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

Agustin Lobo alobolistas at gmail.com
Tue Sep 12 13:32:09 CEST 2017 

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...

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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>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
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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
>>>>>>> R-sig-Geo at r-project.org
>>>>>>> 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
>>>>> 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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