[R-sig-Geo] Errors at installing rgdal on Debian Buster
Roger Bivand
Roger.Bivand at nhh.no
Tue Sep 12 13:09:50 CEST 2017
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
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>>>>>>>>
>>>>>>>>
>>>>>>>> [[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/
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> R-sig-Geo mailing list
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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
>>>> _______________________________________________
>>>> R-sig-Geo mailing list
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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
>>
>> _______________________________________________
>> 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
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