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

[Ege Rubak]

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)
```

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 that my sf installation was out of date.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
> > 
> > 
> > 
> 
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian using r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian