Trouble installing rgdal
Hi Roger,
I just tried re-installing withou using the argument and got this:
teaiii at teaiii-Leopard-WS:~$ sudo R CMD INSTALL rgdal_1.5-13.tar.gz
* installing to library ?/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0?
* installing *source* package ?rgdal? ...
** using staged installation
configure: R_HOME: /usr/local/lib/R
configure: CC: gcc
configure: CXX: g++ -std=gnu++11
configure: CFLAGS: -g -O2
configure: CPPFLAGS: -I/usr/local/include
configure: CXXFLAGS: -g -O2
configure: LDFLAGS: -L/usr/local/lib
configure: LDFLAGS: -L/usr/local/lib
configure: CXX11 is: g++, CXX11STD is: -std=gnu++11
configure: CXX is: g++ -std=gnu++11
configure: C++11 support available
configure: rgdal: 1.5-13
checking for /usr/bin/svnversion... yes
cat: inst/SVN_VERSION: No such file or directory
configure: svn revision:
checking for gdal-config... /usr/local/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.0.0
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/local/share/gdal/stateplane.csv readable... yes
configure: pkg-config proj exists, will use it
configure: PROJ version: 6.1.0
configure: PROJ CPP flags: -DPROJ_H_API -I/usr/local/include
configure: PROJ LIBS: -L/usr/local/lib -lproj
checking PROJ header API:... yes
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 g++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... g++ -std=gnu++11 -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 proj.h usability... yes
checking proj.h presence... yes
checking for proj.h... yes
checking for proj_context_create in -lproj... yes
checking Using GDAL < 3 with PROJ >= 6... no
checking PROJ version >= 4.8.0... yes
checking PROJ: proj.db found and readable... yes
configure: Package CPP flags: -I/usr/local/include -I/usr/local/include
-DPROJ_H_API
configure: Package LIBS: -L/usr/local/lib -lgdal -L/usr/local/lib -lproj
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include
-I/usr/local/include -DPROJ_H_API
-I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
-I/usr/local/include -fpic -g -O2 -c OGR_write.cpp -o OGR_write.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include
-I/usr/local/include -DPROJ_H_API
-I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
-I/usr/local/include -fpic -g -O2 -c gdal-bindings.cpp -o
gdal-bindings.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include
-I/usr/local/include -DPROJ_H_API
-I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
-I/usr/local/include -fpic -g -O2 -c init.c -o init.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include
-I/usr/local/include -DPROJ_H_API
-I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
-I/usr/local/include -fpic -g -O2 -c inverser.c -o inverser.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include
-I/usr/local/include -DPROJ_H_API
-I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
-I/usr/local/include -fpic -g -O2 -c local_stubs.c -o local_stubs.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include
-I/usr/local/include -DPROJ_H_API
-I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
-I/usr/local/include -fpic -g -O2 -c ogr_geom.cpp -o ogr_geom.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include
-I/usr/local/include -DPROJ_H_API
-I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
-I/usr/local/include -fpic -g -O2 -c ogr_polygons.c -o ogr_polygons.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include
-I/usr/local/include -DPROJ_H_API
-I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
-I/usr/local/include -fpic -g -O2 -c ogr_proj.cpp -o ogr_proj.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include
-I/usr/local/include -DPROJ_H_API
-I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
-I/usr/local/include -fpic -g -O2 -c ogrdrivers.cpp -o ogrdrivers.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include
-I/usr/local/include -DPROJ_H_API
-I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
-I/usr/local/include -fpic -g -O2 -c ogrsource.cpp -o ogrsource.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include
-I/usr/local/include -DPROJ_H_API
-I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include'
-I/usr/local/include -fpic -g -O2 -c proj6.cpp -o proj6.o
proj6.cpp: In function ?SEXPREC* transform_ng(SEXP, SEXP, SEXP, SEXP, SEXP,
SEXP, SEXP)?:
proj6.cpp:521:29: error: ?proj_create_crs_to_crs_from_pj? was not declared
in this scope
if ((pj_transform = proj_create_crs_to_crs_from_pj(PJ_DEFAULT_CTX,
source_crs,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
proj6.cpp:521:29: note: suggested alternative: ?proj_create_crs_to_crs?
