[R-sig-Geo] Problem installing rgdal

[Alex M]

On 11/6/18 09:31, Jeremy Kraft wrote:
> Hello,
> 
> I'm trying to reinstall rgdal, but I have a problem with the sqlite
> dependency.
> Below is the R output.
> 
> Does someone knows how to solve the problem?
> 
> Thanks,
> 
> Jeremy
> 
> -------------------------------------------------------------------------------------------------------------------------------
> jeremy using yuri-HP-ProBook-640-G1:/$ R
> 
> R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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> Platform: x86_64-pc-linux-gnu (64-bit)
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> 
>> install.packages('rgdal')
> Installing package into ‘/home/jeremy/R/x86_64-pc-linux-gnu-library/3.4’
> (as ‘lib’ is unspecified)
> trying URL 'https://cloud.r-project.org/src/contrib/rgdal_1.3-6.tar.gz'
> Content type 'application/x-gzip' length 1666975 bytes (1.6 MB)
> ==================================================
> downloaded 1.6 MB
> 
> * installing *source* package ‘rgdal’ ...
> ** package ‘rgdal’ successfully unpacked and MD5 sums checked
> configure: R_HOME: /usr/lib/R
> configure: CC: gcc -std=gnu99
> configure: CXX: g++
> configure: C++11 support available
> configure: rgdal: 1.3-6
> checking for /usr/bin/svnversion... no
> configure: svn revision: 773
> checking for gdal-config... /usr/bin/gdal-config
> checking gdal-config usability... yes
> configure: GDAL: 2.2.3
> checking GDAL version >= 1.11.4... yes
> checking gdal: linking with --libs only... no
> checking gdal: linking with --libs and --dep-libs... no
> /usr/bin/ld: /usr/lib/libgdal.a(genbindataset.o): relocation R_X86_64_32
> against `.rodata.str1.8' can not be used when making a PIE object;
> recompile with -fPIC
> /usr/bin/ld: /usr/lib/libgdal.a(geotiff.o): relocation R_X86_64_32 against
> `.rodata.str1.1' can not be used when making a PIE object; recompile with
> -fPIC
> /usr/bin/ld: /usr/lib/libgdal.a(gff_dataset.o): relocation R_X86_64_32S
> against hidden symbol `_ZTV10GFFDataset' can not be used when making a PIE
> object
> 
> *
> * Long list
> *
> /usr/bin/ld: /usr/lib/libgdal.a(gmlhandler.o): relocation R_X86_64_32
> against `.rodata.str1.1' can not be used when making a PIE object;
> recompile with -fPIC
> /usr/bin/ld: /usr/lib/libgdal.a(ili2handler.o): relocation R_X86_64_32S
> against hidden symbol `_ZTV11ILI2Handler' can not be used when making a PIE
> object
> /usr/bin/ld: /usr/lib/libgdal.a(nashandler.o): relocation R_X86_64_32
> against `.rodata.str1.8' can not be used when making a PIE object;
> recompile with -fPIC
> /usr/bin/ld: /usr/lib/libgdal.a(ntf_codelist.o): relocation R_X86_64_32
> against `.rodata.str1.1' can not be used when making a PIE object;
> recompile with -fPIC
> /usr/bin/ld: /usr/lib/libgdal.a(ntf_estlayers.o): relocation R_X86_64_32S
> against hidden symbol `_ZN11OGRNTFLayer12GetLayerDefnEv' can not be used
> when making a PIE object
> /usr/bin/ld: /usr/lib/libgdal.a(ntf_raster.o): relocation R_X86_64_32S
> against hidden symbol `_ZTV17OGRNTFRasterLayer' can not be used when making
> a PIE object
> /usr/bin/ld: /usr/lib/libgdal.a(ogrmssqlgeometryparser.o): relocation
> R_X86_64_32S against `.rodata' can not be used when making a PIE object;
> recompile with -fPIC
> /usr/bin/ld: final link failed: Nonrepresentable section on output
> collect2: error: ld returned 1 exit status
> /usr/bin/ld: /usr/lib/libgdal.a(ogrsqliteapiroutines.o): undefined
> reference to symbol 'sqlite3_prepare'
> /usr/lib/x86_64-linux-gnu/libsqlite3.so.0: error adding symbols: DSO
> missing from command line
> collect2: error: ld returned 1 exit status
> configure: Install failure: compilation and/or linkage problems.
> configure: error: GDALAllRegister not found in libgdal.
> ERROR: configuration failed for package ‘rgdal’
> * removing ‘/home/jeremy/R/x86_64-pc-linux-gnu-library/3.4/rgdal’
> 
> The downloaded source packages are in
>     ‘/tmp/RtmpKSJ85K/downloaded_packages’
> Warning message:
> In install.packages("rgdal") :
>   installation of package ‘rgdal’ had non-zero exit status
> 
>

Looks like an issue with your system libgdal-dev package, perhaps
reinstall the system dependencies. Which OS are you installing on?

Thanks,
Alex