[R-sig-Geo] rgdal 1.1-3 compilation: error of ogrsource.cpp
Bede-Fazekas Ákos
bfalevlist at gmail.com
Sun Jan 31 12:21:50 CET 2016
Dear Roger,
it is really probable that some gdal versions were mixed. It was long
time ago when I installed gdal but as far as I remember it was compiled
from source. I would be very happy if I could uninstall it and start
again from the base, but don't know how to do it. "make uninstall"
fails, reinstalling also fails, no other ways I'm aware of.
Thanks for any help,
Ákos
2016.01.30. 17:33 keltezéssel, Roger Bivand írta:
> On Sat, 30 Jan 2016, Bede-Fazekas Ákos wrote:
>
>> Dear List,
>> please let me know what I'm doing wrong. Installing package rgdal
>> 1.1-3 with install.packages("rgdal") fails on Ubuntu 14 (gdal
>> version: 2.0.0) with this error message during the compilation:
>> *ogrsource.cpp:413:10: error: ‘OFTInteger64’ was not declared in this
>> scope.*
>>
>> The gdal-version info, verbose output of package installation and
>> sessionInfo() is provided after my signature.
>
> Thanks for a clear report. The GDAL version is declared as 2.0.0. The
> released 2.0.* implement RFC 31:
>
> (https://trac.osgeo.org/gdal/wiki/rfc31_ogr_64)
>
> using long integers for FIDs and allowing them as field values. Since
> the GDAL you are using declares itself as 2.*, the code forks to take
> advantage of the new capability.
>
> How did you install GDAL? Is it possible that the version you have is
> pre-release? The development trunk was named 2.0.0 for quite a long
> time, but implementations of changes happened at different times along
> the way? Is it possible that you have mixed (multiple) GDAL
> installations, with 1.* headers and 2.0 gdal-config?
>
> Roger
>
>> However the R version is the latest (3.2.3), installation of the
>> package failed with similar error message on my previously used R
>> version (3.0.2), and therefore I think that the problem is nothing to
>> do with R.
>> Removing and reinstalling libgdal1-dev, libproj-dev, gdal-bin does
>> not solve the problem. Running R as root user produce similar error.
>>
>> Any help is gratefully appreciated,
>> Ákos Bede-Fazekas
>> Hungarian Academy of Sciences
>>
>>
>> ----------------
>> gdal-config --version
>> 2.0.0
>>
>> ogr2ogr --version
>> GDAL 2.0.0dev, released 2014/04/16
>>
>> ----------------
>> configure: CC: gcc -std=gnu99
>> configure: CXX: g++
>> configure: rgdal: 1.1-3
>> checking for /usr/bin/svnversion... yes
>> configure: svn revision: 594
>> checking for gdal-config... /usr/local/bin/gdal-config
>> checking gdal-config usability... yes
>> configure: GDAL: 2.0.0
>> checking GDAL version >= 1.6.3... yes
>> configure: experimental conditional use of GDAL2
>> checking for gcc... gcc -std=gnu99
>> 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 gcc -std=gnu99 accepts -g... yes
>> checking for gcc -std=gnu99 option to accept ISO C89... none needed
>> checking how to run the C preprocessor... gcc -std=gnu99 -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 gdal.h usability... yes
>> checking gdal.h presence... yes
>> checking for gdal.h... yes
>> checking gdal: linking with --libs only... yes
>> checking GDAL: /usr/local/share/gdal/pcs.csv readable... yes
>> checking proj_api.h usability... yes
>> checking proj_api.h presence... yes
>> checking for proj_api.h... yes
>> checking for pj_init_plus in -lproj... yes
>> configure: PROJ.4 version: 4.8.0
>> checking PROJ.4: epsg found and readable... yes
>> checking PROJ.4: conus found and readable... yes
>> configure: Package CPP flags: -I/usr/local/include
>> configure: Package LIBS: -L/usr/local/lib -lgdal -lproj
>> configure: creating ./config.status
>> config.status: creating src/Makevars
>> ** libs
>> g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I/usr/local/include
>> -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2
>> -fstack-protector --param=ssp-buffer-size=4 -Wformat
>> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c OGR_write.cpp -o
>> OGR_write.o
>> g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I/usr/local/include
>> -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2
