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

[Edzer Pebesma]

IMHO, debugging a problem like this would become so much easier if you
could provide a docker file that creates the machine you are looking at.
Other docker users (like me) could then run it, reproduce your machine,
and look at what is going wrong.

A set of r-spatial targeting rocker (debian)-based docker images are
found here:

https://github.com/rocker-org/geospatial

a set of ubuntu-based docker files are found here:

https://github.com/r-spatial/sf/tree/master/inst/docker

On 13/09/17 09:37, Agustin Lobo wrote:
> The problem seems to be related to the compiler. I had:
> gcc version 5.3.1 20160101 (Debian 5.3.1-5)
> 
> I have now:
> gcc version 7.2.0 (Debian 7.2.0-4)
> 
> All weird previus errors are gone but I still have:
> 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
> 
> and finally
> 
> ** testing if installed package can be loaded
> Fatal error: glibc detected an invalid stdio handle
> Aborted
> ERROR: loading failed
> * removing ‘/home/alobo/R/i686-pc-linux-gnu-library/3.3/rgdal’
> 
> Surprisingly,  I do have 4.9 installed, not 4.8:
> 
> $ dpkg -s proj-bin
> Package: proj-bin
> Status: install ok installed
> Priority: optional
> Section: science
> Installed-Size: 125
> Maintainer: Debian GIS Project <pkg-grass-devel at lists.alioth.debian.org>
> Architecture: i386
> Source: proj
> Version: 4.9.3-2
> 
> and
> $ proj
> Rel. 4.9.3, 15 August 2016
> usage: proj [ -bCeEfiIlormsStTvVwW [args] ] [ +opts[=arg] ] [ files ]
> 
> and I cannot find proj_conf_test anywhere:
> $ sudo find / -name 'proj_conf_test'
> gives no result
> 
> How is the test ./proj_conf_test done so that I can investigate why it
> results into PROJ 4.8 instead of 4.9?
> 
> Thanks
> 
> Agus
> 
> 
> 
> On Tue, Sep 12, 2017 at 1:49 PM, Roger Bivand <Roger.Bivand at nhh.no> wrote:
>> $ g++ -v
>> ...
>> gcc version 7.1.1 20170622 (Red Hat 7.1.1-3) (GCC)
>>
>> in my case on Fedora 26.
>>
>> Recent versions should be OK, but < 5 may be problematic. If you have
>> upgraded in place but not upgraded the compile trains, installing r-base
>> will not force that.
>>
>>
>>
> 
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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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