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

Roger Bivand Roger.Bivand at nhh.no
Tue Sep 12 12:28:16 CEST 2017 

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
>>>>>> _______________________________________________ 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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>>>>>
>>>>>
>>>>> _______________________________________________
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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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>>>
>>>
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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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>

-- 
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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