if ((pj_transform = proj_create_crs_to_crs_from_pj(PJ_DEFAULT_CTX,
source_crs,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
proj_create_crs_to_crs
proj6.cpp: In function ?SEXPREC* project_ng_coordOp(SEXP, SEXP)?:
proj6.cpp:704:33: error: ?proj_create_crs_to_crs_from_pj? was not declared
in this scope
if (use_inv) pj_transform =
proj_create_crs_to_crs_from_pj(PJ_DEFAULT_CTX, target_crs,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
proj6.cpp:704:33: note: suggested alternative: ?proj_create_crs_to_crs?
if (use_inv) pj_transform =
proj_create_crs_to_crs_from_pj(PJ_DEFAULT_CTX, target_crs,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
proj_create_crs_to_crs
proj6.cpp:706:25: error: ?proj_create_crs_to_crs_from_pj? was not declared
in this scope
else pj_transform = proj_create_crs_to_crs_from_pj(PJ_DEFAULT_CTX,
source_crs,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
proj6.cpp:706:25: note: suggested alternative: ?proj_create_crs_to_crs?
else pj_transform = proj_create_crs_to_crs_from_pj(PJ_DEFAULT_CTX,
source_crs,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
proj_create_crs_to_crs
/usr/local/lib/R/etc/Makeconf:176: recipe for target 'proj6.o' failed
make: *** [proj6.o] Error 1
ERROR: compilation failed for package ?rgdal?
* removing ?/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/rgdal?
* restoring previous ?/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/rgdal?
On Fri, Jul 3, 2020 at 5:45 AM Roger Bivand <Roger.Bivand at nhh.no> wrote:
On Thu, 2 Jul 2020, Thomas Adams wrote:
Roger, Thank you so much; after downloading the *.tar.gz file, the that did the trick, using: sudo R CMD INSTALL --configure-args=--with-proj_api="proj_api.h" rgdal_1.5-13.tar.gz
Since you have GDAL: 3.0.0 and PROJ version: 6.1.0, you can drop --configure-args=--with-proj_api="proj_api.h", which is only needed if GDAL < 3 and PROJ >= 6. I'm uncertain how stable a system will be if GDAL
= 3 && PROJ >= 6 with this configure argument, as it is only a
work-around for systems with GDAL < 3 and PROJ >= 6, and onnly tested in that setting. Thanks for reporting back! Roger
Best regards! Tom On Thu, Jul 2, 2020 at 3:15 PM Roger Bivand <Roger.Bivand at nhh.no> wrote:
On Thu, 2 Jul 2020, Thomas Adams wrote:
Hi Bennet! Thank you for your help, but I get the same error...
Tom, Once rgdal revision 1029 completes building (check first) on: https://r-forge.r-project.org/R/?group_id=884 please re-try. The missing function is not in the GDAL 3.0.0 headers,
but
is in the 3.0.1 headers. I've modified the check so as not to try for
just
= 3 to >= 3.0.1.
Roger
Tom On Thu, Jul 2, 2020 at 2:01 PM Bennet Fauber <bennet at umich.edu> wrote:
You might try this
install.packages("rgdal", "/sw/arcts/centos7/Rgeospatial/062020",
repos="http://R-Forge.R-project.org")
as there have been recent patches to rgdal that might help that have
been incorporated there.
On Thu, Jul 2, 2020 at 1:47 PM Thomas Adams <tea3rd at gmail.com> wrote:
Hi all, I have searched the internet and have spent a few days trying to get
to
the
problem when I try to install rgdal into my Ubuntu 18.04 system. I
have
done this many times previously, but cannot seem to track down what I
am
doing wrong now. I have tried a forced install from sources with and without dependencies. Below is what I get. Any help is appreciated. Tom
install.packages("rgdal")
Installing package into
?/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0?
