[R-sig-Geo] Errors at installing rgdal on Debian Buster

Agustin Lobo alobolistas at gmail.com
Tue Sep 12 12:25:38 CEST 2017 

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
>>>>> _______________________________________________ R-sig-Geo mailing list
>>>>> R-sig-Geo at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>
>>>>>
>>>>>         [[alternative HTML version deleted]]
>>>>>
>>>>> _______________________________________________
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>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>
>>>>
>>>> _______________________________________________
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>>>
>>> --
>>> Edzer Pebesma
>>> Institute for Geoinformatics  (ifgi),  University of Münster
>>> Heisenbergstraße 2, 48149 Münster, Germany; +49 251 83 33081
>>> Journal of Statistical Software:   http://www.jstatsoft.org/
>>> Computers & Geosciences:   http://elsevier.com/locate/cageo/
>>>
>>>
>>> _______________________________________________
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>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>
>>
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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
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