I have recently upgraded my Ubuntu version from 20.04 to 22.04 LTS and Rstudio-server to 2023.06.02. The R version is 4.3.1. After that the shiny App I am developing, which ran OK on the previous version, was giving an error of the type 'libproj.so.15 - cannot open shared file'. After reading various possible solutions, I reinstalled the "sf" package, which appeared to work OK. The error message then changed to the same, but referencing 'libproj.so.26', so I tried re-install 'rgdal'. This gave the following error message:
> remove.packages("rgdal")
Removing package from ‘/home/denis/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
Error in remove.packages : there is no package called ‘rgdal’
> install.packages("rgdal")
Installing package into ‘/home/denis/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/rgdal_1.6-7.tar.gz'
Content type 'application/x-gzip' length 4351163 bytes (4.1 MB)
==================================================
downloaded 4.1 MB
* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
** using staged installation
configure: R_HOME: /usr/lib/R
configure: CC: gcc
configure: CXX: g++ -std=gnu++17
configure: CFLAGS: -g -O2 -fdebug-prefix-map=/build/r-base-aeZVAy/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
configure: CPPFLAGS:
configure: CXXFLAGS: -g -O2 -fdebug-prefix-map=/build/r-base-aeZVAy/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
configure: LDFLAGS: -Wl,-Bsymbolic-functions -Wl,-z,relro
configure: LDFLAGS: -Wl,-Bsymbolic-functions -Wl,-z,relro
configure: CXX17 is: g++, CXX17STD is: -std=gnu++17
configure: CXX is: g++ -std=gnu++17
configure: C++17 support available
configure: rgdal: 1.6-7
checking for /usr/bin/svnversion... no
configure: svn revision: 1203
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.4.1
checking GDAL version != 3.6.0... yes
checking GDAL version >= 1.11.4... yes
checking GDAL version <= 2.5 or >= 3.0... yes
checking GDAL: linking with --libs only... yes
checking GDAL: gdal-config data directory readable... yes
checking GDAL: /usr/share/gdal/stateplane.csv readable... yes
configure: pkg-config proj exists, will use it
configure: PROJ version: 8.2.1
configure: PROJ CPP flags: -DPROJ_H_API
configure: PROJ LIBS: -lproj
checking PROJ header API:... yes
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for proj.h... yes
checking for proj_context_create in -lproj... yes
checking Using GDAL < 3 with PROJ >= 6... no
checking PROJ version >= 4.8.0... yes
checking PROJ: proj.db found and readable... yes
configure: Package CPP flags: -I/usr/include/gdal -DPROJ_H_API
configure: Package LIBS: -L/usr/lib -lgdal -lproj
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++17
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal -DPROJ_H_API -I'/usr/local/lib/R/site-library/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-aeZVAy/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c OGR_write.cpp -o OGR_write.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal -DPROJ_H_API -I'/usr/local/lib/R/site-library/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-aeZVAy/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gdal-bindings.cpp -o gdal-bindings.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal -DPROJ_H_API -I'/usr/local/lib/R/site-library/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-aeZVAy/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal -DPROJ_H_API -I'/usr/local/lib/R/site-library/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-aeZVAy/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c inverser.c -o inverser.o
gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal -DPROJ_H_API -I'/usr/local/lib/R/site-library/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-aeZVAy/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c local_stubs.c -o local_stubs.o
In file included from local_stubs.c:3:
/usr/local/lib/R/site-library/sp/include/sp_xports.c: In function ‘RGDAL_Polygon_c’:
/usr/local/lib/R/site-library/sp/include/sp_xports.c:60:22: error: ‘DOUBLE_EPS’ undeclared (first use in this function)
60 | if (fabs(area) < DOUBLE_EPS) {
| ^~~~~~~~~~
/usr/local/lib/R/site-library/sp/include/sp_xports.c:60:22: note: each undeclared identifier is reported only once for each function it appears in
/usr/local/lib/R/site-library/sp/include/sp_xports.c: In function ‘RGDAL_Polygons_c’:
/usr/local/lib/R/site-library/sp/include/sp_xports.c:203:18: error: ‘DOUBLE_EPS’ undeclared (first use in this function)
203 | fuzz = R_pow(DOUBLE_EPS, (2.0/3.0));
| ^~~~~~~~~~
make: *** [/usr/lib/R/etc/Makeconf:191: local_stubs.o] Error 1
ERROR: compilation failed for package ‘rgdal’
* removing ‘/home/denis/R/x86_64-pc-linux-gnu-library/4.3/rgdal’
Warning in install.packages :
installation of package ‘rgdal’ had non-zero exit status
Although the problem is obviously with the installation, a short test script, below, gives the essential code that causes the problems.
library(sf) # various GIS objects and functions
library(rgdal) # for readOGR function (deprecated!)
library(raster) # raster processing, uses GDAL objects
fnms <- c('at', 'ct', 'dams', 'md2', 'smr250', 'snr250')
files <- paste0(fnms, '.tif')
# creates a raster stack with the 6 factors as layers
fL <- raster::stack(files)
The data files if needed are available from https://bio-met.co.uk/file_transfer/EF_maps.zip.
This gives the error:
> source("~/.active-rstudio-document")
Error: package or namespace load failed for ‘rgdal’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/lib/R/library/rgdal/libs/rgdal.so':
libgdal.so.26: cannot open shared object file: No such file or directory
In relation to some similar problems, but with older versions, it is suggested to install gdal libraries at the Ubuntu command line. When I do this, it seems the requisite libraries are already installed, as shown below:
sudo apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
libgdal-dev is already the newest version (3.4.1+dfsg-1build4).
libgeos-dev is already the newest version (3.10.2-1).
libgeos-dev set to manually installed.
libproj-dev is already the newest version (8.2.1-1).
libproj-dev set to manually installed.
libudunits2-dev is already the newest version (2.2.28-3).
The following package was automatically installed and is no longer required:
libssl1.1
Use 'sudo apt autoremove' to remove it.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
At the moment I have run out of ideas as to what to try, not knowing how gdal should properly be configured on Ubuntu 22.04 or why the rgdal installation should give a compiler error on this version when it has worked perfectly in the past. Any suggestions would be very gratefully received. Is there a switch to use when installing rgdal from source to get it to compile properly, for example?
Thank you for those suggestions. I managed to install binaries from r2u, which did indeed solve the problem. Afterwards, I also made a small amendment to the code, retiring a reference to readOGR(), which was the only function from rgdal that was being used, so there is no longer dependence on the deprecated package.