[R-sig-Geo] Problem installing rgdal

Thu Nov 8 10:11:45 CET 2018

Thanks Alex for the help!

I managed to solve the problem:

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
I did:
• ubuntu-gis repository wasn't added correctly, but was added 5 times. I
removed everything ubuntu-gis related from `sources.list.d`
• I removed and purged `r-base`, `r-core`, `gdal-bin`, `libgdal-dev`, and
did autoremove aufterwards.
• rebooted
• added ubuntu-gis correctly (the way their webpage suggested), installed
`gdal-bin`, `libgdal-dev`, `R` + packages. No errors whatsoever.

On Wed, Nov 7, 2018 at 6:33 PM Alex M <tech_dev using wildintellect.com> wrote:

> 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
> >>
> >>
> >
>
>

-- 
Jeremy Kraft
Data Scientist

Parkbob GmbH
jeremy.kraft using parkbob.com <ivan.kasanicky using parkbob.com>
www.parkbob.com
FN 430551 p FB-Gericht: Handelsgericht Wien

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