python3.14-dnachisel-3.2.16
checks.x86_64-linux.pkgs-dnachisel
· build #70
· raw
1Sourcing python-remove-tests-dir-hook2Sourcing python-catch-conflicts-hook.sh3Sourcing python-remove-bin-bytecode-hook.sh4Sourcing pypa-build-hook5Using pypaBuildPhase6Sourcing python-runtime-deps-check-hook7Using pythonRuntimeDepsCheckHook8Sourcing pypa-install-hook9Using pypaInstallPhase10Sourcing python-imports-check-hook.sh11Using pythonImportsCheckPhase12Sourcing python-metadata-check-hook.sh13Using pythonMetadataCheckPhase14Sourcing python-namespaces-hook15Sourcing python-catch-conflicts-hook.sh16Sourcing pytest-check-hook17Using pytestCheckPhase18Using checkPhaseThreadLimitHook
unpackPhase
19unpacking source archive /nix/store/9mmjdsvm7djnn602nrq97pbfwpl14cg6-source20source root is source21setting SOURCE_DATE_EPOCH to timestamp 315619200 of file "source/tests/tests_from_genbanks/test_from_genbanks.py"configurePhase
22no configure script, doing nothingbuildPhase
23Executing pypaBuildPhase24Creating a wheel...25pypa build flags: --no-isolation --outdir dist/ --wheel26* Getting build dependencies for wheel...27running egg_info28creating dnachisel.egg-info29writing dnachisel.egg-info/PKG-INFO30writing dependency_links to dnachisel.egg-info/dependency_links.txt31writing entry points to dnachisel.egg-info/entry_points.txt32writing requirements to dnachisel.egg-info/requires.txt33writing top-level names to dnachisel.egg-info/top_level.txt34writing manifest file 'dnachisel.egg-info/SOURCES.txt'35reading manifest file 'dnachisel.egg-info/SOURCES.txt'36adding license file 'LICENSE'37writing manifest file 'dnachisel.egg-info/SOURCES.txt'38* Building wheel...39running bdist_wheel40running build41running build_py42creating build/lib/dnachisel43copying dnachisel/cli.py -> build/lib/dnachisel44copying dnachisel/Location.py -> build/lib/dnachisel45copying dnachisel/__init__.py -> build/lib/dnachisel46copying dnachisel/version.py -> build/lib/dnachisel47creating build/lib/dnachisel/SequencePattern48copying dnachisel/SequencePattern/DnaNotationPattern.py -> build/lib/dnachisel/SequencePattern49copying dnachisel/SequencePattern/EnzymeSitePattern.py -> build/lib/dnachisel/SequencePattern50copying dnachisel/SequencePattern/HomopolymerPattern.py -> build/lib/dnachisel/SequencePattern51copying dnachisel/SequencePattern/MotifPssmPattern.py -> build/lib/dnachisel/SequencePattern52copying dnachisel/SequencePattern/RepeatedKmerPattern.py -> build/lib/dnachisel/SequencePattern53copying dnachisel/SequencePattern/SequencePattern.py -> build/lib/dnachisel/SequencePattern54copying dnachisel/SequencePattern/__init__.py -> build/lib/dnachisel/SequencePattern55creating build/lib/dnachisel/Specification56copying dnachisel/Specification/FeatureRepresentationMixin.py -> build/lib/dnachisel/Specification57copying dnachisel/Specification/Specification.py -> build/lib/dnachisel/Specification58copying dnachisel/Specification/SpecificationSet.py -> build/lib/dnachisel/Specification59copying dnachisel/Specification/__init__.py -> build/lib/dnachisel/Specification60creating build/lib/dnachisel/biotools61copying dnachisel/biotools/blast_sequence.py -> build/lib/dnachisel/biotools62copying dnachisel/biotools/bowtie.py -> build/lib/dnachisel/biotools63copying dnachisel/biotools/__init__.py -> build/lib/dnachisel/biotools64copying dnachisel/biotools/biotables.py -> build/lib/dnachisel/biotools65copying dnachisel/biotools/enzymes_operations.py -> build/lib/dnachisel/biotools66copying dnachisel/biotools/formatting_operations.py -> build/lib/dnachisel/biotools67copying dnachisel/biotools/gc_content.py -> build/lib/dnachisel/biotools68copying dnachisel/biotools/genbank_operations.py -> build/lib/dnachisel/biotools69copying dnachisel/biotools/indices_operations.py -> build/lib/dnachisel/biotools70copying dnachisel/biotools/random_sequences.py -> build/lib/dnachisel/biotools71copying dnachisel/biotools/sequences_differences.py -> build/lib/dnachisel/biotools72copying dnachisel/biotools/sequences_operations.py -> build/lib/dnachisel/biotools73creating build/lib/dnachisel/builtin_specifications74copying dnachisel/builtin_specifications/AllowPrimer.py -> build/lib/dnachisel/builtin_specifications75copying