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 > -- Emanuele Cordano, PhD Environmental Engineer / Ingegnere per l' Ambiente e il territorio nr. 3587 (Albo A - Provincia di Trento) cell: +39 3282818564 email: emanuele.cord...@gmail.com,emanuele.cord...@rendena100.eu, emanuele.cord...@eurac.edu PEC: emanuele.cord...@ingpec.eu URL: www.rendena100.eu LinkedIn: https://www.linkedin.com/in/emanuele-cordano-31995333 GitHub: https://github.com/ecor [[alternative HTML version deleted]] _______________________________________________ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo