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

[Ege Rubak]

Hi Michael,

I was also pretty sure that the problem was specific to my system, but
I couldn't figure out how to get rid of everything related to PROJ with
apt and then reinstall from scratch.

For future reference it turned out that purging both libproj-dev and
proj-data did it for me:

sudo apt purge libproj-dev proj-data

Afterwards `sudo apt install r-cran-sf` gave me a perfectly working
`sf`.

Thanks for the help (in particular for providing c2d4u for the
community).

Cheers,
Ege

On Mon, 2021-09-13 at 22:16 -0400, Michael Rutter wrote:
> 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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