[R-sig-Geo] Errors at installing rgdal on Debian Buster
Agustin Lobo
alobolistas at gmail.com
Tue Sep 12 12:54:30 CEST 2017
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
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
>>>>> 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
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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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