Package can be installed but not loaded

[santoroma]

Hello, and thank you for your packages. I'm tried unsuccessfully to install lwgeom on centos 7 It fails just at final check.

** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘lwgeom’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/lib64/R/library/00LOCK-lwgeom/00new/lwgeom/libs/lwgeom.so': /usr/lib64/R/library/00LOCK-lwgeom/00new/lwgeom/libs/lwgeom.so: undefined symbol: GEOSClipByRect Errore: loading failed Esecuzione interrotta ERROR: loading failed

Here the overall output:

Installing package into ‘/usr/lib64/R/library’ (as ‘lib’ is unspecified)

• installing source package ‘lwgeom’ ... using staged installation configure: CC: gcc -m64 -std=gnu99 configure: CXX: g++ -m64 -std=gnu++11 checking for gcc... gcc -m64 -std=gnu99 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 -m64 -std=gnu99 accepts -g... yes checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -m64 -std=gnu99 -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 proj.h usability... no checking proj.h presence... no checking for proj.h... no checking for pj_init_plus in -lproj... yes checking PROJ: epsg found and readable... yes configure: POSTGIS_PROJ_VERSION: 48 checking for geos-config... /usr/bin/geos-config checking geos-config usability... yes configure: GEOS: 3.4.2 checking GEOS version >= 3.3.0... yes checking geos: linking with -L/usr/lib64 -lgeos_c... yes checking for GEOS_init_r in -lgeos_c... no configure: Package CPP flags: -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H configure: Package LIBS: -lproj -lproj -L/usr/lib64 -lgeos_c configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/postgis_config.h libs g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c geodetic.cpp -o geodetic.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c lwgeom.cpp -o lwgeom.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c proj.cpp -o proj.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c geos.cpp -o geos.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c io.cpp -o io.o g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c sub.cpp -o sub.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/varint.c -o liblwgeom/varint.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwout_twkb.c -o liblwgeom/lwout_twkb.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwpsurface.c -o liblwgeom/lwpsurface.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwtriangle.c -o liblwgeom/lwtriangle.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwmpoly.c -o liblwgeom/lwmpoly.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lookup3.c -o liblwgeom/lookup3.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwin_wkt.c -o liblwgeom/lwin_wkt.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/gserialized1.c -o liblwgeom/gserialized1.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwgeom.c -o liblwgeom/lwgeom.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/gserialized2.c -o liblwgeom/gserialized2.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwstroke.c -o liblwgeom/lwstroke.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwtin.c -o liblwgeom/lwtin.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwin_twkb.c -o liblwgeom/lwin_twkb.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwgeom_geos_cluster.c -o liblwgeom/lwgeom_geos_cluster.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwmsurface.c -o liblwgeom/lwmsurface.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwgeom_wrapx.c -o liblwgeom/lwgeom_wrapx.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwiterator.c -o liblwgeom/lwiterator.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwgeom_geos_node.c -o liblwgeom/lwgeom_geos_node.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwout_geojson.c -o liblwgeom/lwout_geojson.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwgeom_debug.c -o liblwgeom/lwgeom_debug.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwgeom_median.c -o liblwgeom/lwgeom_median.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwmval.c -o liblwgeom/lwmval.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwkmeans.c -o liblwgeom/lwkmeans.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwgeom_geos.c -o liblwgeom/lwgeom_geos.o liblwgeom/lwgeom_geos.c: In function ‘lwgeom_clip_by_rect’: liblwgeom/lwgeom_geos.c:954:2: warning: implicit declaration of function ‘GEOSClipByRect’ [-Wimplicit-function-declaration] if (!(g3 = GEOSClipByRect(g1, x1, y1, x2, y2))) ^ liblwgeom/lwgeom_geos.c:954:11: warning: assignment makes pointer from integer without a cast [enabled by default] if (!(g3 = GEOSClipByRect(g1, x1, y1, x2, y2))) ^ liblwgeom/lwgeom_geos.c: In function ‘lwgeom_voronoi_diagram’: liblwgeom/lwgeom_geos.c:1926:2: warning: implicit declaration of function ‘GEOSVoronoiDiagram’ [-Wimplicit-function-declaration] geos_result = GEOSVoronoiDiagram(geos_geom, geos_env, tolerance, output_edges); ^ liblwgeom/lwgeom_geos.c:1926:14: warning: assignment makes pointer from integer without a cast [enabled by default] geos_result = GEOSVoronoiDiagram(geos_geom, geos_env, tolerance, output_edges); ^ gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwout_kml.c -o liblwgeom/lwout_kml.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwutil.c -o liblwgeom/lwutil.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwprint.c -o liblwgeom/lwprint.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwrandom.c -o liblwgeom/lwrandom.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwmline.c -o liblwgeom/lwmline.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwgeodetic_tree.c -o liblwgeom/lwgeodetic_tree.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwline.c -o liblwgeom/lwline.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/bytebuffer.c -o liblwgeom/bytebuffer.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwgeodetic.c -o liblwgeom/lwgeodetic.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/measures.c -o liblwgeom/measures.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwgeom_api.c -o liblwgeom/lwgeom_api.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwmcurve.c -o liblwgeom/lwmcurve.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwcollection.c -o liblwgeom/lwcollection.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/gbox.c -o liblwgeom/gbox.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwspheroid.c -o liblwgeom/lwspheroid.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwout_svg.c -o liblwgeom/lwout_svg.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwin_encoded_polyline.c -o liblwgeom/lwin_encoded_polyline.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwout_encoded_polyline.c -o liblwgeom/lwout_encoded_polyline.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwgeom_geos_split.c -o liblwgeom/lwgeom_geos_split.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/effectivearea.c -o liblwgeom/effectivearea.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwboundingcircle.c -o liblwgeom/lwboundingcircle.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwcurvepoly.c -o liblwgeom/lwcurvepoly.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwlinearreferencing.c -o liblwgeom/lwlinearreferencing.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwunionfind.c -o liblwgeom/lwunionfind.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwchaikins.c -o liblwgeom/lwchaikins.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwalgorithm.c -o liblwgeom/lwalgorithm.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwhomogenize.c -o liblwgeom/lwhomogenize.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwgeom_geos_clean.c -o liblwgeom/lwgeom_geos_clean.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/measures3d.c -o liblwgeom/measures3d.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwout_x3d.c -o liblwgeom/lwout_x3d.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwgeom_transform.c -o liblwgeom/lwgeom_transform.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwin_wkt_lex.c -o liblwgeom/lwin_wkt_lex.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwmpoint.c -o liblwgeom/lwmpoint.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/stringbuffer.c -o liblwgeom/stringbuffer.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwcompound.c -o liblwgeom/lwcompound.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/gserialized.c -o liblwgeom/gserialized.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwout_wkt.c -o liblwgeom/lwout_wkt.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwin_wkb.c -o liblwgeom/lwin_wkb.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/ptarray.c -o liblwgeom/ptarray.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwout_wkb.c -o liblwgeom/lwout_wkb.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwpoly.c -o liblwgeom/lwpoly.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwpoint.c -o liblwgeom/lwpoint.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwout_gml.c -o liblwgeom/lwout_gml.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwgeom_topo.c -o liblwgeom/lwgeom_topo.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwcircstring.c -o liblwgeom/lwcircstring.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/include -DPOSTGIS_GEOS_VERSION=34 -I./liblwgeom -DHAVE_LIBGEOM_INTERNAL_H -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/sf/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c liblwgeom/lwin_wkt_parse.c -o liblwgeom/lwin_wkt_parse.o g++ -m64 -std=gnu++11 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o lwgeom.so geodetic.o lwgeom.o RcppExports.o proj.o geos.o io.o sub.o liblwgeom/varint.o liblwgeom/lwout_twkb.o liblwgeom/lwpsurface.o liblwgeom/lwtriangle.o liblwgeom/lwmpoly.o liblwgeom/lookup3.o liblwgeom/lwin_wkt.o liblwgeom/gserialized1.o liblwgeom/lwgeom.o liblwgeom/gserialized2.o liblwgeom/lwstroke.o liblwgeom/lwtin.o liblwgeom/lwin_twkb.o liblwgeom/lwgeom_geos_cluster.o liblwgeom/lwmsurface.o liblwgeom/lwgeom_wrapx.o liblwgeom/lwiterator.o liblwgeom/lwgeom_geos_node.o liblwgeom/lwout_geojson.o liblwgeom/lwgeom_debug.o liblwgeom/lwgeom_median.o liblwgeom/lwmval.o liblwgeom/lwkmeans.o liblwgeom/lwgeom_geos.o liblwgeom/lwout_kml.o liblwgeom/lwutil.o liblwgeom/lwprint.o liblwgeom/lwrandom.o liblwgeom/lwmline.o liblwgeom/lwgeodetic_tree.o liblwgeom/lwline.o liblwgeom/bytebuffer.o liblwgeom/lwgeodetic.o liblwgeom/measures.o liblwgeom/lwgeom_api.o liblwgeom/lwmcurve.o liblwgeom/lwcollection.o liblwgeom/gbox.o liblwgeom/lwspheroid.o liblwgeom/lwout_svg.o liblwgeom/lwin_encoded_polyline.o liblwgeom/lwout_encoded_polyline.o liblwgeom/lwgeom_geos_split.o liblwgeom/effectivearea.o liblwgeom/lwboundingcircle.o liblwgeom/lwcurvepoly.o liblwgeom/lwlinearreferencing.o liblwgeom/lwunionfind.o liblwgeom/lwchaikins.o liblwgeom/lwalgorithm.o liblwgeom/lwhomogenize.o liblwgeom/lwgeom_geos_clean.o liblwgeom/measures3d.o liblwgeom/lwout_x3d.o liblwgeom/lwgeom_transform.o liblwgeom/lwin_wkt_lex.o liblwgeom/lwmpoint.o liblwgeom/stringbuffer.o liblwgeom/lwcompound.o liblwgeom/gserialized.o liblwgeom/lwout_wkt.o liblwgeom/lwin_wkb.o liblwgeom/ptarray.o liblwgeom/lwout_wkb.o liblwgeom/lwpoly.o liblwgeom/lwpoint.o liblwgeom/lwout_gml.o liblwgeom/lwgeom_topo.o liblwgeom/lwcircstring.o liblwgeom/lwin_wkt_parse.o -lproj -lproj -L/usr/lib64 -lgeos_c -lproj -L/usr/lib64 -lgeos_c -L/usr/lib64/R/lib -lR installing to /usr/lib64/R/library/00LOCK-lwgeom/00new/lwgeom/libs R inst byte-compile and prepare package for lazy loading help * installing help indices converting help for package ‘lwgeom’ finding HTML links ... fatto bounding_circle html
  geod html
  Rd warning: /tmp/RtmpZrDOIs/R.INSTALL3cf65815a17/lwgeom/man/geod.Rd:45: file link ‘st_distance’ in package ‘sf’ does not exist and so has been treated as a topic lwgeom_extSoftVersion html
  lwgeom_make_valid html
  perimeter html
  st_as_sfc.TWKB html
  st_astext html
  st_force_polygon_cw html
  st_geod_azimuth html
  st_geohash html
  st_is_polygon_cw html
  st_linesubstring html
  st_snap_to_grid html
  st_split html
  Rd warning: /tmp/RtmpZrDOIs/R.INSTALL3cf65815a17/lwgeom/man/st_split.Rd:12: file link ‘st_combine’ in package ‘sf’ does not exist and so has been treated as a topic st_startpoint html
  st_subdivide html
  st_transform_proj html
  building package indices ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘lwgeom’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/lib64/R/library/00LOCK-lwgeom/00new/lwgeom/libs/lwgeom.so': /usr/lib64/R/library/00LOCK-lwgeom/00new/lwgeom/libs/lwgeom.so: undefined symbol: GEOSClipByRect Errore: loading failed Esecuzione interrotta ERROR: loading failed
• removing ‘/usr/lib64/R/library/lwgeom’ Errore: Failed to install 'lwgeom' from GitHub: (contertito da avviso) installation of package ‘/tmp/RtmpPzlEnB/file2197405a122d/lwgeom_0.2-4.tar.gz’ had non-zero exit status

