[R-sig-Geo] rgdal 1.1-3 compilation: error of ogrsource.cpp
Roger Bivand
Roger.Bivand at nhh.no
Sun Jan 31 13:59:17 CET 2016
On Sun, 31 Jan 2016, Bede-Fazekas Ákos wrote:
> 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.
Looking more closely at your report, I see:
>> > ogr2ogr --version
>> > GDAL 2.0.0dev, released 2014/04/16
2.0.0 was released in June 2015 (and 2.0.2 has just been released). You
very likely have installed headers that date from before the revisions
introducing handling of 64-bit integers, but where the version of GDAL
declares itself to be 2.0.0. I suggest you use locate from the shell to
find any ogr_api.h files on your system. You could use
gdal-config --cflags
but this could be misleading if you have multiple gdal-config installed.
Find out whether any ogr_api.h contains references to GIntBig, and delete
all prior to that. It may be safest to locate all the *gdal*, *cpl* and
*ogr* components and remove them, running make install again from a fresh
source build of GDAL 2.0.2.
Hope this helps,
Roger
> 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
>> >
>> > _______________________________________________
>> > R-sig-Geo mailing list
>> > R-sig-Geo at r-project.org
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>> >
>> >
>>
>
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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; fax +47 55 95 91 00
e-mail: Roger.Bivand at nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
http://depsy.org/person/434412
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