Try fixed versions sqlite, gdal

Dockerfile

@@ -82,7 +82,7 @@ RUN conda config --set default_threads 4 && \
   ete3 \
   flax \
   fqdn \
-  gdal \
+  gdal 3.9.2\
   graph-tool \
   igraph \
   ipydatagrid \
@@ -95,6 +95,7 @@ RUN conda config --set default_threads 4 && \
   pathos \
   pint \
   plotly \
+  pubchempy \
   py3dmol \
   pylatex \
   pymatgen \
@@ -110,6 +111,7 @@ RUN conda config --set default_threads 4 && \
   scikit-learn \
   seaborn \
   sparqlwrapper \
+  sqlite 2.6.0 \
   tabulate \
   tinygp \
   trame \