dnachisel/builtin_specifications/AvoidBlastMatches.py -> build/lib/dnachisel/builtin_specifications76copying dnachisel/builtin_specifications/AvoidChanges.py -> build/lib/dnachisel/builtin_specifications77copying dnachisel/builtin_specifications/AvoidHairpins.py -> build/lib/dnachisel/builtin_specifications78copying dnachisel/builtin_specifications/AvoidHeterodimerization.py -> build/lib/dnachisel/builtin_specifications79copying dnachisel/builtin_specifications/AvoidMatches.py -> build/lib/dnachisel/builtin_specifications80copying dnachisel/builtin_specifications/AvoidPattern.py -> build/lib/dnachisel/builtin_specifications81copying dnachisel/builtin_specifications/AvoidStopCodons.py -> build/lib/dnachisel/builtin_specifications82copying dnachisel/builtin_specifications/CodonSpecification.py -> build/lib/dnachisel/builtin_specifications83copying dnachisel/builtin_specifications/EnforceChanges.py -> build/lib/dnachisel/builtin_specifications84copying dnachisel/builtin_specifications/EnforceChoice.py -> build/lib/dnachisel/builtin_specifications85copying dnachisel/builtin_specifications/EnforceGCContent.py -> build/lib/dnachisel/builtin_specifications86copying dnachisel/builtin_specifications/EnforceMeltingTemperature.py -> build/lib/dnachisel/builtin_specifications87copying dnachisel/builtin_specifications/EnforcePatternOccurence.py -> build/lib/dnachisel/builtin_specifications88copying dnachisel/builtin_specifications/EnforceRegionsCompatibility.py -> build/lib/dnachisel/builtin_specifications89copying dnachisel/builtin_specifications/EnforceSequence.py -> build/lib/dnachisel/builtin_specifications90copying dnachisel/builtin_specifications/EnforceTerminalGCContent.py -> build/lib/dnachisel/builtin_specifications91copying dnachisel/builtin_specifications/EnforceTranslation.py -> build/lib/dnachisel/builtin_specifications92copying dnachisel/builtin_specifications/SequenceLengthBounds.py -> build/lib/dnachisel/builtin_specifications93copying dnachisel/builtin_specifications/TerminalSpecification.py -> build/lib/dnachisel/builtin_specifications94copying dnachisel/builtin_specifications/UniquifyAllKmers.py -> build/lib/dnachisel/builtin_specifications95copying dnachisel/builtin_specifications/__init__.py -> build/lib/dnachisel/builtin_specifications96creating build/lib/dnachisel/DnaOptimizationProblem97copying dnachisel/DnaOptimizationProblem/CircularDnaOptimizationProblem.py -> build/lib/dnachisel/DnaOptimizationProblem98copying dnachisel/DnaOptimizationProblem/DnaOptimizationProblem.py -> build/lib/dnachisel/DnaOptimizationProblem99copying dnachisel/DnaOptimizationProblem/NoSolutionError.py -> build/lib/dnachisel/DnaOptimizationProblem100copying dnachisel/DnaOptimizationProblem/__init__.py -> build/lib/dnachisel/DnaOptimizationProblem101creating build/lib/dnachisel/reports102copying dnachisel/reports/SpecAnnotationsTranslator.py -> build/lib/dnachisel/reports103copying dnachisel/reports/__init__.py -> build/lib/dnachisel/reports104copying dnachisel/reports/colors_cycle.py -> build/lib/dnachisel/reports105copying dnachisel/reports/optimization_reports.py -> build/lib/dnachisel/reports106copying dnachisel/reports/tools.py -> build/lib/dnachisel/reports107creating build/lib/dnachisel/utils108copying dnachisel/utils/__init__.py -> build/lib/dnachisel/utils109copying dnachisel/utils/utils.py -> build/lib/dnachisel/utils110creating build/lib/dnachisel/MutationSpace111copying dnachisel/MutationSpace/MutationChoice.py -> build/lib/dnachisel/MutationSpace112copying dnachisel/MutationSpace/MutationSpace.py -> build/lib/dnachisel/MutationSpace113copying dnachisel/MutationSpace/__init__.py -> build/lib/dnachisel/MutationSpace114creating build/lib/dnachisel/Specification/SpecEvaluation115copying dnachisel/Specification/SpecEvaluation/ProblemConstraintsEvaluations.py -> build/lib/dnachisel/Specification/SpecEvaluation116copying dnachisel/Specification/SpecEvaluation/ProblemObjectivesEvaluations.py -> build/lib/dnachisel/Specification/SpecEvaluation117copying dnachisel/Specification/SpecEvaluation/SpecEvaluation.py -> build/lib/dnachisel/Specification/SpecEvaluation118copying dnachisel/Specification/SpecEvaluation/SpecEvaluations.py -> build/lib/dnachisel/Specification/SpecEvaluation119copying dnachisel/Specification/SpecEvaluation/__init__.py -> build/lib/dnachisel/Specification/SpecEvaluation120creating build/lib/dnachisel/builtin_specifications/codon_optimization121copying dnachisel/builtin_specifications/codon_optimization/AvoidRareCodons.py -> build/lib/dnachisel/builtin_specifications/codon_optimization122copying dnachisel/builtin_specifications/codon_optimization/BaseCodonOptimizationClass.py -> build/lib/dnachisel/builtin_specifications/codon_optimization123copying dnachisel/builtin_specifications/codon_optimization/CodonOptimize.py -> build/lib/dnachisel/builtin_specifications/codon_optimization124copying dnachisel/builtin_specifications/codon_optimization/HarmonizeRCA.py -> build/lib/dnachisel/builtin_specifications/codon_optimization125copying dnachisel/builtin_specifications/codon_optimization/MatchTargetCodonUsage.py -> build/lib/dnachisel/builtin_specifications/codon_optimization126copying dnachisel/builtin_specifications/codon_optimization/MaximizeCAI.py -> build/lib/dnachisel/builtin_specifications/codon_optimization127copying dnachisel/builtin_specifications/codon_optimization/__init__.py -> build/lib/dnachisel/builtin_specifications/codon_optimization128creating build/lib/dnachisel/DnaOptimizationProblem/mixins129copying dnachisel/DnaOptimizationProblem/mixins/ConstraintsSolverMixin.py -> build/lib/dnachisel/DnaOptimizationProblem/mixins130copying dnachisel/DnaOptimizationProblem/mixins/ObjectivesMaximizerMixin.py -> build/lib/dnachisel/DnaOptimizationProblem/mixins131copying dnachisel/DnaOptimizationProblem/mixins/RecordRepresentationMixin.py -> build/lib/dnachisel/DnaOptimizationProblem/mixins132copying dnachisel/DnaOptimizationProblem/mixins/__init__.py -> build/lib/dnachisel/DnaOptimizationProblem/mixins133creating build/lib/dnachisel/reports/constraints_reports134copying dnachisel/reports/constraints_reports/GraphicTranslator.py -> build/lib/dnachisel/reports/constraints_reports135copying dnachisel/reports/constraints_reports/__init__.py -> build/lib/dnachisel/reports/constraints_reports136copying dnachisel/reports/constraints_reports/constraints_breaches_dataframe.py -> build/lib/dnachisel/reports/constraints_reports137copying dnachisel/reports/constraints_reports/constraints_reports.py -> build/lib/dnachisel/reports/constraints_reports138running egg_info139writing dnachisel.egg-info/PKG-INFO140writing dependency_links to dnachisel.egg-info/dependency_links.txt141writing entry points to dnachisel.egg-info/entry_points.txt142writing requirements to dnachisel.egg-info/requires.txt143writing top-level names to dnachisel.egg-info/top_level.txt144reading manifest file 'dnachisel.egg-info/SOURCES.txt'145adding license file 'LICENSE'146writing manifest file 'dnachisel.egg-info/SOURCES.txt'147creating build/lib/dnachisel/biotools/data148copying dnachisel/biotools/data/README.md -> build/lib/dnachisel/biotools/data149copying dnachisel/biotools/data/complements.csv -> build/lib/dnachisel/biotools/data150copying dnachisel/biotools/data/iupac_notation.csv -> build/lib/dnachisel/biotools/data151copying dnachisel/biotools/data/nucleotide_to_regexpr.csv -> build/lib/dnachisel/biotools/data152creating build/lib/dnachisel/reports/assets153copying dnachisel/reports/assets/logo.png -> build/lib/dnachisel/reports/assets154copying dnachisel/reports/assets/optimization_report.pug -> build/lib/dnachisel/reports/assets155copying dnachisel/reports/assets/style.css -> build/lib/dnachisel/reports/assets156installing to build/bdist.linux-x86_64/wheel157running install158running install_lib159creating build/bdist.linux-x86_64/wheel160creating build/bdist.linux-x86_64/wheel/dnachisel161copying build/lib/dnachisel/cli.py -> build/bdist.linux-x86_64/wheel/./dnachisel162copying build/lib/dnachisel/Location.py -> build/bdist.linux-x86_64/wheel/./dnachisel163copying build/lib/dnachisel/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel164copying build/lib/dnachisel/version.py -> build/bdist.linux-x86_64/wheel/./dnachisel165creating build/bdist.linux-x86_64/wheel/dnachisel/SequencePattern166copying build/lib/dnachisel/SequencePattern/DnaNotationPattern.py -> build/bdist.linux-x86_64/wheel/./dnachisel/SequencePattern167copying build/lib/dnachisel/SequencePattern/EnzymeSitePattern.py -> build/bdist.linux-x86_64/wheel/./dnachisel/SequencePattern168copying build/lib/dnachisel/SequencePattern/HomopolymerPattern.py -> build/bdist.linux-x86_64/wheel/./dnachisel/SequencePattern169copying build/lib/dnachisel/SequencePattern/MotifPssmPattern.py -> build/bdist.linux-x86_64/wheel/./dnachisel/SequencePattern170copying build/lib/dnachisel/SequencePattern/RepeatedKmerPattern.py -> build/bdist.linux-x86_64/wheel/./dnachisel/SequencePattern171copying build/lib/dnachisel/SequencePattern/SequencePattern.py -> build/bdist.linux-x86_64/wheel/./dnachisel/SequencePattern172copying build/lib/dnachisel/SequencePattern/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/SequencePattern173creating build/bdist.linux-x86_64/wheel/dnachisel/Specification174copying build/lib/dnachisel/Specification/FeatureRepresentationMixin.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification175copying build/lib/dnachisel/Specification/Specification.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification176copying build/lib/dnachisel/Specification/SpecificationSet.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification177copying build/lib/dnachisel/Specification/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification178creating build/bdist.linux-x86_64/wheel/dnachisel/Specification/SpecEvaluation179copying build/lib/dnachisel/Specification/SpecEvaluation/ProblemConstraintsEvaluations.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification/SpecEvaluation180copying build/lib/dnachisel/Specification/SpecEvaluation/ProblemObjectivesEvaluations.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification/SpecEvaluation181copying build/lib/dnachisel/Specification/SpecEvaluation/SpecEvaluation.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification/SpecEvaluation182copying build/lib/dnachisel/Specification/SpecEvaluation/SpecEvaluations.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification/SpecEvaluation183copying build/lib/dnachisel/Specification/SpecEvaluation/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/Specification/SpecEvaluation184creating build/bdist.linux-x86_64/wheel/dnachisel/biotools185copying build/lib/dnachisel/biotools/blast_sequence.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools186copying build/lib/dnachisel/biotools/bowtie.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools187copying build/lib/dnachisel/biotools/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools188copying build/lib/dnachisel/biotools/biotables.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools189copying build/lib/dnachisel/biotools/enzymes_operations.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools190copying build/lib/dnachisel/biotools/formatting_operations.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools191copying build/lib/dnachisel/biotools/gc_content.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools192copying build/lib/dnachisel/biotools/genbank_operations.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools193copying build/lib/dnachisel/biotools/indices_operations.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools194copying build/lib/dnachisel/biotools/random_sequences.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools195copying build/lib/dnachisel/biotools/sequences_differences.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools196copying build/lib/dnachisel/biotools/sequences_operations.py -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools197creating build/bdist.linux-x86_64/wheel/dnachisel/biotools/data198copying build/lib/dnachisel/biotools/data/README.md -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools/data199copying build/lib/dnachisel/biotools/data/complements.csv -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools/data200copying build/lib/dnachisel/biotools/data/iupac_notation.csv -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools/data201copying build/lib/dnachisel/biotools/data/nucleotide_to_regexpr.csv -> build/bdist.linux-x86_64/wheel/./dnachisel/biotools/data202creating build/bdist.linux-x86_64/wheel/dnachisel/builtin_specifications203copying build/lib/dnachisel/builtin_specifications/AllowPrimer.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications204copying build/lib/dnachisel/builtin_specifications/AvoidBlastMatches.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications205copying build/lib/dnachisel/builtin_specifications/AvoidChanges.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications206copying build/lib/dnachisel/builtin_specifications/AvoidHairpins.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications207copying build/lib/dnachisel/builtin_specifications/AvoidHeterodimerization.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications208copying build/lib/dnachisel/builtin_specifications/AvoidMatches.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications209copying build/lib/dnachisel/builtin_specifications/AvoidPattern.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications210copying build/lib/dnachisel/builtin_specifications/AvoidStopCodons.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications211copying build/lib/dnachisel/builtin_specifications/CodonSpecification.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications212copying build/lib/dnachisel/builtin_specifications/EnforceChanges.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications213copying build/lib/dnachisel/builtin_specifications/EnforceChoice.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications214copying build/lib/dnachisel/builtin_specifications/EnforceGCContent.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications215copying build/lib/dnachisel/builtin_specifications/EnforceMeltingTemperature.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications216copying build/lib/dnachisel/builtin_specifications/EnforcePatternOccurence.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications217copying build/lib/dnachisel/builtin_specifications/EnforceRegionsCompatibility.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications218copying build/lib/dnachisel/builtin_specifications/EnforceSequence.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications219copying build/lib/dnachisel/builtin_specifications/EnforceTerminalGCContent.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications220copying build/lib/dnachisel/builtin_specifications/EnforceTranslation.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications221copying build/lib/dnachisel/builtin_specifications/SequenceLengthBounds.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications222copying build/lib/dnachisel/builtin_specifications/TerminalSpecification.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications223copying build/lib/dnachisel/builtin_specifications/UniquifyAllKmers.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications224copying build/lib/dnachisel/builtin_specifications/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications225creating build/bdist.linux-x86_64/wheel/dnachisel/builtin_specifications/codon_optimization226copying build/lib/dnachisel/builtin_specifications/codon_optimization/AvoidRareCodons.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications/codon_optimization227copying build/lib/dnachisel/builtin_specifications/codon_optimization/BaseCodonOptimizationClass.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications/codon_optimization228copying build/lib/dnachisel/builtin_specifications/codon_optimization/CodonOptimize.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications/codon_optimization229copying build/lib/dnachisel/builtin_specifications/codon_optimization/HarmonizeRCA.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications/codon_optimization230copying build/lib/dnachisel/builtin_specifications/codon_optimization/MatchTargetCodonUsage.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications/codon_optimization231copying build/lib/dnachisel/builtin_specifications/codon_optimization/MaximizeCAI.