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

Agustin Lobo alobolistas at gmail.com
Tue Sep 12 13:45:50 CEST 2017 

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

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