sf fails to install on ubuntu 20.04 (GDAL?)

[maksymiuks]

Hi

to begin with, I'm sorry to start yet another issue regarding installation failures, but I've dug through:

#844
#1377
#2092
https://github.com/r-spatial/sf#ubuntu
https://github.com/r-spatial/sf#multiple-gdal-geos-andor-proj-versions-on-your-system

only to find that none of the suggestions works for me. That's why I decided to start this.

I'm trying to install sf package in the ubuntu 20.04 docker image, unfortunately, this is the output I'm getting

** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘sf’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/opt/autovalidate-r/lib/00LOCK-sf/00new/sf/libs/sf.so':
  /opt/autovalidate-r/lib/00LOCK-sf/00new/sf/libs/sf.so: undefined symbol: _Z21CPL_gdalmdimtranslateN4Rcpp6VectorILi16ENS_15PreserveStorageEEES2_S2_S2_S2_b
Error: loading failed
Execution halted
ERROR: loading failed

where autovalidate-r/ is a custom library to which I install packages. To exclude rule out the problem of double installation I've run which and also search through the entire file system

/home/root# which -a gdal-config
/usr/bin/gdal-config
/bin/gdal-config

/home/root# find / -name "*libgdal*"
/usr/share/lintian/overrides/libgdal-dev
/usr/share/lintian/overrides/libgdal26
/usr/share/doc/libgdal-dev
/usr/share/doc/libgdal26
/usr/lib/libgdal.so
/usr/lib/libgdal.a
/usr/lib/libgdal.so.26
/usr/lib/ogdi/libgdal.so
/usr/lib/libgdal.so.26.0.4
/var/lib/dpkg/info/libgdal-dev.list
/var/lib/dpkg/info/libgdal26.symbols
/var/lib/dpkg/info/libgdal26.triggers
/var/lib/dpkg/info/libgdal-dev.md5sums
/var/lib/dpkg/info/libgdal26.shlibs
/var/lib/dpkg/info/libgdal26.list
/var/lib/dpkg/info/libgdal26.md5sums

/home/root# find / -name "*libproj*"
/usr/share/doc/libproj-dev
/usr/share/doc/libproj15
/usr/lib/x86_64-linux-gnu/libproj.so.15
/usr/lib/x86_64-linux-gnu/libproj.a
/usr/lib/x86_64-linux-gnu/libproj.so.15.3.1
/usr/lib/x86_64-linux-gnu/libproj.so
/usr/lib/x86_64-linux-gnu/libproj.la
/var/lib/dpkg/info/libproj-dev:amd64.list
/var/lib/dpkg/info/libproj15:amd64.symbols
/var/lib/dpkg/info/libproj-dev:amd64.md5sums
/var/lib/dpkg/info/libproj15:amd64.md5sums
/var/lib/dpkg/info/libproj15:amd64.triggers
/var/lib/dpkg/info/libproj15:amd64.shlibs
/var/lib/dpkg/info/libproj15:amd64.list

/home/root# find / -name "*libgeos*"
/usr/share/lintian/overrides/libgeos-3.8.0
/usr/share/doc/libgeos-dev
/usr/share/doc/libgeos-3.8.0
/usr/share/doc/libgeos-c1v5
/usr/lib/x86_64-linux-gnu/libgeos_c.so.1
/usr/lib/x86_64-linux-gnu/libgeos_c.so
/usr/lib/x86_64-linux-gnu/libgeos_c.so.1.13.1
/usr/lib/x86_64-linux-gnu/libgeos_c.a
/usr/lib/x86_64-linux-gnu/libgeos-3.8.0.so
/var/lib/dpkg/info/libgeos-c1v5:amd64.shlibs
/var/lib/dpkg/info/libgeos-dev.list
/var/lib/dpkg/info/libgeos-c1v5:amd64.md5sums
/var/lib/dpkg/info/libgeos-3.8.0:amd64.list
/var/lib/dpkg/info/libgeos-c1v5:amd64.symbols
/var/lib/dpkg/info/libgeos-c1v5:amd64.triggers
/var/lib/dpkg/info/libgeos-3.8.0:amd64.triggers
/var/lib/dpkg/info/libgeos-c1v5:amd64.list
/var/lib/dpkg/info/libgeos-3.8.0:amd64.symbols
/var/lib/dpkg/info/libgeos-3.8.0:amd64.shlibs
/var/lib/dpkg/info/libgeos-dev.md5sums
/var/lib/dpkg/info/libgeos-3.8.0:amd64.md5sums

Surprisingly, the problem occurs only for versions 1.0-11 (latest) and 1.0-10 (archive). Installation of the old release 1.0-9 succeeds without any issues. Therefore I also attach session info with attached sf 1.0-9 to capture R dependencies.

loaded via a namespace (and not attached):
 [1] compiler_4.2.2     magrittr_2.0.3     class_7.3-21       tools_4.2.2       
 [5] DBI_1.1.3          units_0.8-1        proxy_0.4-27       Rcpp_1.0.10       
 [9] KernSmooth_2.23-20 grid_4.2.2         e1071_1.7-13       classInt_0.4-9 

I've tried playing with LD_LIBRARY_PATH, preloading libs with dyn.load() and obviously reinstalling all packages. Neither approach succeeded. And what bugs me the most is the fact everything works for the old realease.

I'll appreciate any bit of advice on how I could address this issue.

[edzer]

If you'd share a minimal Dockerfile that reproduces your problem, I could take a look.

[bart1]

I can confirm I get the same error installing on my desktop ubuntu 20.04 machine

[edzer]

Thanks, 1d0302a might have fixed this.

[bart1]

@edzer the development version from github now installs without a problem

[maksymiuks]

@edzer Installing the package from the commit you've provided succeeded! 🥳 Thank you so much for such a fast reaction.

May I ask if you are intending to bring these changes to CRAN reasonably soon? Or do you prefer to wait considering recent releases?

[ssj1739]

Just as an FYI, I was having the same issue on Ubuntu 18.04, using GDAL 3.0.4, GEOS 3.8.0, and proj 7.0.0. Checked up and down for any extra GDAL/GEOS/PROJ versions, removed and reinstalled existing installs.
Solved by installing latest GitHub version from remotes::install_github("r-spatial/sf").

Thank you!

[edzer]

Thanks!