Source: python-cobra
Version: 0.14.2-2
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200402 ftbfs-bullseye
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> debian/rules build
> dh build --with python3 --buildsystem=pybuild
> dh_update_autotools_config -O--buildsystem=pybuild
> dh_autoreconf -O--buildsystem=pybuild
> dh_auto_configure -O--buildsystem=pybuild
> I: pybuild base:217: python3.7 setup.py config
> running config
> I: pybuild base:217: python3.8 setup.py config
> running config
> dh_auto_build -O--buildsystem=pybuild
> I: pybuild base:217: /usr/bin/python3.7 setup.py build
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra
> copying cobra/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra
> copying cobra/exceptions.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/util
> copying cobra/util/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/util
> copying cobra/util/array.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/util
> copying cobra/util/util.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/util
> copying cobra/util/solver.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/util
> copying cobra/util/context.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/util
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
> copying cobra/core/configuration.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
> copying cobra/core/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
> copying cobra/core/object.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
> copying cobra/core/species.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
> copying cobra/core/singleton.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
> copying cobra/core/gene.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
> copying cobra/core/dictlist.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
> copying cobra/core/metabolite.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
> copying cobra/core/reaction.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
> copying cobra/core/model.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
> copying cobra/core/formula.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
> copying cobra/core/solution.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/core
> creating
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/geometric.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/room.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/loopless.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/deletion.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/gapfilling.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/phenotype_phase_plane.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/variability.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/sampling.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/parsimonious.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/summary.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/moma.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/reaction.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/flux_analysis
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test
> copying cobra/test/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test
> copying cobra/test/test_manipulation.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test
> copying cobra/test/test_medium.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test
> copying cobra/test/conftest.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation
> copying cobra/manipulation/validate.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation
> copying cobra/manipulation/modify.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation
> copying cobra/manipulation/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation
> copying cobra/manipulation/delete.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation
> copying cobra/manipulation/annotate.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/manipulation
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/medium
> copying cobra/medium/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/medium
> copying cobra/medium/annotations.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/medium
> copying cobra/medium/boundary_types.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/medium
> copying cobra/medium/minimal_medium.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/medium
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/io
> copying cobra/io/dict.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/io
> copying cobra/io/sbml.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/io
> copying cobra/io/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/io
> copying cobra/io/json.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/io
> copying cobra/io/yaml.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/io
> copying cobra/io/mat.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/io
> copying cobra/io/sbml3.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/io
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/test_sbml3.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/test_mat.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/test_sbml.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/test_pickle.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/conftest.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/test_yaml.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/test_json.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/test_io_order.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/test_io
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/iJO1366.xml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/invalid0.xml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/mini_fbc1.xml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/mini_cobra.xml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/mini.pickle ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/salmonella.pickle ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/update_pickles.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/raven.mat ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/textbook.xml.gz ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/mini_fbc2.xml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/textbook_fva.json ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/salmonella.genes ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/textbook_pfba_fva.json ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/salmonella.xml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/raven.pickle ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/invalid2.xml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/iJO1366.pickle ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/invalid1.xml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/salmonella.media ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/textbook_solution.pickle ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/mini.mat ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/mini.yml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/mini.json ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/mini_fbc2.xml.bz2 ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> copying cobra/test/data/mini_fbc2.xml.gz ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/data
> I: pybuild base:217: /usr/bin/python3 setup.py build
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra
> copying cobra/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra
> copying cobra/exceptions.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/util
> copying cobra/util/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/util
> copying cobra/util/array.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/util
> copying cobra/util/util.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/util
> copying cobra/util/solver.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/util
> copying cobra/util/context.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/util
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
> copying cobra/core/configuration.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
> copying cobra/core/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
> copying cobra/core/object.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
> copying cobra/core/species.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
> copying cobra/core/singleton.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
> copying cobra/core/gene.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
> copying cobra/core/dictlist.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
> copying cobra/core/metabolite.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
> copying cobra/core/reaction.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
> copying cobra/core/model.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
> copying cobra/core/formula.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
