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

Tue Sep 12 13:49:12 CEST 2017

$ 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
>>>>>>>>>>>> _______________________________________________ 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]]
>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> R-sig-Geo mailing list
>>>>>>>>>>>> R-sig-Geo at r-project.org
>>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> R-sig-Geo mailing list
>>>>>>>>>>> R-sig-Geo at r-project.org
>>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> 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/
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> R-sig-Geo mailing list
>>>>>>>>>> R-sig-Geo at r-project.org
>>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> R-sig-Geo mailing list
>>>>>>>>> R-sig-Geo at r-project.org
>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> 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
>>>>>>>> _______________________________________________
>>>>>>>> R-sig-Geo mailing list
>>>>>>>> R-sig-Geo at r-project.org
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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
>>>>>>
>>>>>> _______________________________________________
>>>>>> R-sig-Geo mailing list
>>>>>> R-sig-Geo at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> 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
>>>>
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
>>>> R-sig-Geo at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>>>
>>>
>>
>> --
>> 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
>>
>> _______________________________________________
>> R-sig-Geo mailing list
>> R-sig-Geo at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

-- 
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