[R-sig-Geo] Problem installing rgdal

[Alex M]

Jeremy,

Please keep the thread on list so every-one can see the
discussion/solution (reply-all).

I don't have a 18.10 box to test on quickly. But can you review what
steps you did, ie: what system packages did you install before
attempting to install rgdal? Usually you need libgdal-dev libproj-dev
and perhaps libsqlite3-dev libgeos-dev (all of these are supposed to be
dependencies of libgdal-dev).

Also it might be good to jump this over to the R-sig-debian list where
many people are familiar with the OS
https://stat.ethz.ch/mailman/listinfo/r-sig-debian (also covers ubuntu &
mint, all debian derivatives). One option is usually the marutter ppa
which has system packages for cran libraries, however it doesn't appear
to support 18.10 yet
http://sites.psu.edu/theubunturblog/installing-r-in-ubuntu/

Thanks,
Alex


On 11/7/18 01:51, Jeremy Kraft wrote:
> I'm on linux, ubuntu 18.10. I've been trying to reinstall  libgdal-dev but
> that did not solve the problem.
> 
> Thanks,
> 
> On Tue, Nov 6, 2018 at 7:12 PM Alex M <tech_dev using wildintellect.com> wrote:
> 
>> 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"
>>> Copyright (C) 2018 The R Foundation for Statistical Computing
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>
>>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>>> You are welcome to redistribute it under certain conditions.
>>> Type 'license()' or 'licence()' for distribution details.
>>>
>>>   Natural language support but running in an English locale
>>>
>>> R is a collaborative project with many contributors.
>>> Type 'contributors()' for more information and
>>> 'citation()' on how to cite R or R packages in publications.
>>>
>>> Type 'demo()' for some demos, 'help()' for on-line help, or
>>> 'help.start()' for an HTML browser interface to help.
>>> Type 'q()' to quit R.
>>>
>>>> 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
>>
>>
>