(as ?lib? is unspecified) trying URL 'https://cran.case.edu/src/contrib/rgdal_1.5-12.tar.gz' Content type 'application/x-gzip' length 2302403 bytes (2.2 MB) ================================================== downloaded 2.2 MB * installing *source* package ?rgdal? ... ** package ?rgdal? successfully unpacked and MD5 sums checked ** using staged installation configure: R_HOME: /usr/local/lib/R configure: CC: gcc configure: CXX: g++ -std=gnu++11 configure: CXX11 is: g++, CXX11STD is: -std=gnu++11 configure: CXX is: g++ -std=gnu++11 configure: C++11 support available configure: rgdal: 1.5-12 checking for /usr/bin/svnversion... yes configure: svn revision: 1018 checking for gdal-config... /usr/local/bin/gdal-config checking gdal-config usability... yes configure: GDAL: 3.0.0 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/local/share/gdal/stateplane.csv readable... yes configure: pkg-config proj exists, will use it configure: PROJ version: 6.1.0 configure: PROJ CPP flags: -DPROJ_H_API -I/usr/local/include configure: PROJ LIBS: -L/usr/local/lib -lproj checking PROJ header API:... yes 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 g++ -std=gnu++11 accepts -g... yes checking how to run the C++ preprocessor... g++ -std=gnu++11 -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 proj.h usability... yes checking proj.h presence... yes checking for proj.h... yes checking for proj_context_create in -lproj... yes checking Using GDAL < 3 with PROJ >= 6... no checking PROJ version >= 4.8.0... yes checking PROJ: proj.db found and readable... yes configure: Package CPP flags: -I/usr/local/include
-I/usr/local/include
-DPROJ_H_API configure: Package LIBS: -L/usr/local/lib -lgdal -L/usr/local/lib
-lproj
configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG
-I/usr/local/include
-I/usr/local/include -DPROJ_H_API -I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include' -I/usr/local/include -fpic -g -O2 -c OGR_write.cpp -o OGR_write.o g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG
-I/usr/local/include
-I/usr/local/include -DPROJ_H_API -I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include' -I/usr/local/include -fpic -g -O2 -c gdal-bindings.cpp -o gdal-bindings.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DPROJ_H_API -I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include' -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DPROJ_H_API -I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include' -I/usr/local/include -fpic -g -O2 -c inverser.c -o inverser.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DPROJ_H_API -I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include' -I/usr/local/include -fpic -g -O2 -c local_stubs.c -o
local_stubs.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG
-I/usr/local/include
-I/usr/local/include -DPROJ_H_API -I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include' -I/usr/local/include -fpic -g -O2 -c ogr_geom.cpp -o ogr_geom.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DPROJ_H_API -I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include' -I/usr/local/include -fpic -g -O2 -c ogr_polygons.c -o
ogr_polygons.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG
-I/usr/local/include
-I/usr/local/include -DPROJ_H_API -I'/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/sp/include' -I/usr/local/include -fpic -g -O2 -c ogr_proj.cpp -o ogr_proj.o ogr_proj.cpp: In function ?SEXPREC* R_GDAL_OSR_PROJ()?: ogr_proj.cpp:163:9: error: ?OSRGetPROJVersion? was not declared in
this
scope
OSRGetPROJVersion(&pnMajor, &pnMinor, &pnPatch);
^~~~~~~~~~~~~~~~~
ogr_proj.cpp:163:9: note: suggested alternative: ?OSRProjVersion?
OSRGetPROJVersion(&pnMajor, &pnMinor, &pnPatch);
^~~~~~~~~~~~~~~~~
OSRProjVersion
/usr/local/lib/R/etc/Makeconf:176: recipe for target 'ogr_proj.o'
failed
make: *** [ogr_proj.o] Error 1
ERROR: compilation failed for package ?rgdal?
* removing ?/home/teaiii/R/x86_64-pc-linux-gnu-library/4.0/rgdal?
The downloaded source packages are in
?/tmp/RtmpNkdFOf/downloaded_packages?
Warning message:
In install.packages("rgdal") :
installation of package ?rgdal? had non-zero exit status
--
Thomas E Adams, III
1724 Sage Lane
Blacksburg, VA 24060
tea3rd at gmail.com (personal)
tea at terrapredictions.org (work)
1 (513) 739-9512 (cell)
[[alternative HTML version deleted]]
_______________________________________________ R-sig-Geo mailing list R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
-- 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 at nhh.no https://orcid.org/0000-0003-2392-6140 https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
-- 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 at nhh.no https://orcid.org/0000-0003-2392-6140 https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
Thomas E Adams, III 1724 Sage Lane Blacksburg, VA 24060 tea3rd at gmail.com (personal) tea at terrapredictions.org (work) 1 (513) 739-9512 (cell) [[alternative HTML version deleted]]