[R-sig-Geo] Error in the installation of rgdal on the docker osgeo/gdal:ubuntu-small
Roger Bivand
Roger@B|v@nd @end|ng |rom nhh@no
Tue Jan 28 20:47:32 CET 2020
Thanks for this. The configure script does not check that sqlite is available, and should do that. For now, make sqlite available in the image (PROJ needs it from PROJ 6). Did you know that you are pulling GDAL 3.1.0, which has not been released or checked with R packages (not the problem here)? If the problem with the configure failure gets resolved, you'll need to install from rgdal from R-Forge, no more patch releases for 1.4.*. If you want to experiment with WKT2 CRS, also grab sp from my github master.
Roger
--
Roger Bivand
Norwegian School of Economics
Helleveien 30, 5045 Bergen, Norway
Roger.Bivand using nhh.no
________________________________________
Fra: R-sig-Geo <r-sig-geo-bounces using r-project.org> på vegne av Arnaud De Groof <Arnaud.DeGroof using spacebel.be>
Sendt: tirsdag 28. januar 2020 16.46
Til: r-sig-geo using r-project.org
Emne: [R-sig-Geo] Error in the installation of rgdal on the docker osgeo/gdal:ubuntu-small
Hi,
I am trying to install the rgdal package on a docker image based on osgeo/gdal:ubuntu-small (latest) but I encounter the following issue:
> install.packages('rgdal', repos='http://cran.rstudio.com', configure.args = c('--with-gdal-config=/usr/bin/gdal-config','--with-gdal-share=/usr/share/gdal', '--with-proj-include=/usr/include', '--with-proj-lib=/usr/share/proj'))
Installing package into '/usr/local/lib/R/site-library'
(as 'lib' is unspecified)
also installing the dependency 'sp'
trying URL 'http://cran.rstudio.com/src/contrib/sp_1.3-2.tar.gz'
Content type 'application/x-gzip' length 1132347 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
trying URL 'http://cran.rstudio.com/src/contrib/rgdal_1.4-8.tar.gz'
Content type 'application/x-gzip' length 1698902 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
* installing *source* package 'sp' ...
** package 'sp' successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rcentroid.c -o Rcentroid.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gcdist.c -o gcdist.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -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 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pip.c -o pip.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pip2.c -o pip2.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sp_xports.c -o sp_xports.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c surfaceArea.c -o surfaceArea.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c zerodist.c -o zerodist.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o sp.so Rcentroid.o gcdist.o init.o pip.o pip2.o sp_xports.o surfaceArea.o zerodist.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-sp/00new/sp/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sp)
* installing *source* package 'rgdal' ...
** package 'rgdal' successfully unpacked and MD5 sums checked
** using staged installation
configure: R_HOME: /usr/lib/R
configure: CC: gcc -std=gnu99
configure: CXX: g++ -std=gnu++11
configure: C++11 support available
configure: rgdal: 1.4-7
checking for /usr/bin/svnversion... no
configure: svn revision: 845
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.1.0
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/pcs.csv readable... no
configure: pkg-config proj exists, will use it
configure: PROJ version: 6.3.0
configure: Support for PROJ >= 6.0.0 not yet available, deprecated API defined
configure: proj CPP flags: -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/local/include
configure: PROJ LIBS: -L/usr/local/lib -lproj
checking PROJ header API:... proj_api.h
checking proj_api.h presence and usability... yes
checking PROJ version agreement... yes
checking PROJ version >= 4.8.0... yes
/usr/bin/ld: cannot find -lsqlite3
collect2: error: ld returned 1 exit status
./configure: line 2437: ./proj_conf_test2: No such file or directory
checking PROJ: proj.db found and readable... yes
configure: Package CPP flags: -I/usr/include -I/usr/local/include -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H
configure: Package LIBS: -L/usr/lib -lgdal -L/usr/local/lib -lproj
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -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 -I/usr/local/include -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -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 -I/usr/local/include -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -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 -I/usr/local/include -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -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 -I/usr/local/include -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -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 -I/usr/local/include -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -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 -I/usr/local/include -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -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 -I/usr/local/include -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -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 -I/usr/local/include -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ogrdrivers.cpp -o ogrdrivers.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ogrsource.cpp -o ogrsource.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c proj_info6.cpp -o proj_info6.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I/usr/local/include -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-t3diwe/r-base-3.6.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c projectit.cpp -o projectit.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o proj_info6.o projectit.o -L/usr/lib -lgdal -L/usr/local/lib -lproj -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-rgdal/00new/rgdal/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'rgdal' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/site-library/00LOCK-rgdal/00new/rgdal/libs/rgdal.so':
/usr/local/lib/R/site-library/00LOCK-rgdal/00new/rgdal/libs/rgdal.so: undefined symbol: proj_list_operations
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/usr/local/lib/R/site-library/rgdal'
The downloaded source packages are in
'/tmp/RtmpeD6Lq2/downloaded_packages'
Warning message:
In install.packages("rgdal", repos = "http://cran.rstudio.com", :
installation of package 'rgdal' had non-zero exit status
Here the dockerfile:
FROM osgeo/gdal:ubuntu-small-latest
ENV DEBIAN_FRONTEND=noninteractive
#######################
### Install
RUN apt-get update && apt-get install -y\
zip\
bc\
curl\
lsb-release\
libfreetype6\
#r-base\
default-jre\
pkg-config\
wget\
git\
libproj-dev\
proj-data\
proj-bin\
libcurl4-openssl-dev\
python-pip && \
pip install pip==9.0.1 && \
pip install\
numpy==1.14.1 \
Jinja2 \
geojson \
requests \
rasterstats \
pandas \
pyshp \
Pillow \
scipy
RUN apt install -y apt-transport-https software-properties-common
RUN gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
RUN gpg -a --export E298A3A825C0D65DFD57CBB651716619E084DAB9 | apt-key add -
RUN add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/' && \
apt-get update
RUN apt install -y r-base r-base-core r-recommended
RUN R --version
ENV GDAL_DATA /usr/share/gdal/
ENV PROJ_LIB /usr/share/proj/
RUN R -e "install.packages('rgdal', repos='http://cran.rstudio.com', configure.args = c('--with-gdal-config=/usr/bin/gdal-config','--with-gdal-share=/usr/share/gdal', '--with-proj-include=/usr/include', '--with-proj-lib=/usr/share/proj'))"
Thanks,
Arnaud
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