Install on Ubuntu 24.04 failed

[Marc-Girondot]

System: Ubuntu 24.04 R 4.4.1

In R:

devtools::install_github("thomasp85/transformr")

It returns an error (all the logs are at the end of this report): Erreur dans dyn.load(file, DLLpath = DLLpath, ...) : impossible de charger l'objet partagé '/usr/local/lib/R/site-library/sf/libs/sf.so' : libgdal.so.32: cannot open shared object file: No such file or directory

Indeed, I have the last version of libgdal.so installed which is version 34: mgirond@caretta:~$ cd /usr/lib/x86_64-linux-gnu mgirond@caretta:/usr/lib/x86_64-linux-gnu$ ls -a libgdal* libgdal.so libgdal.so.34 libgdal.so.34.3.8.4

Using a hack to symlink 34 to 32 does not work either: sudo ln -s /usr/lib/x86_64-linux-gnu/libgdal.so /usr/lib/x86_64-linux-gnu/libgdal.so.32

will return: Erreur dans dyn.load(file, DLLpath = DLLpath, ...) : impossible de charger l'objet partagé '/usr/local/lib/R/site-library/sf/libs/sf.so' : /usr/local/lib/R/site-library/sf/libs/sf.so: undefined symbol: _ZN18OGRGeometryFactory13createFromWkbEPKvP19OGRSpatialReferencePP11OGRGeometrym13OGRwkbVariant

All the logs are here:

devtools::install_github("thomasp85/transformr") Downloading GitHub repo thomasp85/transformr@HEAD ── R CMD build ────────────────────────────────────────────────────────────────────────── ✔ checking for file ‘/tmp/RtmpaALtTp/remotes85b47a4fd5/thomasp85-transformr-0f7262d/DESCRIPTION’ (361ms) ─ preparing ‘transformr’: ✔ checking DESCRIPTION meta-information ─ cleaning src ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘transformr_0.1.5.9000.tar.gz’

Installation du package dans ‘/usr/local/lib/R/site-library’ (car ‘lib’ n'est pas spécifié)

• installing source package ‘transformr’ ... using staged installation libs using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-avGvPq/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c align_rings.cpp -o align_rings.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-avGvPq/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cpp11.cpp -o cpp11.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-avGvPq/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fill_down.cpp -o fill_down.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/cpp11/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-avGvPq/r-base-4.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sf_packing.cpp -o sf_packing.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o transformr.so align_rings.o cpp11.o fill_down.o sf_packing.o -L/usr/lib/R/lib -lR installing to /usr/local/lib/R/site-library/00LOCK-transformr/00new/transformr/libs R byte-compile and prepare package for lazy loading Erreur dans dyn.load(file, DLLpath = DLLpath, ...) : impossible de charger l'objet partagé '/usr/local/lib/R/site-library/sf/libs/sf.so' : libgdal.so.32: cannot open shared object file: No such file or directory Appels : ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Exécution arrêtée ERROR: lazy loading failed for package ‘transformr’
• removing ‘/usr/local/lib/R/site-library/transformr’ Message d'avis : Dans i.p(...) : l'installation du package ‘/tmp/RtmpaALtTp/file85b705d3294/transformr_0.1.5.9000.tar.gz’ a eu un statut de sortie non nul

mgirond@caretta:~$ cd /usr/lib/x86_64-linux-gnu mgirond@caretta:/usr/lib/x86_64-linux-gnu$ ls -a libgdal* libgdal.so libgdal.so.34 libgdal.so.34.3.8.4

mgirond@caretta:/usr/lib/x86_64-linux-gnu$ sudo ln -s /usr/lib/x86_64-linux-gnu/libgdal.so /usr/lib/x86_64-linux-gnu/libgdal.so.32

Erreur dans dyn.load(file, DLLpath = DLLpath, ...) : impossible de charger l'objet partagé '/usr/local/lib/R/site-library/sf/libs/sf.so' : /usr/local/lib/R/site-library/sf/libs/sf.so: undefined symbol: _ZN18OGRGeometryFactory13createFromWkbEPKvP19OGRSpatialReferencePP11OGRGeometrym13OGRwkbVariant Appels : ... asNamespace -> loadNamespace -> library.dynam -> dyn.load Exécution arrêtée

[The-Dub]

Hi,

I got a similar issue installing transformr on a docker container.

• for error : unable to load shared object '/usr/local/lib/R/site-library/units/libs/units.so': libudunits2.so.0: then run in terminal sudo apt-get install -y libudunits2-dev

• for error : unable to load shared object '/usr/local/lib/R/site-library/sf/libs/sf.so': libproj.so.22: then run in terminal sudo apt-get install libproj-dev

• for error :unable to load shared object '/usr/local/lib/R/site-library/sf/libs/sf.so': libgdal.so.30: then run in terminal sudo apt-get install libudunits2-dev libgdal-dev libgeos-dev libproj-dev (similar as this issue)

hope this helps!