[R-sig-Geo] Trouble installing rgdal

Thomas Adams te@3rd @end|ng |rom gm@||@com
Fri Jul 3 11:52:13 CEST 2020 

Hi Roger,

I just tried re-installing withou using the argument and got this:

teaiii using 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 using 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 using 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 using 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 using 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 using gmail.com (personal)
> >>>>> tea using terrapredictions.org (work)
> >>>>>
> >>>>> 1 (513) 739-9512 (cell)
> >>>>>
> >>>>>         [[alternative HTML version deleted]]
> >>>>>
> >>>>> _______________________________________________
> >>>>> R-sig-Geo mailing list
> >>>>> R-sig-Geo using 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 using 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 using 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 using gmail.com (personal)
tea using terrapredictions.org (work)

1 (513) 739-9512 (cell)

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