[R-sig-Geo] rgdal segmentation fault during installation
Emanuele Cordano
em@nuele@cord@no @ending from gm@il@com
Sat Nov 17 13:57:41 CET 2018
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 using 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)
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[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.cordano using gmail.com,emanuele.cordano using rendena100.eu,
emanuele.cordano using eurac.edu
PEC: emanuele.cordano using ingpec.eu
URL: www.rendena100.eu
LinkedIn: https://www.linkedin.com/in/emanuele-cordano-31995333
GitHub: https://github.com/ecor
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