Trouble installing rgdal

Roger,

OK; I'll update GDAL and PROJ to 3.0.4 and 6.3.1 and get back to you... you
anticipated my question... thank you!

Best,
Tom

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 '
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)

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 _______________________________________________
 R-sig-Geo mailing list
 R-sig-Geo at r-project.org
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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

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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Trouble installing rgdal

Thread (13 messages)