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<p>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','<span style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:12pt; background-color:rgb(255,255,255)">with-proj-share</span>',..)?<br>
<br>
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<div><span style="font-size:10pt"> 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'))<br style="">
Installing package into '/usr/local/lib/R/site-library'<br style="">
(as 'lib' is unspecified)<br style="">
trying URL 'http://R-Forge.R-project.org/src/contrib/rgdal_1.5-3.tar.gz'<br style="">
Content type 'application/x-gzip' length 1774321 bytes (1.7 MB)<br style="">
==================================================<br style="">
downloaded 1.7 MB<br style="">
<br style="">
* installing *source* package 'rgdal' ...<br style="">
** using staged installation<br style="">
configure: R_HOME: /usr/lib/R<br style="">
configure: CC: gcc -std=gnu99<br style="">
configure: CXX: g++ -std=gnu++11<br style="">
configure: C++11 support available<br style="">
configure: rgdal: 1.5-3<br style="">
checking for /usr/bin/svnversion... no<br style="">
cat: inst/SVN_VERSION: No such file or directory<br style="">
configure: svn revision: <br style="">
configure: gdal-config set to /usr/bin/gdal-config<br style="">
checking gdal-config exists... yes<br style="">
checking gdal-config executable... yes<br style="">
checking gdal-config usability... yes<br style="">
configure: GDAL: 3.1.0<br style="">
checking GDAL version >= 1.11.4... yes<br style="">
checking GDAL version <= 2.5 or >= 3.0... yes<br style="">
checking gdal: linking with --libs only... yes<br style="">
checking GDAL: gdal-config data directory readable... yes<br style="">
checking GDAL: /usr/share/gdal/stateplane.csv readable... yes<br style="">
configure: pkg-config proj exists, will use it<br style="">
configure: PROJ version: 6.3.0<br style="">
configure: Support for PROJ >= 6.0.0 not yet available, deprecated API defined<br style="">
configure: proj CPP flags: -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -I/usr/local/include <br style="">
configure: PROJ LIBS: -L/usr/local/share/proj <br style="">
checking PROJ header API:... proj_api.h<br style="">
checking proj_api.h presence and usability... yes<br style="">
checking PROJ version agreement... yes<br style="">
checking Using GDAL < 3 with PROJ >= 6... no<br style="">
checking PROJ version >= 4.8.0... yes<br style="">
configure: PROJ_LIB: /usr/local/share/proj<br style="">
checking for gcc... gcc -std=gnu99<br style="">
checking whether the C compiler works... yes<br style="">
checking for C compiler default output file name... a.out<br style="">
checking for suffix of executables... <br style="">
checking whether we are cross compiling... no<br style="">
checking for suffix of object files... o<br style="">
checking whether we are using the GNU C compiler... yes<br style="">
checking whether gcc -std=gnu99 accepts -g... yes<br style="">
checking for gcc -std=gnu99 option to accept ISO C89... none needed<br style="">
checking how to run the C preprocessor... gcc -std=gnu99 -E<br style="">
checking for grep that handles long lines and -e... /bin/grep<br style="">
checking for egrep... /bin/grep -E<br style="">
checking for ANSI C header files... yes<br style="">
checking for sys/types.h... yes<br style="">
checking for sys/stat.h... yes<br style="">
checking for stdlib.h... yes<br style="">
checking for string.h... yes<br style="">
checking for memory.h... yes<br style="">
checking for strings.h... yes<br style="">
checking for inttypes.h... yes<br style="">
checking for stdint.h... yes<br style="">
checking for unistd.h... yes<br style="">
checking sqlite3.h usability... yes<br style="">
checking sqlite3.h presence... yes<br style="">
checking for sqlite3.h... yes<br style="">
checking for sqlite3_libversion in -lsqlite3... yes<br style="">
checking PROJ: proj.db found and readable... yes<br style="">
configure: Package CPP flags: -I/usr/include -I/usr/local/include -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H<br style="">
configure: Package LIBS: -L/usr/lib -lgdal -L/usr/local/share/proj -lproj -lsqlite3<br style="">