[federicotallis]

I am having the same issue when trying to deploy to Shinyapps.io. Locally, it works just fine.

• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing source package ‘lwgeom’ ... package ‘lwgeom’ successfully unpacked and MD5 sums checked using staged installation configure: CC: gcc configure: CXX: g++ -std=gnu++11 configure: pkg-config proj exists, will use it checking proj_api.h usability... no checking proj_api.h presence... no checking for proj_api.h... no configure: error: proj_api.h not found in standard or given locations. ERROR: configuration failed for package ‘lwgeom’
• removing ‘/opt/R/3.6.3/lib/R/library/lwgeom’ ################################# End Task Log ################################# Error: Unhandled Exception: Child Task 725622758 failed: Error building image: Error building lwgeom (0.2-3). Build exited with non-zero status: 1 Execution halted

[edzer]

liblwgeom in the version of PostGIS 3.0.0, shipped in released lwgeom, requires GEOS version to be >= 3.6.0; I failed to indicate and check this properly.

[federicotallis]

Still getting the same error when trying to deploy.

configure: CC: gcc configure: CXX: g++ -std=gnu++11 configure: pkg-config proj exists, will use it checking proj_api.h usability... no checking proj_api.h presence... no checking for proj_api.h... no configure: error: proj_api.h not found in standard or given locations. ERROR: configuration failed for package ‘lwgeom’

• removing ‘/opt/R/3.6.3/lib/R/library/lwgeom’

[edzer]

Yes, I meant to solve the issue brought up by @santoroma - yours is a different one. Did you look at #57?

[edzer]

... and have you tried installing from github?

[federicotallis]

Yes, I went ahead and installed it, but that didn't solve my issue. Here's my full log:

[2020-05-04T14:08:50.165242960+0000] Execute script: packages/build/units.sh

• set -e
• apt-get update -qq
• apt-get install -y libudunits2-dev Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libudunits2-0 The following NEW packages will be installed: libudunits2-0 libudunits2-dev 0 upgraded, 2 newly installed, 0 to remove and 114 not upgraded. Need to get 430 kB of archives. After this operation, 992 kB of additional disk space will be used. Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libudunits2-0 amd64 2.2.20-1 [69.5 kB] Get:2 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libudunits2-dev amd64 2.2.20-1 [360 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 430 kB in 0s (19.3 MB/s) Selecting previously unselected package libudunits2-0:amd64. (Reading database ... 119718 files and directories currently installed.) Preparing to unpack .../libudunits2-0_2.2.20-1_amd64.deb ... Unpacking libudunits2-0:amd64 (2.2.20-1) ... Selecting previously unselected package libudunits2-dev. Preparing to unpack .../libudunits2-dev_2.2.20-1_amd64.deb ... Unpacking libudunits2-dev (2.2.20-1) ... Processing triggers for libc-bin (2.23-0ubuntu11) ... Setting up libudunits2-0:amd64 (2.2.20-1) ... Setting up libudunits2-dev (2.2.20-1) ... Processing triggers for libc-bin (2.23-0ubuntu11) ... [2020-05-04T14:08:53.069069163+0000] Execute script: packages/build/sf.sh
• set -e
• apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 0x089EBE08314DF160 Executing: /tmp/tmp.rSRCyWRMcd/gpg.1.sh --keyserver keyserver.ubuntu.com --recv-keys 0x089EBE08314DF160 gpg: requesting key 314DF160 from hkp server keyserver.ubuntu.com gpg: key 314DF160: public key "Launchpad ubuntugis-stable" imported gpg: Total number processed: 1 gpg: imported: 1 (RSA: 1) ++ lsb_release -cs
• echo 'deb http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial main'
• apt-get update -qq
• apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev Reading package lists... Building dependency tree... Reading state information... libproj-dev is already the newest version (4.9.2-2). libudunits2-dev is already the newest version (2.2.20-1). The following packages were automatically installed and are no longer required: libgdal1i libgeos-3.5.0 libjasper-dev libjasper1 Use 'apt autoremove' to remove them. The following additional packages will be installed: gdal-data libarmadillo-dev libarpack2-dev libepsilon-dev libfreexl-dev libfyba-dev libfyba0 libgdal20 libgeos-3.5.1 libgeos-c1v5 libgeotiff-dev libgeotiff2 libjbig-dev libjson-c-dev libkml-dev libkmlconvenience1 libkmlregionator1 libkmlxsd1 libminizip-dev libogdi3.2-dev libopenjp2-7-dev libpoppler-dev libpoppler-private-dev libqhull-dev libqhull7 libsuperlu-dev libtiff5 libtiff5-dev libtiffxx5 liburiparser-dev Suggested packages: libitpp-dev libgdal-doc libgeotiff-epsg geotiff-bin gdal-bin libsuperlu-doc The following NEW packages will be installed: gdal-data libarmadillo-dev libarpack2-dev libepsilon-dev libfreexl-dev libfyba-dev libfyba0 libgdal20 libgeos-3.5.1 libgeotiff-dev libgeotiff2 libjbig-dev libjson-c-dev libkml-dev libkmlconvenience1 libkmlregionator1 libkmlxsd1 libminizip-dev libogdi3.2-dev libopenjp2-7-dev libpoppler-dev libpoppler-private-dev libqhull-dev libqhull7 libsuperlu-dev libtiff5-dev libtiffxx5 liburiparser-dev The following packages will be upgraded: libgdal-dev libgeos-c1v5 libgeos-dev libtiff5 4 upgraded, 28 newly installed, 0 to remove and 113 not upgraded. Need to get 17.1 MB of archives. After this operation, 54.0 MB of additional disk space will be used. Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libarpack2-dev amd64 3.3.0-1build2 [94.7 kB] Get:2 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libsuperlu-dev amd64 4.3+dfsg-3 [174 kB] Get:3 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libarmadillo-dev amd64 1:6.500.5+dfsg-1 [297 kB] Get:4 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libfyba0 amd64 4.1.1-2 [111 kB] Get:5 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libfyba-dev amd64 4.1.1-2 [392 kB] Get:6 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libtiff5 amd64 4.0.6-1ubuntu0.7 [149 kB] Get:7 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libgeotiff2 amd64 1.4.1-2 [55.9 kB] Get:8 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libqhull7 amd64 2015.2-1 [152 kB] Get:9 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libepsilon-dev amd64 0.9.2-3ubuntu1 [48.9 kB] Get:10 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/universe amd64 libfreexl-dev amd64 1.0.2-1ubuntu0.1 [30.5 kB] Get:11 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libjbig-dev amd64 2.1-3.1 [24.8 kB] Get:12 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libtiffxx5 amd64 4.0.6-1ubuntu0.7 [5598 B] Get:13 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libtiff5-dev amd64 4.0.6-1ubuntu0.7 [269 kB] Get:14 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libgeotiff-dev amd64 1.4.1-2 [77.3 kB] Get:15 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libjson-c-dev amd64 0.11-4ubuntu2 [30.6 kB] Get:16 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libkmlconvenience1 amd64 1.3.0-1 [44.2 kB] Get:17 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libkmlregionator1 amd64 1.3.0-1 [19.8 kB] Get:18 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libkmlxsd1 amd64 1.3.0-1 [28.0 kB] Get:19 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libminizip-dev amd64 1.1-8 [26.7 kB] Get:20 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 liburiparser-dev amd64 0.8.4-1 [10.0 kB] Get:21 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libkml-dev amd64 1.3.0-1 [936 kB] Get:22 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libogdi3.2-dev amd64 3.2.0~beta2-7.1build1 [23.0 kB] Get:23 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/universe amd64 libopenjp2-7-dev amd64 2.1.2-1.1+deb9u3build0.16.04.1 [25.4 kB] Get:24 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libpoppler-dev amd64 0.41.0-0ubuntu1.14 [762 kB] Get:25 http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial/main amd64 gdal-data all 2.2.2+dfsg-1~xenial1 [567 kB] Get:26 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libpoppler-private-dev amd64 0.41.0-0ubuntu1.14 [165 kB] Get:27 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libqhull-dev amd64 2015.2-1 [240 kB] Get:28 http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial/main amd64 libgeos-dev amd64 3.5.1-3~xenial0 [72.9 kB] Get:29 http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial/main amd64 libgeos-3.5.1 amd64 3.5.1-3~xenial0 [481 kB] Get:30 http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial/main amd64 libgeos-c1v5 amd64 3.5.1-3~xenial0 [58.0 kB] Get:31 http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial/main amd64 libgdal20 amd64 2.2.2+dfsg-1~xenial1 [5208 kB] Get:32 http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial/main amd64 libgdal-dev amd64 2.2.2+dfsg-1~xenial1 [6503 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.1 MB in 3s (4751 kB/s) Selecting previously unselected package gdal-data. (Reading database ... 