Please post plain text only.
I am not going to waste time installing the docker image on a desktop
machine in my office when I'm not there. You can easily check out the SVN
source of the package, debug your system, and contribute your patch back.
You have not motivated your need to install in this way, nor have I seen
any contributions to the development marathon of adapting sp/rgdal or sf
to PROJ6/GDAL3:
https://www.youtube.com/watch?v=Rgn4Ns2UgAg&list=PLXUoTpMa_9s10NVk4dBQljNOaOXAOhcE0&index=4&t=0s
Your implicit affiliation is with a company, you can helpfully debug this
and contribute back - you do not seem to be reading around this problem,
but push it back to me as maintainer regardless. It is your problem on
your odddish configuration. I look forward to receiving patches for the
SVN repo.
If you think that:
'--with-proj-lib=/usr/local/share/proj'
looks odd (it does, '--with-proj-lib=/usr/local/lib' is much more likely,
and if you register proj.pc with pkg-config, you don't need to use those
configure arguments), you are the best person to try alternatives.
Further, the error message now looks like multiple installed versions of
the proj shared object: https://github.com/r-spatial/sf/issues/844.
For an alternative docker image, see
https://github.com/r-spatial/discuss/issues/28#issuecomment-551241421 -
correct GDAL and PROJ versions to current.
On Wed, 29 Jan 2020, Arnaud De Groof wrote:
There is alway an error with the installation of rgdal. Is it linked to an
issue in the definition of the arguments
('with-proj-lib','with-proj-share',..)?
install.packages('rgdal', repos='http://R-Forge.R-project.org',
configure.args = c('--with-gdal-config=/usr/bin/gdal-config',
'--with-proj-include=/usr/local/include',
'--with-proj-lib=/usr/local/share/proj',
'--with-proj-share=/usr/local/share/proj'))
Installing package into '/usr/local/lib/R/site-library'
(as 'lib' is unspecified)
trying URL 'http://R-Forge.R-project.org/src/contrib/rgdal_1.5-3.tar.gz'
Content type 'application/x-gzip' length 1774321 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
* installing *source* package 'rgdal' ...
** 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: 1.5-3
checking for /usr/bin/svnversion... no
cat: inst/SVN_VERSION: No such file or directory
configure: svn revision:
configure: gdal-config set to /usr/bin/gdal-config
checking gdal-config exists... yes
checking gdal-config executable... yes
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/stateplane.csv readable... yes
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/share/proj
checking PROJ header API:... proj_api.h
checking proj_api.h presence and usability... yes
checking PROJ version agreement... yes
checking Using GDAL < 3 with PROJ >= 6... no
checking PROJ version >= 4.8.0... yes
configure: PROJ_LIB: /usr/local/share/proj
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 sqlite3.h usability... yes
checking sqlite3.h presence... yes
checking for sqlite3.h... yes
checking for sqlite3_libversion in -lsqlite3... yes
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/share/proj -lproj
-lsqlite3
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/share/proj -lproj
-lsqlite3 -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_create
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/usr/local/lib/R/site-library/rgdal'
>
>
The downloaded source packages are in
'/tmp/Rtmpvt7qpB/downloaded_packages'
Warning message:
In install.packages("rgdal", repos = "http://R-Forge.R-project.org", :
installation of package 'rgdal' had non-zero exit status
____________________________________________________________________________
De : Roger Bivand <roger.biv...@nhh.no>
Envoyé : mercredi 29 janvier 2020 16:06
À : r-sig-geo@r-project.org; Arnaud De Groof
Objet : Re: [R-sig-Geo] Error in the installation of rgdal on the docker
osgeo/gdal:ubuntu-small
For sp, install from CRAN, or for the development version,
remotes::install_github("rsbivand/sp").
Roger
Roger Bivand
Norwegian School of Economics
Bergen, Norway
____________________________________________________________________________
From: Arnaud De Groof <arnaud.degr...@spacebel.be>
Sent: Wednesday, January 29, 2020 4:02:15 PM
To: r-sig-geo@r-project.org <r-sig-geo@r-project.org>; roger.biv...@nhh.no
<roger.biv...@nhh.no>
Subject: RE: [R-sig-Geo] Error in the installation of rgdal on the docker
osgeo/gdal:ubuntu-small
Thanks Roger,
I have modified the Dockerfile aiming to integrate sqlite3, libsqlite3-dev
and rgdal from R-Forge:
RUN R -e "install.packages('rgdal', repos='http://R-Forge.R-project.org',
configure.args
=c('--with-gdal-config=/usr/bin/gdal-config','--with-gdal-share=/usr/share/g
dal', '--with-proj-include=/usr/include',
'--with-proj-lib=/usr/share/proj',
'--with-proj-share=/usr/local/share/proj'))"
Unfortunately, this package have a dependency to 'sp'.
> install.packages('rgdal', repos='http://R-Forge.R-project.org',
configure.args
=c('--with-gdal-config=/usr/bin/gdal-config','--with-gdal-share=/usr/share/g
dal', '--with-proj-include=/usr/include',
'--with-proj-lib=/usr/share/proj',
'--with-proj-share=/usr/local/share/proj'))
Installing package into '/usr/local/lib/R/site-library'
(as 'lib' is unspecified)
Warning: dependency 'sp' is not available
trying URL 'http://R-Forge.R-project.org/src/contrib/rgdal_1.5-3.tar.gz';
Content type 'application/x-gzip' length 1774321 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
ERROR: dependency 'sp' is not available for package 'rgdal'
* removing '/usr/local/lib/R/site-library/rgdal'
The downloaded source packages are in
'/tmp/Rtmp0aIlx7/downloaded_packages'
Warning message:
In install.packages("rgdal", repos = "http://R-Forge.R-project.org", :
installation of package 'rgdal' had non-zero exit status
So, I added the package 'sp' :
RUN R -e "install.packages('sp', repos='http://R-Forge.R-project.org')";
But this package seems not available for the version of R 3.6.2:
install.packages('sp', repos='http://R-Forge.R-project.org')
Installing package into '/usr/local/lib/R/site-library'
(as 'lib' is unspecified)
Warning message:
package 'sp' is not available (for R version 3.6.2)
Solution : downgrade R?
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.biv...@nhh.no
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
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