configure: creating ./config.status<br style="">
config.status: creating src/Makevars<br style="">
** libs<br style="">
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<br style="">
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<br style="">
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<br style="">
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<br style="">
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<br style="">
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<br style="">
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<br style="">
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<br style="">
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<br style="">
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<br style="">
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<br style="">
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<br style="">
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<br style="">
installing to /usr/local/lib/R/site-library/00LOCK-rgdal/00new/rgdal/libs<br style="">
** R<br style="">
** data<br style="">
** inst<br style="">
** byte-compile and prepare package for lazy loading<br style="">
** help<br style="">
*** installing help indices<br style="">
** building package indices<br style="">
** installing vignettes<br style="">
** testing if installed package can be loaded from temporary location<br style="">
Error: package or namespace load failed for 'rgdal' in dyn.load(file, DLLpath = DLLpath, ...):<br style="">
unable to load shared object '/usr/local/lib/R/site-library/00LOCK-rgdal/00new/rgdal/libs/rgdal.so':<br style="">
/usr/local/lib/R/site-library/00LOCK-rgdal/00new/rgdal/libs/rgdal.so: undefined symbol: proj_create<br style="">
Error: loading failed<br style="">
Execution halted<br style="">
ERROR: loading failed<br style="">
* removing '/usr/local/lib/R/site-library/rgdal'<br style="">
> <br style="">
> <br style="">
<br style="">
The downloaded source packages are in<br style="">
'/tmp/Rtmpvt7qpB/downloaded_packages'<br style="">
Warning message:<br style="">
In install.packages("rgdal", repos = "http://R-Forge.R-project.org", :<br style="">
installation of package 'rgdal' had non-zero exit status<br style="">
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De :</b> Roger Bivand <Roger.Bivand@nhh.no><br>
<b>Envoyé :</b> mercredi 29 janvier 2020 16:06<br>
<b>À :</b> r-sig-geo@r-project.org; Arnaud De Groof<br>
<b>Objet :</b> Re: [R-sig-Geo] Error in the installation of rgdal on the docker osgeo/gdal:ubuntu-small</font>
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<div dir="auto" style="color:rgb(33,33,33); background-color:rgb(255,255,255); text-align:left">
For sp, install from CRAN, or for the development version, remotes::install_github("rsbivand/sp").</div>
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<br>
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<div dir="auto" style="color:rgb(33,33,33); background-color:rgb(255,255,255); text-align:left">
Roger</div>
<div id="ms-outlook-mobile-signature">
<div><br>
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Roger Bivand<br>
Norwegian School of Economics<br>
Bergen, Norway</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Arnaud De Groof <Arnaud.DeGroof@spacebel.be><br>
<b>Sent:</b> Wednesday, January 29, 2020 4:02:15 PM<br>
<b>To:</b> r-sig-geo@r-project.org <r-sig-geo@r-project.org>; Roger.Bivand@nhh.no <Roger.Bivand@nhh.no><br>
<b>Subject:</b> RE: [R-sig-Geo] Error in the installation of rgdal on the docker osgeo/gdal:ubuntu-small</font>
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<p></p>
Thanks Roger,<br>
<br>
I have modified the Dockerfile aiming to integrate sqlite3, libsqlite3-dev and rgdal from R-Forge:
<br>
<br>
<span style="font-size:10pt">RUN R -e "install.packages('rgdal', repos='</span><a href="https://clicktime.symantec.com/3W1CRQBg3PcUEAHSfQiiBZ86H2?u=http%3A%2F%2FR-Forge.R-project.org%27" target="_blank"><span style="font-size:10pt">http://R-Forge.R-project.org'</span></a><span style="font-size:10pt">,
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', '--with-proj-share=/usr/local/share/proj'))"</span><br>