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications/codon_optimization232copying build/lib/dnachisel/builtin_specifications/codon_optimization/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/builtin_specifications/codon_optimization233creating build/bdist.linux-x86_64/wheel/dnachisel/DnaOptimizationProblem234copying build/lib/dnachisel/DnaOptimizationProblem/CircularDnaOptimizationProblem.py -> build/bdist.linux-x86_64/wheel/./dnachisel/DnaOptimizationProblem235copying build/lib/dnachisel/DnaOptimizationProblem/DnaOptimizationProblem.py -> build/bdist.linux-x86_64/wheel/./dnachisel/DnaOptimizationProblem236copying build/lib/dnachisel/DnaOptimizationProblem/NoSolutionError.py -> build/bdist.linux-x86_64/wheel/./dnachisel/DnaOptimizationProblem237copying build/lib/dnachisel/DnaOptimizationProblem/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/DnaOptimizationProblem238creating build/bdist.linux-x86_64/wheel/dnachisel/DnaOptimizationProblem/mixins239copying build/lib/dnachisel/DnaOptimizationProblem/mixins/ConstraintsSolverMixin.py -> build/bdist.linux-x86_64/wheel/./dnachisel/DnaOptimizationProblem/mixins240copying build/lib/dnachisel/DnaOptimizationProblem/mixins/ObjectivesMaximizerMixin.py -> build/bdist.linux-x86_64/wheel/./dnachisel/DnaOptimizationProblem/mixins241copying build/lib/dnachisel/DnaOptimizationProblem/mixins/RecordRepresentationMixin.py -> build/bdist.linux-x86_64/wheel/./dnachisel/DnaOptimizationProblem/mixins242copying build/lib/dnachisel/DnaOptimizationProblem/mixins/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/DnaOptimizationProblem/mixins243creating build/bdist.linux-x86_64/wheel/dnachisel/reports244copying build/lib/dnachisel/reports/SpecAnnotationsTranslator.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports245copying build/lib/dnachisel/reports/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports246copying build/lib/dnachisel/reports/colors_cycle.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports247copying build/lib/dnachisel/reports/optimization_reports.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports248copying build/lib/dnachisel/reports/tools.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports249creating build/bdist.linux-x86_64/wheel/dnachisel/reports/constraints_reports250copying build/lib/dnachisel/reports/constraints_reports/GraphicTranslator.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports/constraints_reports251copying build/lib/dnachisel/reports/constraints_reports/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports/constraints_reports252copying build/lib/dnachisel/reports/constraints_reports/constraints_breaches_dataframe.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports/constraints_reports253copying build/lib/dnachisel/reports/constraints_reports/constraints_reports.py -> build/bdist.linux-x86_64/wheel/./dnachisel/reports/constraints_reports254creating build/bdist.linux-x86_64/wheel/dnachisel/reports/assets255copying build/lib/dnachisel/reports/assets/logo.png -> build/bdist.linux-x86_64/wheel/./dnachisel/reports/assets256copying build/lib/dnachisel/reports/assets/optimization_report.pug -> build/bdist.linux-x86_64/wheel/./dnachisel/reports/assets257copying build/lib/dnachisel/reports/assets/style.css -> build/bdist.linux-x86_64/wheel/./dnachisel/reports/assets258creating build/bdist.linux-x86_64/wheel/dnachisel/utils259copying build/lib/dnachisel/utils/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/utils260copying build/lib/dnachisel/utils/utils.py -> build/bdist.linux-x86_64/wheel/./dnachisel/utils261creating build/bdist.linux-x86_64/wheel/dnachisel/MutationSpace262copying build/lib/dnachisel/MutationSpace/MutationChoice.py -> build/bdist.linux-x86_64/wheel/./dnachisel/MutationSpace263copying build/lib/dnachisel/MutationSpace/MutationSpace.py -> build/bdist.linux-x86_64/wheel/./dnachisel/MutationSpace264copying build/lib/dnachisel/MutationSpace/__init__.py -> build/bdist.linux-x86_64/wheel/./dnachisel/MutationSpace265running install_egg_info266Copying dnachisel.egg-info to build/bdist.linux-x86_64/wheel/./dnachisel-3.2.16-py3.14.egg-info267running install_scripts268creating build/bdist.linux-x86_64/wheel/dnachisel-3.2.16.dist-info/WHEEL269creating '/build/source/dist/.tmp-14xpzmmz/dnachisel-3.2.16-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it270adding 'dnachisel/Location.py'271adding 'dnachisel/__init__.py'272adding 'dnachisel/cli.py'273adding 'dnachisel/version.py'274adding 'dnachisel/DnaOptimizationProblem/CircularDnaOptimizationProblem.py'275adding 