Problem installing rgdal
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 at 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