<br>
Unfortunately, this package have a dependency to 'sp'. <br>
<br>
<span style="font-size:10pt">> install.packages('rgdal', repos='</span><a href="https://clicktime.symantec.com/3W1CRQBg3PcUEAHSfQiiBZ86H2?u=http%3A%2F%2FR-Forge.R-project.org%27" target="_blank"><span style="font-size:10pt">http://R-Forge.R-project.org'</span></a><span style="font-size:10pt">,
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', '--with-proj-share=/usr/local/share/proj'))</span><br style="font-size:10pt">
<span style="font-size:10pt">Installing package into '/usr/local/lib/R/site-library'</span><br style="font-size:10pt">
<span style="font-size:10pt">(as 'lib' is unspecified)</span><br style="font-size:10pt">
<span style="font-size:10pt">Warning: dependency 'sp' is not available</span><br style="font-size:10pt">
<span style="font-size:10pt">trying URL '</span><a href="https://clicktime.symantec.com/3J8mQkekNwnwWDJ5Keiid4f6H2?u=http%3A%2F%2FR-Forge.R-project.org%2Fsrc%2Fcontrib%2Frgdal_1.5-3.tar.gz%27" target="_blank"><span style="font-size:10pt">http://R-Forge.R-project.org/src/contrib/rgdal_1.5-3.tar.gz'</span></a><span style="font-size:10pt">;</span><br style="font-size:10pt">
<span style="font-size:10pt">Content type 'application/x-gzip' length 1774321 bytes (1.7 MB)</span><br style="font-size:10pt">
<span style="font-size:10pt">==================================================</span><br style="font-size:10pt">
<span style="font-size:10pt">downloaded 1.7 MB</span><br style="font-size:10pt">
<br style="font-size:10pt">
<span style="font-size:10pt">ERROR: dependency 'sp' is not available for package 'rgdal'</span><br style="font-size:10pt">
<span style="font-size:10pt">* removing '/usr/local/lib/R/site-library/rgdal'</span><br style="font-size:10pt">
<br style="font-size:10pt">
<span style="font-size:10pt">The downloaded source packages are in</span><br style="font-size:10pt">
<span style="font-size:10pt"> '/tmp/Rtmp0aIlx7/downloaded_packages'</span><br style="font-size:10pt">
<span style="font-size:10pt">Warning message:</span><br style="font-size:10pt">
<span style="font-size:10pt">In install.packages("rgdal", repos = "</span><a href="https://clicktime.symantec.com/3VzPWa39wDWRwnrEvCtCR6X6H2?u=http%3A%2F%2FR-Forge.R-project.org%2522" target="_blank"><span style="font-size:10pt">http://R-Forge.R-project.org"</span></a><span style="font-size:10pt">,
:</span><br style="font-size:10pt">
<span style="font-size:10pt"> installation of package 'rgdal' had non-zero exit status</span><br>
<br>
So, I added the package 'sp' : <br>
<br>
<span style="font-size:10pt">RUN R -e "install.packages('sp', repos='</span><a href="https://clicktime.symantec.com/3D1euyd15gp6hTrrvhrqbW76H2?u=http%3A%2F%2FR-Forge.R-project.org%27%29%2522" target="_blank"><span style="font-size:10pt">http://R-Forge.R-project.org')"</span></a><span style="font-size:10pt">;</span><br>
<br>
But this package seems not available for the version of R 3.6.2:<br>
<br>
<span style="font-size:10pt">install.packages('sp', repos='</span><a href="https://clicktime.symantec.com/3VhFK9P7V8QSvRQchfSEzwk6H2?u=http%3A%2F%2FR-Forge.R-project.org%27%29" target="_blank"><span style="font-size:10pt">http://R-Forge.R-project.org')</span></a><br style="font-size:10pt">
<span style="font-size:10pt">Installing package into '/usr/local/lib/R/site-library'</span><br style="font-size:10pt">
<span style="font-size:10pt">(as 'lib' is unspecified)</span><br style="font-size:10pt">
<span style="font-size:10pt">Warning message:</span><br style="font-size:10pt">
<span style="font-size:10pt">package 'sp' is not available (for R version 3.6.2) </span>
<div><span style="font-size:13.3333px"><br>
</span></div>
<div><span style="font-size:12pt">Solution : downgrade R?</span><br>
</div>
<div><span style="font-size:13.3333px"><span style="font-size:12pt"><br>
</span></span></div>
<div><span style="font-size:13.3333px"><span style="font-size:12pt">Thanks,</span><br style="font-size:12pt">
<br style="font-size:12pt">
<span style="font-size:12pt">Arnaud</span><br>
</span></div>
<div><span style="font-size:13.3333px"><br>
</span></div>
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