[R-sig-Geo] Trouble installing rgdal

Roger Bivand Roger@B|v@nd @end|ng |rom nhh@no
Fri Jul 3 12:08:09 CEST 2020 

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.

Roger

>
> 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
>
>
>
>

-- 
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

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