'dnachisel/DnaOptimizationProblem/DnaOptimizationProblem.py'276adding 'dnachisel/DnaOptimizationProblem/NoSolutionError.py'277adding 'dnachisel/DnaOptimizationProblem/__init__.py'278adding 'dnachisel/DnaOptimizationProblem/mixins/ConstraintsSolverMixin.py'279adding 'dnachisel/DnaOptimizationProblem/mixins/ObjectivesMaximizerMixin.py'280adding 'dnachisel/DnaOptimizationProblem/mixins/RecordRepresentationMixin.py'281adding 'dnachisel/DnaOptimizationProblem/mixins/__init__.py'282adding 'dnachisel/MutationSpace/MutationChoice.py'283adding 'dnachisel/MutationSpace/MutationSpace.py'284adding 'dnachisel/MutationSpace/__init__.py'285adding 'dnachisel/SequencePattern/DnaNotationPattern.py'286adding 'dnachisel/SequencePattern/EnzymeSitePattern.py'287adding 'dnachisel/SequencePattern/HomopolymerPattern.py'288adding 'dnachisel/SequencePattern/MotifPssmPattern.py'289adding 'dnachisel/SequencePattern/RepeatedKmerPattern.py'290adding 'dnachisel/SequencePattern/SequencePattern.py'291adding 'dnachisel/SequencePattern/__init__.py'292adding 'dnachisel/Specification/FeatureRepresentationMixin.py'293adding 'dnachisel/Specification/Specification.py'294adding 'dnachisel/Specification/SpecificationSet.py'295adding 'dnachisel/Specification/__init__.py'296adding 'dnachisel/Specification/SpecEvaluation/ProblemConstraintsEvaluations.py'297adding 'dnachisel/Specification/SpecEvaluation/ProblemObjectivesEvaluations.py'298adding 'dnachisel/Specification/SpecEvaluation/SpecEvaluation.py'299adding 'dnachisel/Specification/SpecEvaluation/SpecEvaluations.py'300adding 'dnachisel/Specification/SpecEvaluation/__init__.py'301adding 'dnachisel/biotools/__init__.py'302adding 'dnachisel/biotools/biotables.py'303adding 'dnachisel/biotools/blast_sequence.py'304adding 'dnachisel/biotools/bowtie.py'305adding 'dnachisel/biotools/enzymes_operations.py'306adding 'dnachisel/biotools/formatting_operations.py'307adding 'dnachisel/biotools/gc_content.py'308adding 'dnachisel/biotools/genbank_operations.py'309adding 'dnachisel/biotools/indices_operations.py'310adding 'dnachisel/biotools/random_sequences.py'311adding 'dnachisel/biotools/sequences_differences.py'312adding 'dnachisel/biotools/sequences_operations.py'313adding 'dnachisel/biotools/data/README.md'314adding 'dnachisel/biotools/data/complements.csv'315adding 'dnachisel/biotools/data/iupac_notation.csv'316adding 'dnachisel/biotools/data/nucleotide_to_regexpr.csv'317adding 'dnachisel/builtin_specifications/AllowPrimer.py'318adding 'dnachisel/builtin_specifications/AvoidBlastMatches.py'319adding 'dnachisel/builtin_specifications/AvoidChanges.py'320adding 'dnachisel/builtin_specifications/AvoidHairpins.py'321adding 'dnachisel/builtin_specifications/AvoidHeterodimerization.py'322adding 'dnachisel/builtin_specifications/AvoidMatches.py'323adding 'dnachisel/builtin_specifications/AvoidPattern.py'324adding 'dnachisel/builtin_specifications/AvoidStopCodons.py'325adding 'dnachisel/builtin_specifications/CodonSpecification.py'326adding 'dnachisel/builtin_specifications/EnforceChanges.py'327adding 'dnachisel/builtin_specifications/EnforceChoice.py'328adding 'dnachisel/builtin_specifications/EnforceGCContent.py'329adding 'dnachisel/builtin_specifications/EnforceMeltingTemperature.py'330adding 'dnachisel/builtin_specifications/EnforcePatternOccurence.py'331adding 'dnachisel/builtin_specifications/EnforceRegionsCompatibility.py'332adding 'dnachisel/builtin_specifications/EnforceSequence.py'333adding 'dnachisel/builtin_specifications/EnforceTerminalGCContent.py'334adding 'dnachisel/builtin_specifications/EnforceTranslation.py'335adding 'dnachisel/builtin_specifications/SequenceLengthBounds.py'336adding 'dnachisel/builtin_specifications/TerminalSpecification.py'337adding 'dnachisel/builtin_specifications/UniquifyAllKmers.py'338adding 'dnachisel/builtin_specifications/__init__.py'339adding 'dnachisel/builtin_specifications/codon_optimization/AvoidRareCodons.py'340adding 'dnachisel/builtin_specifications/codon_optimization/BaseCodonOptimizationClass.py'341adding 'dnachisel/builtin_specifications/codon_optimization/CodonOptimize.py'342adding 'dnachisel/builtin_specifications/codon_optimization/HarmonizeRCA.py'343adding 'dnachisel/builtin_specifications/codon_optimization/MatchTargetCodonUsage.py'344adding 