[R-sig-Debian] Unable to update r-cran-sf

[Michael Rutter]

Ege,


On 9/12/21 3:59 PM, Ege Rubak wrote:
> Thanks for the promt reply, Michael.
> 
> I managed to add the UbuntuGIS PPA and installed everything. However,
> when I load the new version of sf I all the sudden get corruptions when
> I exit R. I haven't had a real crash while running R yet, but I also
> didn't really test anything yet. Have anyone seen something like this
> before? My gut feeling is to try to remove/purge any apt packages
> related to spatial stuff, and reinstall, but I'm not sure what the
> easiest way to do this is. I tried
> 
> sudo apt remove libproj-dev
> 
> Which caused a lot of packages to be removed, and then I reinstalled r-
> cran-sf and others, but I still get the corruption as before.
> 
> At the moment a vanilla R session gives the following:
> 
> ```
>> library(sf)
> Linking to GEOS 3.9.0, GDAL 3.2.1, PROJ 7.2.1
>> q("no")
> double free or corruption (out)
> Aborted (core dumped)
> ```

I think this is something specific to your system.  I started with a 
fresh Docker container for 20.04, installed the required PPAs, and this 
exited without issue.

 > library(sf)
Linking to GEOS 3.9.0, GDAL 3.2.1, PROJ 7.2.1
 > q("no")

Hard to diagnose what could be causing this.  Could be related to 
packages installed within R, not with apt.

Hope this helps,
Michael

> Good advice is appreciated.
> 
> Best,
> Ege
> 
> 
> On Fri, 2021-09-10 at 10:06 -0400, Michael Rutter wrote:
>> Ege,
>>
>> Thanks for the quesion.
>>
>> On 9/10/21 6:42 AM, Ege Rubak wrote:
>>> Hi,
>>>
>>> I'm an absolute fan of binary packages provided by c2d4u.team, and
>>> try
>>> to install as many packages as possible this way. This includes the
>>> Rspatial suite of packages with r-cran-sf as the main building
>>> block.
>>> This has worked out of the box on Ubuntu 20.04, but recently I
>>> noticed
>>> that my sf installation was out of date. Trying to update I get the
>>> following error:
>>>
>>> ```
>>> $ sudo apt install r-cran-sf
>>> [sudo] password for rubak:
>>> Reading package lists... Done
>>> Building dependency tree
>>> Reading state information... Done
>>> Some packages could not be installed. This may mean that you have
>>> requested an impossible situation or if you are using the unstable
>>> distribution that some required packages have not yet been created
>>> or been moved out of Incoming.
>>> The following information may help to resolve the situation:
>>>
>>> The following packages have unmet dependencies:
>>>    r-cran-sf : Depends: libgdal28 (>= 3.1.0) but it is not
>>> installable
>>>                Depends: libgeos-c1v5 (>= 3.9.0) but 3.8.0-1build1 is
>>> to
>>> be installed
>>>                Depends: libproj19 (>= 7.1.0) but it is not
>>> installable
>>> E: Unable to correct problems, you have held broken packages.
>>> ```
>>>
>>> How do I best update libgdal, libgeos and libproj to required
>>> versions?
>>> Does anyone know how it is handled by the machine used by
>>> c2d4u.team?
>>>
>>> [This tutorial][1] mentions that it is recommended to use [UbuntGIS
>>> PPA][2] for spatial packages in R, but warns that it doesn't work
>>> with
>>> the binaries provided by c2d4u.team.
>>
>> I would disagree with the warning.  If you look look at the
>> "Technical
>> details about this PPA" on the c2d4u4.0 page, you will see that it
>> does
>> depend on the the ubuntugis-stable PPA.  You will need to install
>> that
>> PPA in order to use a majority of the spatial packages.  I have not
>> had
>> issues with installing the packages on my Focal machine.
>>
>> The warnings you see above as usual an indication that you are
>> missing
>> one of the dependent PPAs.  If you add the ubuntugis-stable PPA and
>> you
>> still get the errors, please let me know.
>>
>> Hope this helps,
>> Michael
>>
>>
>>> Any suggestions of how to approach this? I really want to stay as
>>> close
>>> as possible to plain Ubuntu binaries and the binaries provided by
>>> c2d4u.team.
>>>
>>> Cheers,
>>> Ege
>>>
>>> [1]:
>>> https://rtask.thinkr.fr/installation-of-r-4-0-on-ubuntu-20-04-lts-and-tips-for-spatial-packages/
>>> [2]: https://launchpad.net/~ubuntugis
>>>
>>>
>>>
>>
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