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Errors at installing rgdal on Debian Buster

Roger Bivand

Tue, Sep 12, 2017 4:49 AM

$ g++ -v
...
gcc version 7.1.1 20170622 (Red Hat 7.1.1-3) (GCC)

in my case on Fedora 26.

Recent versions should be OK, but < 5 may be problematic. If you have 
upgraded in place but not upgraded the compile trains, installing r-base 
will not force that.

On Tue, 12 Sep 2017, Agustin Lobo wrote:

How do I find out that?
Agus

On Tue, Sep 12, 2017 at 1:39 PM, Roger Bivand <Roger.Bivand at nhh.no> wrote:

On Tue, 12 Sep 2017, Agustin Lobo wrote:

Yes, r-base in Buster is 3.3.3.1:
https://packages.debian.org/buster/r-base

I'll wait to see if the maintainers answer...


What is the version of g++ on your buster system - the buster r-base does
not seem to require a version that supports CXX11 or later?

Roger

Thanks


On Tue, Sep 12, 2017 at 1:09 PM, Roger Bivand <Roger.Bivand at nhh.no> wrote:

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

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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

Thread (14 messages)

Agustin Lobo Errors at installing rgdal on Debian Buster Sep 8 Roger Bivand Errors at installing rgdal on Debian Buster Sep 8 Agustin Lobo Errors at installing rgdal on Debian Buster Sep 12 Edzer Pebesma Errors at installing rgdal on Debian Buster Sep 12 Agustin Lobo Errors at installing rgdal on Debian Buster Sep 12 Roger Bivand Errors at installing rgdal on Debian Buster Sep 12 Agustin Lobo Errors at installing rgdal on Debian Buster Sep 12 Roger Bivand Errors at installing rgdal on Debian Buster Sep 12 Agustin Lobo Errors at installing rgdal on Debian Buster Sep 12 Roger Bivand Errors at installing rgdal on Debian Buster Sep 12 Agustin Lobo Errors at installing rgdal on Debian Buster Sep 12 Roger Bivand Errors at installing rgdal on Debian Buster Sep 12 Agustin Lobo Errors at installing rgdal on Debian Buster Sep 12 Roger Bivand Errors at installing rgdal on Debian Buster Sep 12