H -I/usr/local/include -I/usr/local/include -I'/usr/local/lib/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zm_range.cpp -o zm_range.o
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -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 ops.o polygonize.o proj.o proj_info.o raster2sf.o 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/local/lib -lgeos_c -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/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”
** 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)
>

edzer closed this as completed in 1ace5ce Dec 8, 2020

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The dev version of sf does not install on the rocker/geospatial:dev-osgeo container but the CRAN version does #1553

The dev version of sf does not install on the rocker/geospatial:dev-osgeo container but the CRAN version does #1553

Robinlovelace commented Dec 8, 2020

Robinlovelace commented Dec 8, 2020

edzer commented Dec 8, 2020

Robinlovelace commented Dec 8, 2020

The dev version of sf does not install on the rocker/geospatial:dev-osgeo container but the CRAN version does #1553

The dev version of sf does not install on the rocker/geospatial:dev-osgeo container but the CRAN version does #1553

Comments

Robinlovelace commented Dec 8, 2020

Robinlovelace commented Dec 8, 2020

edzer commented Dec 8, 2020

Robinlovelace commented Dec 8, 2020