119745 files and directories currently installed.) Preparing to unpack .../gdal-data_2.2.2+dfsg-1~xenial1_all.deb ... Unpacking gdal-data (2.2.2+dfsg-1~xenial1) ... Selecting previously unselected package libarpack2-dev. Preparing to unpack .../libarpack2-dev_3.3.0-1build2_amd64.deb ... Unpacking libarpack2-dev (3.3.0-1build2) ... Selecting previously unselected package libsuperlu-dev:amd64. Preparing to unpack .../libsuperlu-dev_4.3+dfsg-3_amd64.deb ... Unpacking libsuperlu-dev:amd64 (4.3+dfsg-3) ... Selecting previously unselected package libarmadillo-dev. Preparing to unpack .../libarmadillo-dev_1%3a6.500.5+dfsg-1_amd64.deb ... Unpacking libarmadillo-dev (1:6.500.5+dfsg-1) ... Selecting previously unselected package libfyba0:amd64. Preparing to unpack .../libfyba0_4.1.1-2_amd64.deb ... Unpacking libfyba0:amd64 (4.1.1-2) ... Selecting previously unselected package libfyba-dev:amd64. Preparing to unpack .../libfyba-dev_4.1.1-2_amd64.deb ... Unpacking libfyba-dev:amd64 (4.1.1-2) ... Preparing to unpack .../libgeos-dev_3.5.1-3~xenial0_amd64.deb ... Unpacking libgeos-dev (3.5.1-3~xenial0) over (3.5.0-1ubuntu2) ... Selecting previously unselected package libgeos-3.5.1. Preparing to unpack .../libgeos-3.5.1_3.5.1-3~xenial0_amd64.deb ... Unpacking libgeos-3.5.1 (3.5.1-3~xenial0) ... Preparing to unpack .../libgeos-c1v5_3.5.1-3~xenial0_amd64.deb ... Unpacking libgeos-c1v5 (3.5.1-3~xenial0) over (3.5.0-1ubuntu2) ... Preparing to unpack .../libtiff5_4.0.6-1ubuntu0.7_amd64.deb ... Unpacking libtiff5:amd64 (4.0.6-1ubuntu0.7) over (4.0.6-1ubuntu0.6) ... Selecting previously unselected package libgeotiff2:amd64. Preparing to unpack .../libgeotiff2_1.4.1-2_amd64.deb ... Unpacking libgeotiff2:amd64 (1.4.1-2) ... Selecting previously unselected package libqhull7:amd64. Preparing to unpack .../libqhull7_2015.2-1_amd64.deb ... Unpacking libqhull7:amd64 (2015.2-1) ... Selecting previously unselected package libgdal20. Preparing to unpack .../libgdal20_2.2.2+dfsg-1~xenial1_amd64.deb ... Unpacking libgdal20 (2.2.2+dfsg-1~xenial1) ... Selecting previously unselected package libepsilon-dev:amd64. Preparing to unpack .../libepsilon-dev_0.9.2-3ubuntu1_amd64.deb ... Unpacking libepsilon-dev:amd64 (0.9.2-3ubuntu1) ... Selecting previously unselected package libfreexl-dev:amd64. Preparing to unpack .../libfreexl-dev_1.0.2-1ubuntu0.1_amd64.deb ... Unpacking libfreexl-dev:amd64 (1.0.2-1ubuntu0.1) ... Selecting previously unselected package libjbig-dev:amd64. Preparing to unpack .../libjbig-dev_2.1-3.1_amd64.deb ... Unpacking libjbig-dev:amd64 (2.1-3.1) ... Selecting previously unselected package libtiffxx5:amd64. Preparing to unpack .../libtiffxx5_4.0.6-1ubuntu0.7_amd64.deb ... Unpacking libtiffxx5:amd64 (4.0.6-1ubuntu0.7) ... Selecting previously unselected package libtiff5-dev:amd64. Preparing to unpack .../libtiff5-dev_4.0.6-1ubuntu0.7_amd64.deb ... Unpacking libtiff5-dev:amd64 (4.0.6-1ubuntu0.7) ... Selecting previously unselected package libgeotiff-dev:amd64. Preparing to unpack .../libgeotiff-dev_1.4.1-2_amd64.deb ... Unpacking libgeotiff-dev:amd64 (1.4.1-2) ... Selecting previously unselected package libjson-c-dev:amd64. Preparing to unpack .../libjson-c-dev_0.11-4ubuntu2_amd64.deb ... Unpacking libjson-c-dev:amd64 (0.11-4ubuntu2) ... Selecting previously unselected package libkmlconvenience1:amd64. Preparing to unpack .../libkmlconvenience1_1.3.0-1_amd64.deb ... Unpacking libkmlconvenience1:amd64 (1.3.0-1) ... Selecting previously unselected package libkmlregionator1:amd64. Preparing to unpack .../libkmlregionator1_1.3.0-1_amd64.deb ... Unpacking libkmlregionator1:amd64 (1.3.0-1) ... Selecting previously unselected package libkmlxsd1:amd64. Preparing to unpack .../libkmlxsd1_1.3.0-1_amd64.deb ... Unpacking libkmlxsd1:amd64 (1.3.0-1) ... Selecting previously unselected package libminizip-dev:amd64. Preparing to unpack .../libminizip-dev_1.1-8_amd64.deb ... Unpacking libminizip-dev:amd64 (1.1-8) ... Selecting previously unselected package liburiparser-dev. Preparing to unpack .../liburiparser-dev_0.8.4-1_amd64.deb ... Unpacking liburiparser-dev (0.8.4-1) ... Selecting previously unselected package libkml-dev:amd64. Preparing to unpack .../libkml-dev_1.3.0-1_amd64.deb ... Unpacking libkml-dev:amd64 (1.3.0-1) ... Selecting previously unselected package libogdi3.2-dev. Preparing to unpack .../libogdi3.2-dev_3.2.0~beta2-7.1build1_amd64.deb ... Unpacking libogdi3.2-dev (3.2.0~beta2-7.1build1) ... Selecting previously unselected package libopenjp2-7-dev. Preparing to unpack .../libopenjp2-7-dev_2.1.2-1.1+deb9u3build0.16.04.1_amd64.deb ... Unpacking libopenjp2-7-dev (2.1.2-1.1+deb9u3build0.16.04.1) ... Selecting previously unselected package libpoppler-dev:amd64. Preparing to unpack .../libpoppler-dev_0.41.0-0ubuntu1.14_amd64.deb ... Unpacking libpoppler-dev:amd64 (0.41.0-0ubuntu1.14) ... Selecting previously unselected package libpoppler-private-dev:amd64. Preparing to unpack .../libpoppler-private-dev_0.41.0-0ubuntu1.14_amd64.deb ... Unpacking libpoppler-private-dev:amd64 (0.41.0-0ubuntu1.14) ... Selecting previously unselected package libqhull-dev:amd64. Preparing to unpack .../libqhull-dev_2015.2-1_amd64.deb ... Unpacking libqhull-dev:amd64 (2015.2-1) ... Preparing to unpack .../libgdal-dev_2.2.2+dfsg-1~xenial1_amd64.deb ... Unpacking libgdal-dev (2.2.2+dfsg-1~xenial1) over (1.11.3+dfsg-3build2) ... Processing triggers for man-db (2.7.5-1) ... Processing triggers for libc-bin (2.23-0ubuntu11) ... Setting up gdal-data (2.2.2+dfsg-1~xenial1) ... Setting up libarpack2-dev (3.3.0-1build2) ... Setting up libsuperlu-dev:amd64 (4.3+dfsg-3) ... Setting up libarmadillo-dev (1:6.500.5+dfsg-1) ... Setting up libfyba0:amd64 (4.1.1-2) ... Setting up libfyba-dev:amd64 (4.1.1-2) ... Setting up libgeos-3.5.1 (3.5.1-3~xenial0) ... Setting up libgeos-c1v5 (3.5.1-3~xenial0) ... Setting up libgeos-dev (3.5.1-3~xenial0) ... Setting up libtiff5:amd64 (4.0.6-1ubuntu0.7) ... Setting up libgeotiff2:amd64 (1.4.1-2) ... Setting up libqhull7:amd64 (2015.2-1) ... Setting up libgdal20 (2.2.2+dfsg-1~xenial1) ... Setting up libepsilon-dev:amd64 (0.9.2-3ubuntu1) ... Setting up libfreexl-dev:amd64 (1.0.2-1ubuntu0.1) ... Setting up libjbig-dev:amd64 (2.1-3.1) ... Setting up libtiffxx5:amd64 (4.0.6-1ubuntu0.7) ... Setting up libtiff5-dev:amd64 (4.0.6-1ubuntu0.7) ... Setting up libgeotiff-dev:amd64 (1.4.1-2) ... Setting up libjson-c-dev:amd64 (0.11-4ubuntu2) ... Setting up libkmlconvenience1:amd64 (1.3.0-1) ... Setting up libkmlregionator1:amd64 (1.3.0-1) ... Setting up libkmlxsd1:amd64 (1.3.0-1) ... Setting up libminizip-dev:amd64 (1.1-8) ... Setting up liburiparser-dev (0.8.4-1) ... Setting up libkml-dev:amd64 (1.3.0-1) ... Setting up libogdi3.2-dev (3.2.0~beta2-7.1build1) ... Setting up libopenjp2-7-dev (2.1.2-1.1+deb9u3build0.16.04.1) ... Setting up libpoppler-dev:amd64 (0.41.0-0ubuntu1.14) ... Setting up libpoppler-private-dev:amd64 (0.41.0-0ubuntu1.14) ... Setting up libqhull-dev:amd64 (2015.2-1) ... Setting up libgdal-dev (2.2.2+dfsg-1~xenial1) ... Processing triggers for libc-bin (2.23-0ubuntu11) ... [2020-05-04T14:09:04.967748285+0000] Execute script: packages/build/lwgeom.sh
• set -e
• apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 0x089EBE08314DF160 Executing: /tmp/tmp.vrouLUifqS/gpg.1.sh --keyserver keyserver.ubuntu.com --recv-keys 0x089EBE08314DF160 gpg: requesting key 314DF160 from hkp server keyserver.ubuntu.com gpg: key 314DF160: "Launchpad ubuntugis-stable" not changed gpg: Total number processed: 1 gpg: unchanged: 1 ++ lsb_release -cs
• echo 'deb http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial main'
• apt-get update -qq W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list.d/ubuntugis-ppa.list:1 and /etc/apt/sources.list.d/ubuntugis-ppa.list:2 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/ubuntugis-ppa.list:1 and /etc/apt/sources.list.d/ubuntugis-ppa.list:2 W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list.d/ubuntugis-ppa.list:1 and /etc/apt/sources.list.d/ubuntugis-ppa.list:2 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/ubuntugis-ppa.list:1 and /etc/apt/sources.list.d/ubuntugis-ppa.list:2
• apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev Reading package lists... Building dependency tree... Reading state information... libproj-dev is already the newest version (4.9.2-2). libudunits2-dev is already the newest version (2.2.20-1). libgdal-dev is already the newest version (2.2.2+dfsg-1~xenial1). libgeos-dev is already the newest version (3.5.1-3~xenial0). The following packages were automatically installed and are no longer required: libgdal1i libgeos-3.5.0 libjasper-dev libjasper1 Use 'apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 113 not upgraded. W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list.d/ubuntugis-ppa.list:1 and /etc/apt/sources.list.d/ubuntugis-ppa.list:2 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/ubuntugis-ppa.list:1 and /etc/apt/sources.list.d/ubuntugis-ppa.list:2 [2020-05-04T14:09:10.329118761+0000] Installing R package: rlang (0.4.5)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘rlang’ ...
