It looks like you have multiple versions of GDAL and/or PROJ installed on your system; see https://github.com/r-spatial/sf the section on "Multiple GDAL, GEOS and/or PROJ versions on your system" and there the link to https://github.com/r-spatial/sf/issues/844 which contains a very ugly solution (setting LD_LIBRARY_PATH from within R).
On 11/17/18 1:57 PM, Emanuele Cordano wrote: > Dear list, > > I got the following segmentation fault error when I try to install rgdal on > my local Ubuntu 16.04 LTS machine. Did anyone encounter something similar? > Please below the error message with traceback and R session info. > Similar problems appears on > https://stackoverflow.com/questions/50064673/cannot-install-rgdal-package-in-local-server-an-irrecoverable-exception-occurre > which remains unsolved . In my case (see below) all checks, PROJ4 > included, were OK! > > Thank you for any kind of feedback > Best > Emanuele Cordano > > user@machine:~$ R > > R version 3.5.1 (2018-07-02) -- "Feather Spray" > 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. > > [Previously saved workspace restored] > >> install.packages("rgdal") > Installing package into ‘/home/ecor/R/x86_64-pc-linux-gnu-library/3.5’ > (as ‘lib’ is unspecified) > trying URL 'http://cran.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... yes > configure: svn revision: 773 > checking for gdal-config... /usr/bin/gdal-config > checking gdal-config usability... yes > configure: GDAL: 2.1.3 > checking GDAL version >= 1.11.4... yes > checking gdal: linking with --libs only... yes > checking GDAL: /usr/share/gdal/2.1/pcs.csv readable... yes > configure: pkg-config proj exists, will use it > configure: PROJ version: 4.9.2 > checking proj_api.h presence and usability... yes > checking PROJ version >= 4.8.0... yes > checking projects.h presence and usability... yes > checking PROJ.4: epsg found and readable... yes > checking PROJ.4: conus found and readable... yes > configure: Package CPP flags: -I/usr/include/gdal > configure: Package LIBS: -L/usr/lib -lgdal -lproj > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal > -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include" -fpic -g > -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g -c OGR_write.cpp -o OGR_write.o > g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal > -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include" -fpic -g > -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g -c gdal-bindings.cpp -o gdal-bindings.o > gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal > -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include" -fpic -g > -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o > gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal > -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include" -fpic -g > -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g -c inverser.c -o inverser.o > gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal > -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include" -fpic -g > -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g -c local_stubs.c -o local_stubs.o > g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal > -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include" -fpic -g > -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g -c ogr_geom.cpp -o ogr_geom.o > gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal > -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include" -fpic -g > -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g -c ogr_polygons.c -o ogr_polygons.o > g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal > -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include" -fpic -g > -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g -c ogr_proj.cpp -o ogr_proj.o > g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal > -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include" -fpic -g > -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g -c ogrdrivers.cpp -o ogrdrivers.o > g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal > -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include" -fpic -g > -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g -c ogrsource.cpp -o ogrsource.o > g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/gdal > -I"/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/sp/include" -fpic -g > -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g -c projectit.cpp -o projectit.o > g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions > -Wl,-z,relro -o rgdal.so OGR_write.o gdal-bindings.o init.o inverser.o > local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o ogrdrivers.o ogrsource.o > projectit.o -L/usr/lib -lgdal -lproj -L/usr/lib/R/lib -lR > installing to /home/ecor/R/x86_64-pc-linux-gnu-library/3.5/rgdal/libs > ** R > ** data > ** inst > ** byte-compile and prepare package for lazy loading > ** help > *** installing help indices > ** building package indices > ** installing vignettes > ** testing if installed package can be loaded > > *** caught segfault *** > address 0x20, cause 'memory not mapped' > > Traceback: > 1: assign("has_proj_def.dat", .Call("PROJ4_proj_def_dat_Installed", > PACKAGE = "rgdal"), envir = .RGDAL_CACHE) > 2: fun(libname, pkgname) > 3: doTryCatch(return(expr), name, parentenv, handler) > 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 5: tryCatchList(expr, classes, parentenv, handlers) > 6: tryCatch(fun(libname, pkgname), error = identity) > 7: runHook(".onLoad", env, package.lib, package) > 8: loadNamespace(package, lib.loc) > 9: doTryCatch(return(expr), name, parentenv, handler) > 10: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 11: tryCatchList(expr, classes, parentenv, handlers) > 12: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- > loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, > deps)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) > paste(" in", deparse(cc)[1L]) else "" msg <- > gettextf("package or namespace load failed for %s%s:\n %s", > sQuote(package), P, conditionMessage(e)) if (logical.return) > message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, > domain = NA)}) > 13: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return > = TRUE) > 14: withCallingHandlers(expr, packageStartupMessage = function(c) > invokeRestart("muffleMessage")) > 15: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, > character.only = TRUE, logical.return = TRUE)) > 16: doTryCatch(return(expr), name, parentenv, handler) > 17: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 18: tryCatchList(expr, classes, parentenv, handlers) > 19: tryCatch(expr, error = function(e) { call <- conditionCall(e) if > (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) > call <- sys.call(-4L) dcall <- deparse(call)[1L] > prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- > strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, > type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w > <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = > "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } > else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), > "\n") .Internal(seterrmessage(msg[1L])) if (!silent && > isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) > .Internal(printDeferredWarnings()) } invisible(structure(msg, > class = "try-error", condition = e))}) > 20: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib, > character.only = TRUE, logical.return = TRUE))) > 21: tools:::.test_load_package("rgdal", > "/home/ecor/R/x86_64-pc-linux-gnu-library/3.5") > An irrecoverable exception occurred. R is aborting now ... > Segmentation fault (core dumped) > ERROR: loading failed > * removing ‘/home/ecor/R/x86_64-pc-linux-gnu-library/3.5/rgdal’ > > The downloaded source packages are in > ‘/tmp/Rtmpq9SibK/downloaded_packages’ > Warning message: > In install.packages("rgdal") : > installation of package ‘rgdal’ had non-zero exit status >> sessionInfo() > R version 3.5.1 (2018-07-02) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 16.04.5 LTS > > Matrix products: default > BLAS: /usr/lib/libblas/libblas.so.3.6.0 > LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_IE.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_IE.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_IE.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_IE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] compiler_3.5.1 tools_3.5.1 >> > -- Edzer Pebesma Institute for Geoinformatics Heisenbergstrasse 2, 48151 Muenster, Germany Phone: +49 251 8333081
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