Re: [R-sig-Geo] rgdal segmentation fault during installation
It looks like you have multiple versions of GDAL and/or PROJ installed
on your system; see https://github.com/r-spatial/sf the section on
"Multiple GDAL, GEOS and/or PROJ versions on your system" and there the
link to https://github.com/r-spatial/sf/issues/844 which contains a very
ugly solution (setting LD_LIBRARY_PATH from within R).
On 11/17/18 1:57 PM, Emanuele Cordano wrote:
> Dear list,
>
> I got the following segmentation fault error when I try to install rgdal on
> my local Ubuntu 16.04 LTS machine. Did anyone encounter something similar?
> Please below the error message with traceback and R session info.
> Similar problems appears on
> https://stackoverflow.com/questions/50064673/cannot-install-rgdal-package-in-local-server-an-irrecoverable-exception-occurre
> which remains unsolved . In my case (see below) all checks, PROJ4
> included, were OK!
>
> Thank you for any kind of feedback
> Best
> Emanuele Cordano
>
> user@machine:~$ R
>
> R version 3.5.1 (2018-07-02) -- "Feather Spray"
> Copyright (C) 2018 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> [Previously saved workspace restored]
>
>> install.packages("rgdal")
> Installing package into ‘/home/ecor/R/x86_64-pc-linux-gnu-library/3.5’
> (as ‘lib’ is unspecified)
> trying URL 'http://cran.r-project.org/src/contrib/rgdal_1.3-6.tar.gz'
> Content type 'application/x-gzip' length 1666975 bytes (1.6 MB)
> ==
> downloaded 1.6 MB
>
> * installing *source* package ‘rgdal’ ...
> ** package ‘rgdal’ successfully unpacked and MD5 sums checked
> configure: R_HOME: /usr/lib/R
> configure: CC: gcc -std=gnu99
> configure: CXX: g++
> configure: C++11 support available
> configure: rgdal: 1.3-6
> checking for /usr/bin/svnversion... yes
> configure: svn revision: 773
> checking for gdal-config... /usr/bin/gdal-config
> checking gdal-config usability... yes
> configure: GDAL: 2.1.3
> checking GDAL version >= 1.11.4... yes
> checking gdal: linking with --libs only... yes
> checking GDAL: /usr/share/gdal/2.1/pcs.csv readable... yes
> configure: pkg-config proj exists, will use it
> configure: PROJ version: 4.9.2
> checking proj_api.h presence and usability... yes
> checking PROJ version >= 4.8.0... yes
> checking projects.h presence and usability... yes
> checking PROJ.4: epsg found and readable... yes
> checking PROJ.4: conus found and readable... yes
> configure: Package CPP flags: -I/usr/include/gdal
> configure: Package LIBS: -L/usr/lib -lgdal -lproj
> 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"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include"-fpic -g
> -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -c OGR_write.cpp -o OGR_write.o
> g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal
> -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include"-fpic -g
> -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -c gdal-bindings.cpp -o gdal-bindings.o
> gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal
> -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include"-fpic -g
> -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
> gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal
> -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include"-fpic -g
> -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -c inverser.c -o inverser.o
> gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal
> -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include"-fpic -g
> -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -c local_stubs.c -o local_stubs.o
> g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal
> -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include"-fpic -g
> -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
> -D_FORTIFY_SOURCE=2 -g -c ogr_geom.cpp -o ogr_geom.o
> gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal
> -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include"
[R-sig-Geo] rgdal segmentation fault during installation
Dear list,
I got the following segmentation fault error when I try to install rgdal on
my local Ubuntu 16.04 LTS machine. Did anyone encounter something similar?
Please below the error message with traceback and R session info.
Similar problems appears on
https://stackoverflow.com/questions/50064673/cannot-install-rgdal-package-in-local-server-an-irrecoverable-exception-occurre
which remains unsolved . In my case (see below) all checks, PROJ4
included, were OK!
Thank you for any kind of feedback
Best
Emanuele Cordano
user@machine:~$ R
R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
> install.packages("rgdal")
Installing package into ‘/home/ecor/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
trying URL 'http://cran.r-project.org/src/contrib/rgdal_1.3-6.tar.gz'
Content type 'application/x-gzip' length 1666975 bytes (1.6 MB)
==
downloaded 1.6 MB
* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
configure: R_HOME: /usr/lib/R
configure: CC: gcc -std=gnu99
configure: CXX: g++
configure: C++11 support available
configure: rgdal: 1.3-6
checking for /usr/bin/svnversion... yes
configure: svn revision: 773
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.1.3
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... yes
checking GDAL: /usr/share/gdal/2.1/pcs.csv readable... yes
configure: pkg-config proj exists, will use it
configure: PROJ version: 4.9.2
checking proj_api.h presence and usability... yes
checking PROJ version >= 4.8.0... yes
checking projects.h presence and usability... yes
checking PROJ.4: epsg found and readable... yes
checking PROJ.4: conus found and readable... yes
configure: Package CPP flags: -I/usr/include/gdal
configure: Package LIBS: -L/usr/lib -lgdal -lproj
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"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include"-fpic -g
-O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c OGR_write.cpp -o OGR_write.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal
-I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include"-fpic -g
-O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c gdal-bindings.cpp -o gdal-bindings.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal
-I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include"-fpic -g
-O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal
-I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include"-fpic -g
-O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c inverser.c -o inverser.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal
-I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include"-fpic -g
-O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c local_stubs.c -o local_stubs.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal
-I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include"-fpic -g
-O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c ogr_geom.cpp -o ogr_geom.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal
-I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include"-fpic -g
-O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c ogr_polygons.c -o ogr_polygons.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal
-I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include"-fpic -g
-O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c ogr_proj.cpp -o ogr_proj.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal
-I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include"-fpic -g
-O2