• DONE (rlang) [2020-05-04T14:09:10.569654432+0000] Installing R package: sourcetools (0.1.7)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘sourcetools’ ...
• DONE (sourcetools) [2020-05-04T14:09:10.793966205+0000] Installing R package: stringi (1.4.6)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘stringi’ ...
• DONE (stringi) [2020-05-04T14:09:11.136502690+0000] Installing R package: fansi (0.4.1)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘fansi’ ...
• DONE (fansi) [2020-05-04T14:09:11.344389371+0000] Installing R package: leaflet.providers (1.9.0)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘leaflet.providers’ ...
• DONE (leaflet.providers) [2020-05-04T14:09:11.533509876+0000] Installing R package: utf8 (1.1.4)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘utf8’ ...
• DONE (utf8) [2020-05-04T14:09:11.746882317+0000] Installing R package: assertthat (0.2.1)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘assertthat’ ...
• DONE (assertthat) [2020-05-04T14:09:11.930133593+0000] Installing R package: praise (1.0.0)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘praise’ ...
• DONE (praise) [2020-05-04T14:09:12.116218229+0000] Installing R package: base64enc (0.1-3)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘base64enc’ ...
• DONE (base64enc) [2020-05-04T14:09:12.302094117+0000] Installing R package: magrittr (1.5)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘magrittr’ ...
• DONE (magrittr) [2020-05-04T14:09:12.504047105+0000] Installing R package: png (0.1-7)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘png’ ...
• DONE (png) [2020-05-04T14:09:12.694179963+0000] Installing R package: plogr (0.2.0)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘plogr’ ...
• DONE (plogr) [2020-05-04T14:09:12.885129808+0000] Installing R package: fastmap (1.0.1)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘fastmap’ ...
• DONE (fastmap) [2020-05-04T14:09:13.093860896+0000] Installing R package: MASS (7.3-51.5)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘MASS’ ...
• DONE (MASS) [2020-05-04T14:09:13.457416644+0000] Installing R package: class (7.3-15)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘class’ ...
• DONE (class) [2020-05-04T14:09:13.727482136+0000] Installing R package: pkgconfig (2.0.3)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘pkgconfig’ ...
• DONE (pkgconfig) [2020-05-04T14:09:13.917341097+0000] Installing R package: lattice (0.20-38)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘lattice’ ...
• DONE (lattice) [2020-05-04T14:09:14.255301133+0000] Installing R package: sp (1.4-1)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘sp’ ...
• DONE (sp) [2020-05-04T14:09:14.530522280+0000] Installing R package: ps (1.3.2)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘ps’ ...
• DONE (ps) [2020-05-04T14:09:14.735720421+0000] Installing R package: farver (2.0.3)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘farver’ ...
• DONE (farver) [2020-05-04T14:09:15.028421251+0000] Installing R package: Matrix (1.2-18)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘Matrix’ ...
• DONE (Matrix) [2020-05-04T14:09:15.665285515+0000] Installing R package: prettyunits (1.1.1)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘prettyunits’ ...
• DONE (prettyunits) [2020-05-04T14:09:15.850742043+0000] Installing R package: mime (0.9)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘mime’ ...
• DONE (mime) [2020-05-04T14:09:16.036379523+0000] Installing R package: gtable (0.3.0)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘gtable’ ...
• DONE (gtable) [2020-05-04T14:09:16.285069869+0000] Installing R package: gridExtra (2.3)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘gridExtra’ ...
• DONE (gridExtra) [2020-05-04T14:09:16.530306792+0000] Installing R package: viridisLite (0.3.0)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘viridisLite’ ...
• DONE (viridisLite) [2020-05-04T14:09:16.721784026+0000] Installing R package: RColorBrewer (1.1-2)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘RColorBrewer’ ...
• DONE (RColorBrewer) [2020-05-04T14:09:16.906678788+0000] Installing R package: ellipsis (0.3.0)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘ellipsis’ ...
• DONE (ellipsis) [2020-05-04T14:09:17.092091595+0000] Installing R package: KernSmooth (2.23-16)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘KernSmooth’ ...
• DONE (KernSmooth) [2020-05-04T14:09:17.351798878+0000] Installing R package: e1071 (1.7-3)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘e1071’ ...
• DONE (e1071) [2020-05-04T14:09:17.581898818+0000] Installing R package: classInt (0.4-3)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘classInt’ ...
• DONE (classInt) [2020-05-04T14:09:17.796468849+0000] Installing R package: backports (1.1.6)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘backports’ ...
• DONE (backports) [2020-05-04T14:09:17.981488361+0000] Installing R package: rprojroot (1.3-2)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘rprojroot’ ...
• DONE (rprojroot) [2020-05-04T14:09:18.174774188+0000] Installing R package: xtable (1.8-4)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘xtable’ ...
• DONE (xtable) [2020-05-04T14:09:18.395898186+0000] Installing R package: Rcpp (1.0.4.6)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘Rcpp’ ...
• DONE (Rcpp) [2020-05-04T14:09:19.202502756+0000] Installing R package: raster (3.1-5)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘raster’ ...
• DONE (raster) [2020-05-04T14:09:19.706921255+0000] Installing R package: units (0.6-6)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘units’ ...
• DONE (units) [2020-05-04T14:09:20.012313996+0000] Installing R package: rstudioapi (0.11)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘rstudioapi’ ...
• DONE (rstudioapi) [2020-05-04T14:09:20.224039002+0000] Installing R package: colorspace (1.4-1)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘colorspace’ ...
• DONE (colorspace) [2020-05-04T14:09:20.593938196+0000] Installing R package: munsell (0.5.0)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘munsell’ ...
• DONE (munsell) [2020-05-04T14:09:20.798560742+0000] Installing R package: withr (2.1.2)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘withr’ ...
• DONE (withr) [2020-05-04T14:09:20.997380970+0000] Installing R package: nlme (3.1-144)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘nlme’ ...
• DONE (nlme) [2020-05-04T14:09:21.398922788+0000] Installing R package: mgcv (1.8-31)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘mgcv’ ...
• DONE (mgcv) [2020-05-04T14:09:21.802081194+0000] Installing R package: labeling (0.3)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘labeling’ ...
• DONE (labeling) [2020-05-04T14:09:21.988916758+0000] Installing R package: DBI (1.1.0)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘DBI’ ...
• DONE (DBI) [2020-05-04T14:09:22.211167595+0000] Installing R package: sf (0.9-2)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘sf’ ...
• DONE (sf) [2020-05-04T14:09:23.144190327+0000] Building R package: lwgeom (0.2-3) /mnt/packages/build /mnt
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing source package ‘lwgeom’ ... package ‘lwgeom’ successfully unpacked and MD5 sums checked using staged installation configure: CC: gcc configure: CXX: g++ -std=gnu++11 configure: pkg-config proj exists, will use it checking proj_api.h usability... no checking proj_api.h presence... no checking for proj_api.h... no configure: error: proj_api.h not found in standard or given locations. ERROR: configuration failed for package ‘lwgeom’
• removing ‘/opt/R/3.6.3/lib/R/library/lwgeom’ ################################# End Task Log ################################# Error: Unhandled Exception: Child Task 725835879 failed: Error building image: Error building lwgeom (0.2-3). Build exited with non-zero status: 1 Execution halted

