Can't install SF in Ubuntu 16.04: Error "polygonize.o" failed

[inder-tg]

Hi, I'm trying to install sf in my computer that runs on an Ubuntu 16.04, R 3.4 version but I keep getting the following error message:

Installing package into ‘/home/inder/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/sf_0.7-1.tar.gz'
Content type 'application/x-gzip' length 8330564 bytes (7.9 MB)

downloaded 7.9 MB

• installing source package ‘sf’ ...
  ** package ‘sf’ successfully unpacked and MD5 sums checked
  configure: CC: gcc -std=gnu99
  configure: CXX: g++ -std=gnu++11
  checking for gdal-config... /usr/bin/gdal-config
  checking gdal-config usability... yes
  configure: GDAL: 2.6.0
  checking GDAL version >= 2.0.0... yes
  checking for gcc... gcc -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 -std=gnu99 accepts -g... yes
  checking for gcc -std=gnu99 option to accept ISO C89... none needed
  checking how to run the C preprocessor... gcc -std=gnu99 -E
  checking for grep that handles long lines and -e... /bin/grep
  checking for egrep... /bin/grep -E
  checking for ANSI C header files... yes
  checking for sys/types.h... yes
  checking for sys/stat.h... yes
  checking for stdlib.h... yes
  checking for string.h... yes
  checking for memory.h... yes
  checking for strings.h... yes
  checking for inttypes.h... yes
  checking for stdint.h... yes
  checking for unistd.h... yes
  checking gdal.h usability... yes
  checking gdal.h presence... yes
  checking for gdal.h... yes
  checking GDAL: linking with --libs only... yes
  checking GDAL: /usr/share/gdal/2.6/pcs.csv readable... yes
  checking GDAL: checking whether PROJ is available for linking:... yes
  checking GDAL: checking whether PROJ is available fur running:... yes
  configure: pkg-config proj exists, will use it
  checking proj_api.h usability... yes
  checking proj_api.h presence... yes
  checking for proj_api.h... yes
  configure: PROJ: 4.9.2
  checking for pj_init_plus in -lproj... yes
  checking PROJ: epsg found and readable... yes
  checking PROJ: conus found and readable... yes
  checking for geos-config... /usr/bin/geos-config
  checking geos-config usability... yes
  configure: GEOS: 3.5.0
  checking GEOS version >= 3.4.0... yes
  checking geos_c.h usability... yes
  checking geos_c.h presence... yes
  checking for geos_c.h... yes
  checking geos: linking with -L/usr/lib/x86_64-linux-gnu -lgeos_c -L/usr/lib/x86_64-linux-gnu -lgeos-3.5.0... yes
  configure: Package CPP flags: -I/usr/include/gdal -I/usr/include
  configure: Package LIBS: -lproj -L/usr/lib/x86_64-linux-gnu -lgdal -L/usr/lib/x86_64-linux-gnu -lgeos_c -L/usr/lib/x86_64-linux-gnu -lgeos-3.5.0
  configure: creating ./config.status
  config.status: creating src/Makevars
  ** libs
  g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/inder/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
  g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/inder/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bbox.cpp -o bbox.o
  g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/inder/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gdal.cpp -o gdal.o
  g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/inder/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gdal_geom.cpp -o gdal_geom.o
  g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/inder/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gdal_read.cpp -o gdal_read.o
  g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/inder/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gdal_utils.cpp -o gdal_utils.o
  g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/inder/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gdal_write.cpp -o gdal_write.o
  g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/inder/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c geos.cpp -o geos.o
  g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/inder/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c hex.cpp -o hex.o
  g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal -I/usr/include -I"/home/inder/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include" -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c polygonize.cpp -o polygonize.o
  polygonize.cpp: In function ‘Rcpp::List CPL_polygonize(Rcpp::CharacterVector, Rcpp::CharacterVector, Rcpp::CharacterVector, Rcpp::CharacterVector, Rcpp::CharacterVector, Rcpp::CharacterVector, Rcpp::IntegerVector, Rcpp::CharacterVector, bool, bool)’:
  polygonize.cpp:113:75: error: ‘GDALContourGenerateEx’ was not declared in this scope
  create_options(contour_options).data(), NULL, NULL) != OGRERR_NONE)
  ^
  /usr/lib/R/etc/Makeconf:168: recipe for target 'polygonize.o' failed
  make: *** [polygonize.o] Error 1
  ERROR: compilation failed for package ‘sf’
• removing ‘/home/inder/R/x86_64-pc-linux-gnu-library/3.4/sf’
  Warning in install.packages :
  installation of package ‘sf’ had non-zero exit status

Any help will be really appreciated.

[edzer]

Your configure sais:

configure: GDAL: 2.6.0

which is very odd, since the dev version of GDAL is currently 2.3.2. Something is wrong with your GDAL install (or gdal-config); the routine GDALContourGenerateEx requires gdal >= 2.4.x (dev github version), and has been tested to run against that.

[inder-tg]

Hi, I removed gdal and proj from my system. Then I am trying to install the latest version of gdal and I am getting this: inder@inder-PORTEGE-R835:~$ sudo apt-cache policy libgdal-dev libgdal-dev: Installed: (none) Candidate: 2.6.0+2-0xenial1 Version table: 2.6.0+2-0xenial1 500 500 http://ppa.launchpad.net/nextgis/dev/ubuntu xenial/main amd64 Packages 2.1.3+dfsg-1~xenial2 500 500 http://ppa.launchpad.net/ubuntugis/ppa/ubuntu xenial/main amd64 Packages 1.11.3+dfsg-3build2 500 500 http://archive.ubuntu.com/ubuntu xenial/universe amd64 Packages If I am getting it right, the latest version is 2.6.0. Also, if GDALContourGenerateEx has been tested against gdal >= 2.4 I do not understand why wouldn't run against a 2.6.0, I am puzzled. Or is the dev github version so much different to the one that I am trying to get from this repository: ppa:ubuntugis/ubuntugis-unstable Thanks, Inder

…

On Sat, Nov 3, 2018 at 11:20 AM Edzer Pebesma ***@***.***> wrote: Your configure sais: configure: GDAL: 2.6.0 which is very odd, since the dev version of GDAL is currently 2.3.2 <https://download.osgeo.org/gdal/CURRENT/>. Something is wrong with your GDAL install (or gdal-config); the routine GDALContourGenerateEx requires gdal >= 2.4.x (dev github version), and has been tested to run against that. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#884 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AK7T2JSRQ20NUVGhgjRWRFLnCxrAECYLks5urbQugaJpZM4YMqJK> .

-- Hasta pronto, Inder.

[edzer]

Please look here: https://github.com/OSGeo/gdal/blob/master/gdal/VERSION - I take that as authorative. Please use either ubuntugis-unstable, which will give you GDAL 2.2.3, or install from source, which will give you 2.4.0 with GDALContourGenerateEx in it.

Looks like nextgis is going its own way with assigning version numbers; I take OSGEO as the one deciding about this.