> copying cobra/core/solution.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/core
> creating
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/geometric.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/room.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/loopless.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/deletion.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/gapfilling.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/phenotype_phase_plane.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/variability.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/sampling.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/parsimonious.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/summary.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/moma.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
> copying cobra/flux_analysis/reaction.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/flux_analysis
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test
> copying cobra/test/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test
> copying cobra/test/test_manipulation.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test
> copying cobra/test/test_medium.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test
> copying cobra/test/conftest.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/manipulation
> copying cobra/manipulation/validate.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/manipulation
> copying cobra/manipulation/modify.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/manipulation
> copying cobra/manipulation/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/manipulation
> copying cobra/manipulation/delete.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/manipulation
> copying cobra/manipulation/annotate.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/manipulation
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/medium
> copying cobra/medium/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/medium
> copying cobra/medium/annotations.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/medium
> copying cobra/medium/boundary_types.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/medium
> copying cobra/medium/minimal_medium.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/medium
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/io
> copying cobra/io/dict.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/io
> copying cobra/io/sbml.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/io
> copying cobra/io/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/io
> copying cobra/io/json.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/io
> copying cobra/io/yaml.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/io
> copying cobra/io/mat.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/io
> copying cobra/io/sbml3.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/io
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/test_sbml3.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/test_mat.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/test_sbml.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/test_pickle.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/conftest.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/test_yaml.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/test_json.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
> copying cobra/test/test_io/test_io_order.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/test_io
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/iJO1366.xml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/invalid0.xml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/mini_fbc1.xml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/mini_cobra.xml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/mini.pickle ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/salmonella.pickle ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/update_pickles.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/raven.mat ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/textbook.xml.gz ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/mini_fbc2.xml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/textbook_fva.json ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/salmonella.genes ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/textbook_pfba_fva.json ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/salmonella.xml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/raven.pickle ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/invalid2.xml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/iJO1366.pickle ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/invalid1.xml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/salmonella.media ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/textbook_solution.pickle ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/mini.mat ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/mini.yml ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/mini.json ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/mini_fbc2.xml.bz2 ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> copying cobra/test/data/mini_fbc2.xml.gz ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_cobra/build/cobra/test/data
> dh_auto_test -O--buildsystem=pybuild
> I: pybuild base:217: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build;
> python3.7 -m pytest
> ============================= test session starts
> ==============================
> platform linux -- Python 3.7.7, pytest-4.6.9, py-1.8.1, pluggy-0.13.0
> benchmark: 3.2.2 (defaults: timer=time.perf_counter disable_gc=False
> min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10
> warmup=False warmup_iterations=100000)
> rootdir: /<<PKGBUILDDIR>>, inifile: setup.cfg
> plugins: benchmark-3.2.2
> collected 0 items / 1 errors
>
> ==================================== ERRORS
> ====================================
> ________________________ ERROR collecting test session
> _________________________
> /usr/lib/python3/dist-packages/_pytest/config/__init__.py:440: in
> _importconftest
> return self._conftestpath2mod[conftestpath]
> E KeyError:
> local('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/conftest.py')
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3/dist-packages/_pytest/config/__init__.py:446: in
> _importconftest
> mod = conftestpath.pyimport()
> /usr/lib/python3/dist-packages/py/_path/local.py:701: in pyimport
> __import__(modname)
> cobra/__init__.py:11: in <module>
> from cobra.core import (
> cobra/core/__init__.py:5: in <module>
> from cobra.core.configuration import Configuration
> cobra/core/configuration.py:16: in <module>
> from cobra.util.solver import interface_to_str, solvers
> cobra/util/__init__.py:5: in <module>
> from cobra.util.array import *
> cobra/util/array.py:8: in <module>
> import pandas as pd
> /usr/lib/python3/dist-packages/pandas/__init__.py:182: in <module>
> import pandas.testing
> /usr/lib/python3/dist-packages/pandas/testing.py:7: in <module>
> from pandas.util.testing import (
> /usr/lib/python3/dist-packages/pandas/util/testing.py:18: in <module>
> from matplotlib.cbook import MatplotlibDeprecationWarning
> E ModuleNotFoundError: No module named 'matplotlib'
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3/dist-packages/py/_path/common.py:383: in visit
> for x in Visitor(fil, rec, ignore, bf, sort).gen(self):
> /usr/lib/python3/dist-packages/py/_path/common.py:435: in gen
> for p in self.gen(subdir):
> /usr/lib/python3/dist-packages/py/_path/common.py:424: in gen
> dirs = self.optsort([p for p in entries
> /usr/lib/python3/dist-packages/py/_path/common.py:425: in <listcomp>
> if p.check(dir=1) and (rec is None or rec(p))])
> /usr/lib/python3/dist-packages/_pytest/main.py:667: in _recurse
> ihook = self.gethookproxy(dirpath)
> /usr/lib/python3/dist-packages/_pytest/main.py:482: in gethookproxy
> my_conftestmodules = pm._getconftestmodules(fspath)
> /usr/lib/python3/dist-packages/_pytest/config/__init__.py:424: in
> _getconftestmodules
> mod = self._importconftest(conftestpath.realpath())
> /usr/lib/python3/dist-packages/_pytest/config/__init__.py:463: in
> _importconftest
> raise ConftestImportFailure(conftestpath, sys.exc_info())
> E _pytest.config.ConftestImportFailure:
> (local('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build/cobra/test/conftest.py'),
> (<class 'ModuleNotFoundError'>, ModuleNotFoundError("No module named
> 'matplotlib'"), <traceback object at 0x7f5afd189140>))
> !!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection
> !!!!!!!!!!!!!!!!!!!!
> =========================== 1 error in 0.70 seconds
> ============================
> E: pybuild pybuild:352: test: plugin distutils failed with: exit code=2: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_cobra/build; python3.7 -m pytest
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.7
> 3.8" returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2020/04/02/python-cobra_0.14.2-2_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
