sf installation issues on R4.0 / Ubuntu18.04

LarsR · January 21, 2021, 10:37am

Hi, I get stuck when I try to install package sf on R4.0 / Ubuntu 18.04. Anyone facing the same issues?
install.packages("sf")
...
checking GDAL: linking with --libs only... yes
checking GDAL: /usr/share/gdal/pcs.csv readable... no
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available fur running:... ERROR 1: PROJ: proj_create_from_database: SQLite error on SELECT name, type, coordinate_system_auth_name, coordinate_system_code, datum_auth_name, datum_code, area_of_use_auth_name, area_of_use_code, text_definition, deprecated FROM geodetic_crs WHERE auth_name = ? AND code = ?: no such column: area_of_use_auth_name
ERROR 1: PROJ: proj_create_from_database: SQLite error on SELECT name, coordinate_system_auth_name, coordinate_system_code, geodetic_crs_auth_name, geodetic_crs_code, conversion_auth_name, conversion_code, area_of_use_auth_name, area_of_use_code, text_definition, deprecated FROM projected_crs WHERE auth_name = ? AND code = ?: no such column: area_of_use_auth_name
ERROR 1: PROJ: proj_create: unrecognized format / unknown name
ERROR 6: Cannot find coordinate operations from ' to '
no
configure: error: OGRCoordinateTransformation() does not return a coord.trans: PROJ not available?
ERROR: configuration failed for package ‘sf’

andresrcs · January 21, 2021, 12:50pm

Have you checked that you have the correct versions of the system dependencies installed?

C++11, GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0), sqlite3

LarsR · January 21, 2021, 1:18pm

How do I check this from Rstudio?

LarsR · January 21, 2021, 1:38pm

(base) larsrh@pc4225:~$ c++ --version
c++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0
Do I need to have c++ 11?

andresrcs · January 21, 2021, 2:00pm

Well, those are the advertised minimum requirements so I would guess, yes.

LarsR · January 21, 2021, 2:44pm

Ok, so then it is impossible to install?

andresrcs · January 21, 2021, 3:06pm

Not at all, I have it installed in Ubuntu 18, try with the RStudio package manager to have access to binaries https://packagemanager.rstudio.com/client/#/

LarsR · January 21, 2021, 3:11pm

Well, this is what I did

LarsR · January 21, 2021, 3:17pm

How can I upgrade to c++11 ?

gab1109 · January 26, 2021, 1:49am

I got the same problem. I'm on Ubuntu 18.04 and upgraded R from 3.6 to 4.0.3.

installing source package ‘sf’ ...
** package ‘sf’ successfully unpacked and MD5 sums checked
** using staged installation
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: 3.0.4
checking GDAL version >= 2.0.1... 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/pcs.csv readable... no
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available fur running:... ERROR 1: PROJ: proj_create_from_database: SQLite error on SELECT name, type, coordinate_system_auth_name, coordinate_system_code, datum_auth_name, datum_code, area_of_use_auth_name, area_of_use_code, text_definition, deprecated FROM geodetic_crs WHERE auth_name = ? AND code = ?: no such column: area_of_use_auth_name
ERROR 1: PROJ: proj_create_from_database: SQLite error on SELECT name, coordinate_system_auth_name, coordinate_system_code, geodetic_crs_auth_name, geodetic_crs_code, conversion_auth_name, conversion_code, area_of_use_auth_name, area_of_use_code, text_definition, deprecated FROM projected_crs WHERE auth_name = ? AND code = ?: no such column: area_of_use_auth_name
ERROR 1: PROJ: proj_create: unrecognized format / unknown name
ERROR 6: Cannot find coordinate operations from ' to '
no
configure: error: OGRCoordinateTransformation() does not return a coord.trans: PROJ not available?
ERROR: configuration failed for package ‘sf’

$c++ --version
c++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0

technocrat · January 26, 2021, 5:48am

Missing system dependency. PROJ (>= 4.8.0, Download — PROJ 9.4.0 documentation)

gab1109 · January 26, 2021, 2:52pm

I previously downloaded the PROJ package before my previous post and I am still not being able to download sf. I tried to remove and reinstall the package and nothing change.
Sorry if it is a newbie question, Linux is still very new for me.

