Trouble installing rgdal
The revisions needed to install on PROJ 6.1.0 and GDAL 3.0.0 involved a compiled function that only entered PROJ in 6.2.0, another that only entered GDAL in 3.0.1, and bugs in handling +proj=ob_tran in PROJ 6.0.0, 6.1.0 and 6.1.1. Revision 1031 covering these and letting rgdal install on these (oldish) versions has been committed to R-Forge, and when the build completes will answer the intial question. The package installed using the old PROJ API because that choice also avoided the problem with GDAL, but didn't advance to being able to use WKT2 instead of Proj4 strings internally (with sp >= 1.4). In any case, GDAL 3.0.4 and PROJ 6.3.1 or later is a safer choice, but at least now those obliged to stay with earlier GDAL 3 and PROJ 6 should be covered. Roger
On Sat, 4 Jul 2020, Thomas Adams wrote:
Hi Roger! I updated GDAL and PROJ to 3.0.4 and 6.3.1, respectively... the install worked perfectly using: sudo R CMD INSTALL rgdal_1.5-13.tar.gz Thank you so much! Best, Tom On Fri, Jul 3, 2020 at 11:24 AM Roger Bivand <Roger.Bivand at nhh.no> wrote:
On Fri, 3 Jul 2020, Roger Bivand wrote:
On Fri, 3 Jul 2020, Thomas Adams wrote:
Hi Roger, I just tried re-installing withou using the argument and got this:
Very useful, thanks - painful but another case of staying too close to
the
front. proj_create_crs_to_crs_from_pj() was new in PROJ 6.2.0. I'll try
to
adapt to accommodate older PROJ 6.
Re-creating a GDAL 3.0.0 with PROJ 6.1.0 platform has thrown up another issue which which I'm struggling. I'll try to resolve it, but until then advice would be to update GDAL and PROJ to 3.0.4 and 6.3.1, which we know work (those are the versions in the CRAN Windows binary). Roger
Roger
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 '
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)
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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 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
-- 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