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.biv...@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@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.biv...@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.biv...@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 <ben...@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 <tea...@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
tea...@gmail.com (personal)
t...@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.biv...@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.biv...@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.biv...@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.biv...@nhh.no
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
_______________________________________________
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