Pin libsqlite=3.50.4 to workaround undefined symbol: sqlite3_total_changes64 error

[weiji14]

Pinning to libsqlite==3.50.4 to match repo2docker exactly. Repo2docker first installs some packages (including libsqlite) into the 'notebook' environment, and then upgrades packages based on what's in the environment.yml file. The undefined symbol: sqlite3_total_changes64 error occurs because of some mismatch in sqlite versions it seems.

Test at

This is a hacky fix to the error encountered at #62 (comment). Proper fix might be to rely on upstream changes (in repo2docker?, gdal?, or somewhere else).

[weiji14]

Noticing this warning at the linking step (https://github.com/GenericMappingTools/try-gmt/actions/runs/20699859136/job/59420488037?pr=63#step:6:2195):

Linking libsqlite-3.51.1-h0c1763c_1
Linking libuuid-2.41.3-h5347b49_0
Linking openssl-3.6.0-h26f9b46_0
Linking zstd-1.5.7-hb78ec9c_6
Linking giflib-5.2.2-hd590300_0
Linking json-c-0.18-h6688a6e_0
Linking libdeflate-1.25-h17f619e_0
Linking libjpeg-turbo-3.1.2-hb03c661_0
Linking libpng-1.6.53-h421ea60_0
Linking libwebp-base-1.6.0-hd42ef1d_0
Linking muparser-2.3.5-h5888daf_0
Linking pcre2-10.47-haa7fec5_0
Linking xerces-c-3.3.0-h988505b_0
Linking libbrotlicommon-1.2.0-hb03c661_1
Linking sqlite-3.32.3-hcee41ef_1
warning  libmamba [sqlite-3.32.3-hcee41ef_1] The following files were already present in the environment:
    - include/sqlite3.h
    - include/sqlite3ext.h
    - lib/libsqlite3.so
    - lib/libsqlite3.so.0
    - lib/pkgconfig/sqlite3.pc

Not sure why sqlite 3.32.3 is being pulled in, but thinking that this might be the problem, as it might be conflicting with libsqlite 3.51.1?

[weiji14]

Hmm, I'm starting to think this isn't an issue on GMT but GDAL (specifically conda-forge's libgdal-core=3.12.0=habacd5f_0, possibly others too?). I did a local install, and got:

$ gdal --version
gdal: symbol lookup error: /home/user/mambaforge/envs/pygmt/bin/../lib/libgdal.so.38: undefined symbol: sqlite3_total_changes64

so probably need to investigate https://github.com/conda-forge/gdal-feedstock

Edit: did a clean conda environment install with GDAL 3.12.1 included and the error goes away 😅 But still, should look into what's going on with GDAL and sqlite perhaps.

[weiji14]

Switched from conda install jupyter-repo2docker to pip install jupyter-repo2docker to pull in newer https://pypi.org/project/jupyter-repo2docker/2025.12.0 version since conda-forge is a little behind (xref conda-forge/jupyter-repo2docker-feedstock#16).