[federicotallis]

... and have you tried installing from github?

Yes, I have. I receive the same error.

[edzer]

I have no clue what you are trying to do, what for instance

[2020-05-04T14:08:50.165242960+0000] Execute script: packages/build/units.sh

means. Have you tried starting R, then

install.packages('remotes")
remotes::install_github("r-spatial/lwgeom")

? Please provide the complete output of that.

[federicotallis]

Same error:

• set -e
• apt-get update -qq
• apt-get install -y libudunits2-dev Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libudunits2-0 The following NEW packages will be installed: libudunits2-0 libudunits2-dev 0 upgraded, 2 newly installed, 0 to remove and 114 not upgraded. Need to get 430 kB of archives. After this operation, 992 kB of additional disk space will be used. Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libudunits2-0 amd64 2.2.20-1 [69.5 kB] Get:2 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libudunits2-dev amd64 2.2.20-1 [360 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 430 kB in 0s (23.1 MB/s) Selecting previously unselected package libudunits2-0:amd64. (Reading database ... 119718 files and directories currently installed.) Preparing to unpack .../libudunits2-0_2.2.20-1_amd64.deb ... Unpacking libudunits2-0:amd64 (2.2.20-1) ... Selecting previously unselected package libudunits2-dev. Preparing to unpack .../libudunits2-dev_2.2.20-1_amd64.deb ... Unpacking libudunits2-dev (2.2.20-1) ... Processing triggers for libc-bin (2.23-0ubuntu11) ... Setting up libudunits2-0:amd64 (2.2.20-1) ... Setting up libudunits2-dev (2.2.20-1) ... Processing triggers for libc-bin (2.23-0ubuntu11) ... [2020-05-04T14:26:03.286183547+0000] Execute script: packages/build/sf.sh
• set -e
• apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 0x089EBE08314DF160 Executing: /tmp/tmp.gU1aZ753mu/gpg.1.sh --keyserver keyserver.ubuntu.com --recv-keys 0x089EBE08314DF160 gpg: requesting key 314DF160 from hkp server keyserver.ubuntu.com gpg: key 314DF160: public key "Launchpad ubuntugis-stable" imported gpg: Total number processed: 1 gpg: imported: 1 (RSA: 1) ++ lsb_release -cs
• echo 'deb http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial main'
• apt-get update -qq
• apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev Reading package lists... Building dependency tree... Reading state information... libproj-dev is already the newest version (4.9.2-2). libudunits2-dev is already the newest version (2.2.20-1). The following packages were automatically installed and are no longer required: libgdal1i libgeos-3.5.0 libjasper-dev libjasper1 Use 'apt autoremove' to remove them. The following additional packages will be installed: gdal-data libarmadillo-dev libarpack2-dev libepsilon-dev libfreexl-dev libfyba-dev libfyba0 libgdal20 libgeos-3.5.1 libgeos-c1v5 libgeotiff-dev libgeotiff2 libjbig-dev libjson-c-dev libkml-dev libkmlconvenience1 libkmlregionator1 libkmlxsd1 libminizip-dev libogdi3.2-dev libopenjp2-7-dev libpoppler-dev libpoppler-private-dev libqhull-dev libqhull7 libsuperlu-dev libtiff5 libtiff5-dev libtiffxx5 liburiparser-dev Suggested packages: libitpp-dev libgdal-doc libgeotiff-epsg geotiff-bin gdal-bin libsuperlu-doc The following NEW packages will be installed: gdal-data libarmadillo-dev libarpack2-dev libepsilon-dev libfreexl-dev libfyba-dev libfyba0 libgdal20 libgeos-3.5.1 libgeotiff-dev libgeotiff2 libjbig-dev libjson-c-dev libkml-dev libkmlconvenience1 libkmlregionator1 libkmlxsd1 libminizip-dev libogdi3.2-dev libopenjp2-7-dev libpoppler-dev libpoppler-private-dev libqhull-dev libqhull7 libsuperlu-dev libtiff5-dev libtiffxx5 liburiparser-dev The following packages will be upgraded: libgdal-dev libgeos-c1v5 libgeos-dev libtiff5 4 upgraded, 28 newly installed, 0 to remove and 113 not upgraded. Need to get 17.1 MB of archives. After this operation, 54.0 MB of additional disk space will be used. Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libarpack2-dev amd64 3.3.0-1build2 [94.7 kB] Get:2 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libsuperlu-dev amd64 4.3+dfsg-3 [174 kB] Get:3 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libarmadillo-dev amd64 1:6.500.5+dfsg-1 [297 kB] Get:4 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libfyba0 amd64 4.1.1-2 [111 kB] Get:5 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libfyba-dev amd64 4.1.1-2 [392 kB] Get:6 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libtiff5 amd64 4.0.6-1ubuntu0.7 [149 kB] Get:7 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libgeotiff2 amd64 1.4.1-2 [55.9 kB] Get:8 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libqhull7 amd64 2015.2-1 [152 kB] Get:9 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libepsilon-dev amd64 0.9.2-3ubuntu1 [48.9 kB] Get:10 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/universe amd64 libfreexl-dev amd64 1.0.2-1ubuntu0.1 [30.5 kB] Get:11 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libjbig-dev amd64 2.1-3.1 [24.8 kB] Get:12 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libtiffxx5 amd64 4.0.6-1ubuntu0.7 [5598 B] Get:13 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libtiff5-dev amd64 4.0.6-1ubuntu0.7 [269 kB] Get:14 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libgeotiff-dev amd64 1.4.1-2 [77.3 kB] Get:15 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/main amd64 libjson-c-dev amd64 0.11-4ubuntu2 [30.6 kB] Get:16 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libkmlconvenience1 amd64 1.3.0-1 [44.2 kB] Get:17 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libkmlregionator1 amd64 1.3.0-1 [19.8 kB] Get:18 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libkmlxsd1 amd64 1.3.0-1 [28.0 kB] Get:19 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libminizip-dev amd64 1.1-8 [26.7 kB] Get:20 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 liburiparser-dev amd64 0.8.4-1 [10.0 kB] Get:21 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libkml-dev amd64 1.3.0-1 [936 kB] Get:22 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libogdi3.2-dev amd64 3.2.0~beta2-7.1build1 [23.0 kB] Get:23 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/universe amd64 libopenjp2-7-dev amd64 2.1.2-1.1+deb9u3build0.16.04.1 [25.4 kB] Get:24 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libpoppler-dev amd64 0.41.0-0ubuntu1.14 [762 kB] Get:25 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libpoppler-private-dev amd64 0.41.0-0ubuntu1.14 [165 kB] Get:26 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial/universe amd64 libqhull-dev amd64 2015.2-1 [240 kB] Get:27 http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial/main amd64 gdal-data all 2.2.2+dfsg-1~xenial1 [567 kB] Get:28 http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial/main amd64 libgeos-dev amd64 3.5.1-3~xenial0 [72.9 kB] Get:29 http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial/main amd64 libgeos-3.5.1 amd64 3.5.1-3~xenial0 [481 kB] Get:30 http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial/main amd64 libgeos-c1v5 amd64 3.5.1-3~xenial0 [58.0 kB] Get:31 http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial/main amd64 libgdal20 amd64 2.2.2+dfsg-1~xenial1 [5208 kB] Get:32 http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial/main amd64 libgdal-dev amd64 2.2.2+dfsg-1~xenial1 [6503 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.1 MB in 3s (4475 kB/s) Selecting previously unselected package gdal-data. (Reading database ... 