>> -fstack-protector --param=ssp-buffer-size=4 -Wformat
>> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c gdal-bindings.cpp
>> -o gdal-bindings.o
>> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/local/include
>> -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2
>> -fstack-protector --param=ssp-buffer-size=4 -Wformat
>> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
>> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/local/include
>> -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2
>> -fstack-protector --param=ssp-buffer-size=4 -Wformat
>> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c local_stubs.c -o
>> local_stubs.o
>> g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I/usr/local/include
>> -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2
>> -fstack-protector --param=ssp-buffer-size=4 -Wformat
>> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ogr_geom.cpp -o
>> ogr_geom.o
>> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/local/include
>> -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2
>> -fstack-protector --param=ssp-buffer-size=4 -Wformat
>> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ogr_polygons.c -o
>> ogr_polygons.o
>> g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I/usr/local/include
>> -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2
>> -fstack-protector --param=ssp-buffer-size=4 -Wformat
>> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ogr_proj.cpp -o
>> ogr_proj.o
>> g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I/usr/local/include
>> -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2
>> -fstack-protector --param=ssp-buffer-size=4 -Wformat
>> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ogrdrivers.cpp -o
>> ogrdrivers.o
>> g++ -std=c++11 -I/usr/share/R/include -DNDEBUG -I/usr/local/include
>> -I"/usr/local/lib/R/site-library/sp/include" -fpic -g -O2
>> -fstack-protector --param=ssp-buffer-size=4 -Wformat
>> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ogrsource.cpp -o
>> ogrsource.o
>> ogrsource.cpp: In function ‘SEXPREC* ogrReadColumn(OGRLayer*, SEXP,
>> int, int)’:
>> ogrsource.cpp:413:10: error: ‘OFTInteger64’ was not declared in this
>> scope
>> case OFTInteger64:
>> ^
>> ogrsource.cpp:470:12: error: ‘OFTInteger64’ was not declared in this
>> scope
>> case OFTInteger64:
>> ^
>> ogrsource.cpp:476:45: error: ‘class OGRFeature’ has no member named
>> ‘GetFieldAsInteger64’
>> GIntBig nVal64 = poFeature->GetFieldAsInteger64(iField);
>> ^
>> ogrsource.cpp: In function ‘SEXPREC* ogrReadListColumn(OGRLayer*,
>> SEXP, int, int, int)’:
>> ogrsource.cpp:575:10: error: ‘OFTInteger64List’ was not declared in
>> this scope
>> case OFTInteger64List:
>> ^
>> ogrsource.cpp:618:14: error: ‘OFTInteger64List’ was not declared in
>> this scope
>> case OFTInteger64List:
>> ^
>> ogrsource.cpp:619:28: error: ‘union OGRField’ has no member named
>> ‘Integer64List’
>> nlist = psField->Integer64List.nCount;
>> ^
>> ogrsource.cpp:626:32: error: ‘union OGRField’ has no member named
>> ‘Integer64List’
>> psField->Integer64List.paList[k]);
>> ^
>> ogrsource.cpp:629:43: error: ‘union OGRField’ has no member named
>> ‘Integer64List’
>> GIntBig nVal64 = psField->Integer64List.paList[k];
>> ^
>> make: *** [ogrsource.o] Error 1
>> ERROR: compilation failed for package ‘rgdal’
>> * removing ‘/usr/local/lib/R/site-library/rgdal’
>>
>> The downloaded source packages are in
>> ‘/tmp/RtmpcN1Gpn/downloaded_packages’
>> Warning message:
>> In install.packages("rgdal") :
>> installation of package ‘rgdal’ had non-zero exit status
>>
>>
>> ----------------
>>> sessionInfo()
>> R version 3.2.3 (2015-12-10)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 14.04.3 LTS
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> loaded via a namespace (and not attached):
>> [1] tools_3.2.3
>>
>> _______________________________________________
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>> R-sig-Geo at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>>
>
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