$sudo apt-get install proj-bin
Reading package lists... Done
Building dependency tree       
Reading state information... Done
proj-bin is already the newest version (7.0.0-1~bionic0).

LarsR · January 26, 2021, 3:07pm

It would be great if someone can come up with a solution to this.

andresrcs · January 26, 2021, 6:09pm

Make sure you have these installed in your system

sudo apt install libgdal-dev
sudo apt install gdal-bin
sudo apt install libgeos-dev
sudo apt install libproj-dev

And then install from the RStudio Public Package Manager (as I said before)

options(repos = c(REPO_NAME = "https://packagemanager.rstudio.com/all/__linux__/bionic/latest"))
install.packages("sf")

LarsR · January 26, 2021, 6:40pm

Thanks, I did what you said, and get the following: There still seem to be problems with PROJ.
checking GDAL: /usr/share/gdal/pcs.csv readable... no
checking GDAL: checking whether PROJ is available for linking:... yes
checking GDAL: checking whether PROJ is available fur running:... ERROR 1: PROJ: proj_create_from_database: SQLite error on SELECT name, type, coordinate_system_auth_name, coordinate_system_code, datum_auth_name, datum_code, area_of_use_auth_name, area_of_use_code, text_definition, deprecated FROM geodetic_crs WHERE auth_name = ? AND code = ?: no such column: area_of_use_auth_name
ERROR 1: PROJ: proj_create_from_database: SQLite error on SELECT name, coordinate_system_auth_name, coordinate_system_code, geodetic_crs_auth_name, geodetic_crs_code, conversion_auth_name, conversion_code, area_of_use_auth_name, area_of_use_code, text_definition, deprecated FROM projected_crs WHERE auth_name = ? AND code = ?: no such column: area_of_use_auth_name
ERROR 1: PROJ: proj_create: unrecognized format / unknown name
ERROR 6: Cannot find coordinate operations from ' to '
no
configure: error: OGRCoordinateTransformation() does not return a coord.trans: PROJ not available?
ERROR: configuration failed for package ‘sf’

removing ‘/home/larsrh/R/x86_64-pc-linux-gnu-library/4.0/sf’
Warning in install.packages :
installation of package ‘sf’ had non-zero exit status

technocrat · January 26, 2021, 6:55pm

From the terminal do you get

$ sudo ldconfig -p | grep libproj
        libproj.so.19 (libc6,x86-64) => /lib/x86_64-linux-gnu/libproj.so.19
        libproj.so (libc6,x86-64) => /lib/x86_64-linux-gnu/libproj.so

LarsR · January 26, 2021, 6:59pm

larsrh@pc4225:~/Dropbox/icedata$ sudo ldconfig -p | grep libproj
libproj.so.19 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libproj.so.19
libproj.so.12 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libproj.so.12
libproj.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libproj.so

LarsR · January 26, 2021, 7:00pm

Should I remove libproj.so.12 ?

gab1109 · January 26, 2021, 7:04pm

Thanks @andresrcs for the command precision. It seems I had had installed libgdal-dev (3.0.4), gdal-bin(3.0.4), libgeos-dev(3.8.0) and libproj-dev(7.0.0). Changing the repos allowed me to download sf package, but now I cannot import the library in an R session. I got the following error :

>library(sf)
Error: package or namespace load failed for ‘sf’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/gabriel/R/x86_64-pc-linux-gnu-library/4.0/sf/libs/sf.so':
  libgdal.so.20: cannot open shared object file: No such file or directory

gab1109 · January 26, 2021, 7:08pm

On my side, I got this output:

$ sudo ldconfig -p | grep libproj
	libproj.so.19 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libproj.so.19
	libproj.so.13 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libproj.so.13
	libproj.so.12 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libproj.so.12
	libproj.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libproj.so