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

[Roger Bivand]

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
>>>>
>>>>
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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/
>>
>>
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>
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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