119745 files and directories currently installed.) Preparing to unpack .../gdal-data_2.2.2+dfsg-1~xenial1_all.deb ... Unpacking gdal-data (2.2.2+dfsg-1~xenial1) ... Selecting previously unselected package libarpack2-dev. Preparing to unpack .../libarpack2-dev_3.3.0-1build2_amd64.deb ... Unpacking libarpack2-dev (3.3.0-1build2) ... Selecting previously unselected package libsuperlu-dev:amd64. Preparing to unpack .../libsuperlu-dev_4.3+dfsg-3_amd64.deb ... Unpacking libsuperlu-dev:amd64 (4.3+dfsg-3) ... Selecting previously unselected package libarmadillo-dev. Preparing to unpack .../libarmadillo-dev_1%3a6.500.5+dfsg-1_amd64.deb ... Unpacking libarmadillo-dev (1:6.500.5+dfsg-1) ... Selecting previously unselected package libfyba0:amd64. Preparing to unpack .../libfyba0_4.1.1-2_amd64.deb ... Unpacking libfyba0:amd64 (4.1.1-2) ... Selecting previously unselected package libfyba-dev:amd64. Preparing to unpack .../libfyba-dev_4.1.1-2_amd64.deb ... Unpacking libfyba-dev:amd64 (4.1.1-2) ... Preparing to unpack .../libgeos-dev_3.5.1-3~xenial0_amd64.deb ... Unpacking libgeos-dev (3.5.1-3~xenial0) over (3.5.0-1ubuntu2) ... Selecting previously unselected package libgeos-3.5.1. Preparing to unpack .../libgeos-3.5.1_3.5.1-3~xenial0_amd64.deb ... Unpacking libgeos-3.5.1 (3.5.1-3~xenial0) ... Preparing to unpack .../libgeos-c1v5_3.5.1-3~xenial0_amd64.deb ... Unpacking libgeos-c1v5 (3.5.1-3~xenial0) over (3.5.0-1ubuntu2) ... Preparing to unpack .../libtiff5_4.0.6-1ubuntu0.7_amd64.deb ... Unpacking libtiff5:amd64 (4.0.6-1ubuntu0.7) over (4.0.6-1ubuntu0.6) ... Selecting previously unselected package libgeotiff2:amd64. Preparing to unpack .../libgeotiff2_1.4.1-2_amd64.deb ... Unpacking libgeotiff2:amd64 (1.4.1-2) ... Selecting previously unselected package libqhull7:amd64. Preparing to unpack .../libqhull7_2015.2-1_amd64.deb ... Unpacking libqhull7:amd64 (2015.2-1) ... Selecting previously unselected package libgdal20. Preparing to unpack .../libgdal20_2.2.2+dfsg-1~xenial1_amd64.deb ... Unpacking libgdal20 (2.2.2+dfsg-1~xenial1) ... Selecting previously unselected package libepsilon-dev:amd64. Preparing to unpack .../libepsilon-dev_0.9.2-3ubuntu1_amd64.deb ... Unpacking libepsilon-dev:amd64 (0.9.2-3ubuntu1) ... Selecting previously unselected package libfreexl-dev:amd64. Preparing to unpack .../libfreexl-dev_1.0.2-1ubuntu0.1_amd64.deb ... Unpacking libfreexl-dev:amd64 (1.0.2-1ubuntu0.1) ... Selecting previously unselected package libjbig-dev:amd64. Preparing to unpack .../libjbig-dev_2.1-3.1_amd64.deb ... Unpacking libjbig-dev:amd64 (2.1-3.1) ... Selecting previously unselected package libtiffxx5:amd64. Preparing to unpack .../libtiffxx5_4.0.6-1ubuntu0.7_amd64.deb ... Unpacking libtiffxx5:amd64 (4.0.6-1ubuntu0.7) ... Selecting previously unselected package libtiff5-dev:amd64. Preparing to unpack .../libtiff5-dev_4.0.6-1ubuntu0.7_amd64.deb ... Unpacking libtiff5-dev:amd64 (4.0.6-1ubuntu0.7) ... Selecting previously unselected package libgeotiff-dev:amd64. Preparing to unpack .../libgeotiff-dev_1.4.1-2_amd64.deb ... Unpacking libgeotiff-dev:amd64 (1.4.1-2) ... Selecting previously unselected package libjson-c-dev:amd64. Preparing to unpack .../libjson-c-dev_0.11-4ubuntu2_amd64.deb ... Unpacking libjson-c-dev:amd64 (0.11-4ubuntu2) ... Selecting previously unselected package libkmlconvenience1:amd64. Preparing to unpack .../libkmlconvenience1_1.3.0-1_amd64.deb ... Unpacking libkmlconvenience1:amd64 (1.3.0-1) ... Selecting previously unselected package libkmlregionator1:amd64. Preparing to unpack .../libkmlregionator1_1.3.0-1_amd64.deb ... Unpacking libkmlregionator1:amd64 (1.3.0-1) ... Selecting previously unselected package libkmlxsd1:amd64. Preparing to unpack .../libkmlxsd1_1.3.0-1_amd64.deb ... Unpacking libkmlxsd1:amd64 (1.3.0-1) ... Selecting previously unselected package libminizip-dev:amd64. Preparing to unpack .../libminizip-dev_1.1-8_amd64.deb ... Unpacking libminizip-dev:amd64 (1.1-8) ... Selecting previously unselected package liburiparser-dev. Preparing to unpack .../liburiparser-dev_0.8.4-1_amd64.deb ... Unpacking liburiparser-dev (0.8.4-1) ... Selecting previously unselected package libkml-dev:amd64. Preparing to unpack .../libkml-dev_1.3.0-1_amd64.deb ... Unpacking libkml-dev:amd64 (1.3.0-1) ... Selecting previously unselected package libogdi3.2-dev. Preparing to unpack .../libogdi3.2-dev_3.2.0~beta2-7.1build1_amd64.deb ... Unpacking libogdi3.2-dev (3.2.0~beta2-7.1build1) ... Selecting previously unselected package libopenjp2-7-dev. Preparing to unpack .../libopenjp2-7-dev_2.1.2-1.1+deb9u3build0.16.04.1_amd64.deb ... Unpacking libopenjp2-7-dev (2.1.2-1.1+deb9u3build0.16.04.1) ... Selecting previously unselected package libpoppler-dev:amd64. Preparing to unpack .../libpoppler-dev_0.41.0-0ubuntu1.14_amd64.deb ... Unpacking libpoppler-dev:amd64 (0.41.0-0ubuntu1.14) ... Selecting previously unselected package libpoppler-private-dev:amd64. Preparing to unpack .../libpoppler-private-dev_0.41.0-0ubuntu1.14_amd64.deb ... Unpacking libpoppler-private-dev:amd64 (0.41.0-0ubuntu1.14) ... Selecting previously unselected package libqhull-dev:amd64. Preparing to unpack .../libqhull-dev_2015.2-1_amd64.deb ... Unpacking libqhull-dev:amd64 (2015.2-1) ... Preparing to unpack .../libgdal-dev_2.2.2+dfsg-1~xenial1_amd64.deb ... Unpacking libgdal-dev (2.2.2+dfsg-1~xenial1) over (1.11.3+dfsg-3build2) ... Processing triggers for man-db (2.7.5-1) ... Processing triggers for libc-bin (2.23-0ubuntu11) ... Setting up gdal-data (2.2.2+dfsg-1~xenial1) ... Setting up libarpack2-dev (3.3.0-1build2) ... Setting up libsuperlu-dev:amd64 (4.3+dfsg-3) ... Setting up libarmadillo-dev (1:6.500.5+dfsg-1) ... Setting up libfyba0:amd64 (4.1.1-2) ... Setting up libfyba-dev:amd64 (4.1.1-2) ... Setting up libgeos-3.5.1 (3.5.1-3~xenial0) ... Setting up libgeos-c1v5 (3.5.1-3~xenial0) ... Setting up libgeos-dev (3.5.1-3~xenial0) ... Setting up libtiff5:amd64 (4.0.6-1ubuntu0.7) ... Setting up libgeotiff2:amd64 (1.4.1-2) ... Setting up libqhull7:amd64 (2015.2-1) ... Setting up libgdal20 (2.2.2+dfsg-1~xenial1) ... Setting up libepsilon-dev:amd64 (0.9.2-3ubuntu1) ... Setting up libfreexl-dev:amd64 (1.0.2-1ubuntu0.1) ... Setting up libjbig-dev:amd64 (2.1-3.1) ... Setting up libtiffxx5:amd64 (4.0.6-1ubuntu0.7) ... Setting up libtiff5-dev:amd64 (4.0.6-1ubuntu0.7) ... Setting up libgeotiff-dev:amd64 (1.4.1-2) ... Setting up libjson-c-dev:amd64 (0.11-4ubuntu2) ... Setting up libkmlconvenience1:amd64 (1.3.0-1) ... Setting up libkmlregionator1:amd64 (1.3.0-1) ... Setting up libkmlxsd1:amd64 (1.3.0-1) ... Setting up libminizip-dev:amd64 (1.1-8) ... Setting up liburiparser-dev (0.8.4-1) ... Setting up libkml-dev:amd64 (1.3.0-1) ... Setting up libogdi3.2-dev (3.2.0~beta2-7.1build1) ... Setting up libopenjp2-7-dev (2.1.2-1.1+deb9u3build0.16.04.1) ... Setting up libpoppler-dev:amd64 (0.41.0-0ubuntu1.14) ... Setting up libpoppler-private-dev:amd64 (0.41.0-0ubuntu1.14) ... Setting up libqhull-dev:amd64 (2015.2-1) ... Setting up libgdal-dev (2.2.2+dfsg-1~xenial1) ... Processing triggers for libc-bin (2.23-0ubuntu11) ... [2020-05-04T14:26:14.534494130+0000] Execute script: packages/build/lwgeom.sh
• set -e
• apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 0x089EBE08314DF160 Executing: /tmp/tmp.yrsbhQbvZD/gpg.1.sh --keyserver keyserver.ubuntu.com --recv-keys 0x089EBE08314DF160 gpg: requesting key 314DF160 from hkp server keyserver.ubuntu.com gpg: key 314DF160: "Launchpad ubuntugis-stable" not changed gpg: Total number processed: 1 gpg: unchanged: 1 ++ lsb_release -cs
• echo 'deb http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial main'
• apt-get update -qq W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list.d/ubuntugis-ppa.list:1 and /etc/apt/sources.list.d/ubuntugis-ppa.list:2 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/ubuntugis-ppa.list:1 and /etc/apt/sources.list.d/ubuntugis-ppa.list:2 W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list.d/ubuntugis-ppa.list:1 and /etc/apt/sources.list.d/ubuntugis-ppa.list:2 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/ubuntugis-ppa.list:1 and /etc/apt/sources.list.d/ubuntugis-ppa.list:2
• apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev Reading package lists... Building dependency tree... Reading state information... libproj-dev is already the newest version (4.9.2-2). libudunits2-dev is already the newest version (2.2.20-1). libgdal-dev is already the newest version (2.2.2+dfsg-1~xenial1). libgeos-dev is already the newest version (3.5.1-3~xenial0). The following packages were automatically installed and are no longer required: libgdal1i libgeos-3.5.0 libjasper-dev libjasper1 Use 'apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 113 not upgraded. W: Target Packages (main/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list.d/ubuntugis-ppa.list:1 and /etc/apt/sources.list.d/ubuntugis-ppa.list:2 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list.d/ubuntugis-ppa.list:1 and /etc/apt/sources.list.d/ubuntugis-ppa.list:2 [2020-05-04T14:26:19.195298378+0000] Installing R package: rlang (0.4.5)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘rlang’ ...
• DONE (rlang) [2020-05-04T14:26:19.414436182+0000] Installing R package: sourcetools (0.1.7)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘sourcetools’ ...
• DONE (sourcetools) [2020-05-04T14:26:19.618501267+0000] Installing R package: stringi (1.4.6)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘stringi’ ...
• DONE (stringi) [2020-05-04T14:26:19.934343620+0000] Installing R package: fansi (0.4.1)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘fansi’ ...
• DONE (fansi) [2020-05-04T14:26:20.119494460+0000] Installing R package: leaflet.providers (1.9.0)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘leaflet.providers’ ...
• DONE (leaflet.providers) [2020-05-04T14:26:20.290548804+0000] Installing R package: utf8 (1.1.4)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘utf8’ ...
• DONE (utf8) [2020-05-04T14:26:20.479261232+0000] Installing R package: assertthat (0.2.1)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘assertthat’ ...
• DONE (assertthat) [2020-05-04T14:26:20.645760005+0000] Installing R package: praise (1.0.0)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘praise’ ...
• DONE (praise) [2020-05-04T14:26:20.812031423+0000] Installing R package: base64enc (0.1-3)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘base64enc’ ...
• DONE (base64enc) [2020-05-04T14:26:20.980328741+0000] Installing R package: magrittr (1.5)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘magrittr’ ...
• DONE (magrittr) [2020-05-04T14:26:21.159036711+0000] Installing R package: png (0.1-7)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘png’ ...
• DONE (png) [2020-05-04T14:26:21.330036659+0000] Installing R package: plogr (0.2.0)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘plogr’ ...
• DONE (plogr) [2020-05-04T14:26:21.502779454+0000] Installing R package: fastmap (1.0.1)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘fastmap’ ...
• DONE (fastmap) [2020-05-04T14:26:21.692236528+0000] Installing R package: MASS (7.3-51.5)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘MASS’ ...
• DONE (MASS) [2020-05-04T14:26:22.020293707+0000] Installing R package: class (7.3-15)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘class’ ...
• DONE (class) [2020-05-04T14:26:22.266028824+0000] Installing R package: pkgconfig (2.0.3)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘pkgconfig’ ...
• DONE (pkgconfig) [2020-05-04T14:26:22.434692249+0000] Installing R package: lattice (0.20-38)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘lattice’ ...
• DONE (lattice) [2020-05-04T14:26:22.735675541+0000] Installing R package: sp (1.4-1)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘sp’ ...
• DONE (sp) [2020-05-04T14:26:22.983742951+0000] Installing R package: ps (1.3.2)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘ps’ ...
• DONE (ps) [2020-05-04T14:26:23.174818123+0000] Installing R package: farver (2.0.3)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘farver’ ...
• DONE (farver) [2020-05-04T14:26:23.444462133+0000] Installing R package: Matrix (1.2-18)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘Matrix’ ...
• DONE (Matrix) [2020-05-04T14:26:24.039776244+0000] Installing R package: prettyunits (1.1.1)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘prettyunits’ ...
• DONE (prettyunits) [2020-05-04T14:26:24.207048677+0000] Installing R package: mime (0.9)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘mime’ ...
• DONE (mime) [2020-05-04T14:26:24.374312629+0000] Installing R package: gtable (0.3.0)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘gtable’ ...
• DONE (gtable) [2020-05-04T14:26:24.598167068+0000] Installing R package: gridExtra (2.3)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘gridExtra’ ...
• DONE (gridExtra) [2020-05-04T14:26:24.820311203+0000] Installing R package: viridisLite (0.3.0)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘viridisLite’ ...
• DONE (viridisLite) [2020-05-04T14:26:24.992106917+0000] Installing R package: RColorBrewer (1.1-2)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘RColorBrewer’ ...
• DONE (RColorBrewer) [2020-05-04T14:26:25.160106596+0000] Installing R package: ellipsis (0.3.0)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘ellipsis’ ...
• DONE (ellipsis) [2020-05-04T14:26:25.330377977+0000] Installing R package: KernSmooth (2.23-16)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘KernSmooth’ ...
• DONE (KernSmooth) [2020-05-04T14:26:25.575859907+0000] Installing R package: e1071 (1.7-3)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘e1071’ ...
• DONE (e1071) [2020-05-04T14:26:25.778003402+0000] Installing R package: classInt (0.4-3)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘classInt’ ...
• DONE (classInt) [2020-05-04T14:26:25.972503756+0000] Installing R package: backports (1.1.6)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘backports’ ...
• DONE (backports) [2020-05-04T14:26:26.143778821+0000] Installing R package: rprojroot (1.3-2)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘rprojroot’ ...
• DONE (rprojroot) [2020-05-04T14:26:26.319191986+0000] Installing R package: xtable (1.8-4)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘xtable’ ...
• DONE (xtable) [2020-05-04T14:26:26.522916968+0000] Installing R package: Rcpp (1.0.4.6)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘Rcpp’ ...
• DONE (Rcpp) [2020-05-04T14:26:27.259875471+0000] Installing R package: raster (3.1-5)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘raster’ ...
• DONE (raster) [2020-05-04T14:26:27.718084038+0000] Installing R package: units (0.6-6)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘units’ ...
• DONE (units) [2020-05-04T14:26:27.992834087+0000] Installing R package: rstudioapi (0.11)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘rstudioapi’ ...
• DONE (rstudioapi) [2020-05-04T14:26:28.187319095+0000] Installing R package: colorspace (1.4-1)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘colorspace’ ...
• DONE (colorspace) [2020-05-04T14:26:28.520618327+0000] Installing R package: munsell (0.5.0)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘munsell’ ...
• DONE (munsell) [2020-05-04T14:26:28.704527961+0000] Installing R package: withr (2.1.2)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘withr’ ...
• DONE (withr) [2020-05-04T14:26:28.885800069+0000] Installing R package: nlme (3.1-144)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘nlme’ ...
• DONE (nlme) [2020-05-04T14:26:29.269523359+0000] Installing R package: mgcv (1.8-31)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘mgcv’ ...
• DONE (mgcv) [2020-05-04T14:26:29.636541040+0000] Installing R package: labeling (0.3)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘labeling’ ...
• DONE (labeling) [2020-05-04T14:26:29.803765000+0000] Installing R package: DBI (1.1.0)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘DBI’ ...
• DONE (DBI) [2020-05-04T14:26:30.005975765+0000] Installing R package: sf (0.9-2)
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing binary package ‘sf’ ...
• DONE (sf) [2020-05-04T14:26:30.851207099+0000] Building R package: lwgeom (0.2-3) /mnt/packages/build /mnt
• installing to library ‘/opt/R/3.6.3/lib/R/library’
• installing source package ‘lwgeom’ ... package ‘lwgeom’ successfully unpacked and MD5 sums checked using staged installation configure: CC: gcc configure: CXX: g++ -std=gnu++11 configure: pkg-config proj exists, will use it checking proj_api.h usability... no checking proj_api.h presence... no checking for proj_api.h... no configure: error: proj_api.h not found in standard or given locations. ERROR: configuration failed for package ‘lwgeom’
• removing ‘/opt/R/3.6.3/lib/R/library/lwgeom’ ################################# End Task Log ################################# Error: Unhandled Exception: Child Task 725843413 failed: Error building image: Error building lwgeom (0.2-3). Build exited with non-zero status: 1 Execution halted

[edzer]

You didn't answer my questions.

[federicotallis]

You didn't answer my questions.

Sorry, I'm trying to deploy my ShinyApp onto ShinyApps.io

Preparing to deploy application...DONE Uploading bundle for application: 2197624...DONE Deploying bundle: 3101422 for application: 2197624 ... Waiting for task: 725843412 building: Parsing manifest building: Building image: 3460227 building: Installing system dependencies building: Fetching packages building: Building package: lwgeom ################################ Begin Task Log ################################

[edzer]

Sorry, I can't help you with that.

[federicotallis]

Sorry, I can't help you with that.

I'm not sure I follow. Can't run the app because can't install lwgeom. It seems that I can't install the package onto the instance because of:

"configure: error: proj_api.h not found in standard or given locations. ERROR: configuration failed for package ‘lwgeom'

Need an alternate way to install package. Installing directly from source has failed. Any idea why?