[R-sig-Geo] Error in the installation of rgdal on the docker osgeo/gdal:ubuntu-small

Wed Jan 29 12:00:27 CET 2020

On Tue, 28 Jan 2020, Roger Bivand wrote:

> 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.

Please try revision 926 from https://r-forge.r-project.org/R/?group_id=884 
once it refreshes (and if the build succeeds); this includes a 
non-failing test for sqlite3. Once you report back, I can also modify it 
to hard-fail.

Roger

>
> 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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-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand using nhh.no
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en