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that my sf installation was out of date.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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