Errors at installing rgdal on Debian Buster

On Tue, 12 Sep 2017, Agustin Lobo wrote:

I just installed r-base through synaptic.
alobo at debi:~$ dpkg -s r-base
Package: r-base
Status: install ok installed
Priority: optional
Section: gnu-r
Installed-Size: 60
Maintainer: Dirk Eddelbuettel <edd at debian.org>
Architecture: all
Version: 3.3.3-1
Depends: r-base-core (>= 3.3.3-1), r-recommended (= 3.3.3-1)
Recommends: r-base-html, r-doc-html
Suggests: ess, r-doc-info | r-doc-pdf

This is not current R. An offlist solution for someone else was installing
PROJ, GDAL, and R from source. Is the R 3.3.3-1 binary for your Debian
version?

Roger

I think I'll try to downgrade to stretch...

Agus


On Tue, Sep 12, 2017 at 12:28 PM, Roger Bivand <Roger.Bivand at nhh.no>
wrote:

From the entrails, GDAL was built with a CXX11 compiler, but R was very
possibly not, hence the messages. Where did R come from, and was it
itself
built for the same Debian version?


Roger


On Tue, 12 Sep 2017, Agustin Lobo wrote:

I assume that from the repos I have defined, this is an standard
installation:
deb http://ftp.de.debian.org/debian/ testing main
deb-src http://ftp.de.debian.org/debian/ testing main
deb http://ftp.de.debian.org/debian/ testing-updates main
deb-src http://ftp.de.debian.org/debian/ testing-updates main
deb ftp://security.debian.org/debian-security testing/updates main
deb-src ftp://security.debian.org/debian-security testing/updates main

deb http://deb.debian.org/debian/ testing non-free contrib main
deb-src http://deb.debian.org/debian/ testing non-free contrib main
deb http://deb.debian.org/debian/ testing-updates non-free contrib main
deb-src http://deb.debian.org/debian/ testing-updates non-free contrib
main

Also:
alobo at debi:~$ dpkg -s gdal-bin
Package: gdal-bin
Status: install ok installed
Priority: optional
Section: science
Installed-Size: 724
Maintainer: Debian GIS Project <pkg-grass-devel at lists.alioth.debian.org>
Architecture: i386
Source: gdal (2.2.1+dfsg-2)
Version: 2.2.1+dfsg-2+b2
Depends: gdal-abi-2-2-1, libc6 (>= 2.15), libgcc1 (>= 1:4.2),
libgdal20 (>= 2.2.0), libstdc++6 (>= 5.2)
Suggests: libgdal-grass, python-gdal
Breaks: gdal-bin (<< 1.10.0-0~)

alobo at debi:~$ dpkg -s libgdal-dev
Package: libgdal-dev
Status: install ok installed
Priority: optional
Section: libdevel
Installed-Size: 32633
Maintainer: Debian GIS Project <pkg-grass-devel at lists.alioth.debian.org>
Architecture: i386
Source: gdal (2.2.1+dfsg-2)
Version: 2.2.1+dfsg-2+b2
Depends: libgdal20 (= 2.2.1+dfsg-2+b2), libc6-dev, libarmadillo-dev,
libcurl4-gnutls-dev | libcurl-ssl-dev, libdap-dev, libepsilon-dev,
libexpat1-dev, libfreexl-dev, libfyba-dev, libgeos-dev,
libgeotiff-dev, libgif-dev, libhdf4-alt-dev, libhdf5-dev, libjpeg-dev,
libjson-c-dev, libkml-dev, libltdl-dev, liblzma-dev,
default-libmysqlclient-dev, libnetcdf-dev, libogdi3.2-dev,
libopenjp2-7-dev, libpcre3-dev, libpng-dev, libpoppler-private-dev,
libpq-dev, libproj-dev, libqhull-dev, libspatialite-dev,
libsqlite3-dev, libtiff-dev, liburiparser-dev, libwebp-dev,
libxerces-c-dev, libxml2-dev, unixodbc-dev
Suggests: libgdal-doc

I've contacted pkg-grass-devel at lists.alioth.debian.org

Agus

On Tue, Sep 12, 2017 at 11:37 AM, Roger Bivand <Roger.Bivand at nhh.no>
wrote:

My guess is that your g++ is being used differently to build R and GDAL
(seen before off-list in August). If you install PROJ, GDAL and R from
source on your platform, they will (most likely) match. It looks as
though R
was not built with -std=c++11 or -std=gnu++11. On your current
platform,
you
almost certainly have a more modern g++, and your R should be built
with
this for packages using C++. Do you know where synaptic is getting its
binaries?

Roger


On Tue, 12 Sep 2017, Agustin Lobo wrote:

Using Synaptic.
I just tested with a live usb with Debian Stretch, and with stretch
rgdal installs with no problems (after installing gdal-bin, gdal-dev
and dependencies) .
Agus

On Tue, Sep 12, 2017 at 10:15 AM, Edzer Pebesma
<edzer.pebesma at uni-muenster.de> wrote:

How did you install gdal and proj on that machine?

On 12/09/17 09:10, Agustin Lobo wrote:

Thanks,

As indicated, I do:
$ R CMD INSTALL rgdal_1.2-8.tar.gz 2>&1 | tee rgdal.log

The whole output is here:
https://drive.google.com/open?id=0B_LsZU5NlOztb0ZYQzZZRDQ0WkU

The problem starts at:

configure: PROJ.4 version: 4.8.0
./configure: line 3725:  8390 Segmentation fault
./proj_conf_test
checking PROJ.4: epsg found and readable... yes
./configure: line 3800:  8399 Segmentation fault
./proj_conf_test
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++ -I/usr/share/R/include -DNDEBUG -I/usr/include/gdal
-I"/home/alobo/R/i686-pc-linux-gnu-library/3.3/sp/include"   -fpic
-g
-O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=.
-fstack-protector-strong -Wformat -Werror=format-security
-Wdate-time
-D_FORTIFY_SOURCE=2 -g  -c OGR_write.cpp -o OGR_write.o
In file included from /usr/include/gdal/ogr_feature.h:35:0,
                 from /usr/include/gdal/ogrsf_frmts.h:35,
                 from OGR_write.cpp:2:
/usr/include/gdal/ogr_featurestyle.h:264:17: warning: override
controls (override/final) only available with -std=c++11 or
-std=gnu++11
     GBool Parse() CPL_OVERRIDE;

I'm totally clueless...

Agus

On Fri, Sep 8, 2017 at 4:00 PM, Roger Bivand <Roger.Bivand at nhh.no>
wrote:

Please use the command line: R CMD INSTALL <tarball>  and pipe the
output (tee) 2>&1 to a file. Please do not post the file, read it
to
find
the root cause. Almost certainly the installed GDAL ha different
assumptions
about the g++ compiler than R itself, so you may need to install
GDAL
and R
from source. There have been unclear reports of issues with -std=.

Hope this helps,

Roger

Roger Bivand
Norwegian School of Economics
Bergen, Norway



Fra: Agustin Lobo
Sendt: fredag 8. september, 14.49
Emne: [R-sig-Geo] Errors at installing rgdal on Debian Buster
Til: r-sig-geo


I get lots of errors at installing rgdal on a recently upgraded
machine
to Debian Buster and R3.3.3 There are so many errors that I cannot
scroll up
enough as to get where the errors actually start and report. Is
there
any
way to save the output of install.packages("rgdal") ? Any other
reports on
problems installing rgdal on Debian Buster ? Thanks Agus

--
Edzer Pebesma
Institute for Geoinformatics  (ifgi),  University of M?nster
Heisenbergstra?e 2, 48149 M?nster, Germany; +49 251 83 33081
Journal of Statistical Software:   http://www.jstatsoft.org/
Computers & Geosciences:   http://elsevier.com/locate/cageo/

--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand at nhh.no
Editor-in-Chief of The R Journal,
https://journal.r-project.org/index.html
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand at nhh.no
Editor-in-Chief of The R Journal,
https://journal.r-project.org/index.html
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: Roger.Bivand at nhh.no
Editor-in-Chief of The R Journal, https://journal.r-project.org/index.html
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en