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_...@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@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 >> >> > _______________________________________________ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