'dnachisel/builtin_specifications/codon_optimization/MaximizeCAI.py'345adding 'dnachisel/builtin_specifications/codon_optimization/__init__.py'346adding 'dnachisel/reports/SpecAnnotationsTranslator.py'347adding 'dnachisel/reports/__init__.py'348adding 'dnachisel/reports/colors_cycle.py'349adding 'dnachisel/reports/optimization_reports.py'350adding 'dnachisel/reports/tools.py'351adding 'dnachisel/reports/assets/logo.png'352adding 'dnachisel/reports/assets/optimization_report.pug'353adding 'dnachisel/reports/assets/style.css'354adding 'dnachisel/reports/constraints_reports/GraphicTranslator.py'355adding 'dnachisel/reports/constraints_reports/__init__.py'356adding 'dnachisel/reports/constraints_reports/constraints_breaches_dataframe.py'357adding 'dnachisel/reports/constraints_reports/constraints_reports.py'358adding 'dnachisel/utils/__init__.py'359adding 'dnachisel/utils/utils.py'360adding 'dnachisel-3.2.16.dist-info/licenses/LICENSE'361adding 'dnachisel-3.2.16.dist-info/METADATA'362adding 'dnachisel-3.2.16.dist-info/WHEEL'363adding 'dnachisel-3.2.16.dist-info/entry_points.txt'364adding 'dnachisel-3.2.16.dist-info/top_level.txt'365adding 'dnachisel-3.2.16.dist-info/RECORD'366removing build/bdist.linux-x86_64/wheel367Successfully built dnachisel-3.2.16-py3-none-any.whl368Finished creating a wheel...369Finished executing pypaBuildPhasepythonRuntimeDepsCheckHook
370Executing pythonRuntimeDepsCheck371Checking runtime dependencies for dnachisel-3.2.16-py3-none-any.whl372Finished executing pythonRuntimeDepsCheckinstallPhase
373Executing pypaInstallPhase374Successfully installed dnachisel-3.2.16-py3-none-any.whl375Finished executing pypaInstallPhasepythonOutputDistPhase
376Executing pythonOutputDistPhase377Finished executing pythonOutputDistPhasefixupPhase
378shrinking RPATHs of ELF executables and libraries in /nix/store/chzqq58ij86z01fxab1rkpw6mpfyncy8-python3.14-dnachisel-3.2.16379checking for references to /build/ in /nix/store/chzqq58ij86z01fxab1rkpw6mpfyncy8-python3.14-dnachisel-3.2.16...380patching script interpreter paths in /nix/store/chzqq58ij86z01fxab1rkpw6mpfyncy8-python3.14-dnachisel-3.2.16381stripping (with command strip and flags -S -p) in /nix/store/chzqq58ij86z01fxab1rkpw6mpfyncy8-python3.14-dnachisel-3.2.16/lib /nix/store/chzqq58ij86z01fxab1rkpw6mpfyncy8-python3.14-dnachisel-3.2.16/bin382shrinking RPATHs of ELF executables and libraries in /nix/store/kp4bchrmyhfa21npshjhm9q09mlbrdq2-python3.14-dnachisel-3.2.16-dist383checking for references to /build/ in /nix/store/kp4bchrmyhfa21npshjhm9q09mlbrdq2-python3.14-dnachisel-3.2.16-dist...384patching script interpreter paths in /nix/store/kp4bchrmyhfa21npshjhm9q09mlbrdq2-python3.14-dnachisel-3.2.16-dist385Rewriting #!/nix/store/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-python3-3.14.7/bin/python3.14 to #!/nix/store/b5bpi6zfajzzrwwpgba2q6li3nnya4bs-python3-3.14.7386wrapping `/nix/store/chzqq58ij86z01fxab1rkpw6mpfyncy8-python3.14-dnachisel-3.2.16/bin/dnachisel'...387Executing pythonRemoveTestsDir388Finished executing pythonRemoveTestsDirinstallCheckPhase
389setting known thread variables to default: 1390 OMP_NUM_THREADS=1 OPENBLAS_NUM_THREADS=1 MKL_NUM_THREADS=1 BLIS_NUM_THREADS=1 VECLIB_MAXIMUM_THREADS=1 NUMBA_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1391no Makefile or custom installCheckPhase, doing nothingpythonImportsCheckPhase
392Executing pythonImportsCheckPhase393Check whether the following modules can be imported: dnachisel394mkdir -p failed for path /homeless-shelter/.config/matplotlib: [Errno 13] Permission denied: '/homeless-shelter'395Matplotlib created a temporary cache directory at /build/matplotlib-6d7as6ur because there was an issue with the default path ({configdir}); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.396Fontconfig error: Cannot load default config file: File not found397398Fontconfig error: No writable cache directories399 /var/cache/fontconfig400 /homeless-shelter/.cache/fontconfig401402Fontconfig error: No writable cache directories403 /var/cache/fontconfig404 /homeless-shelter/.cache/fontconfig405406Fontconfig error: No writable cache directories407 /var/cache/fontconfig408 /homeless-shelter/.cache/fontconfig409410Fontconfig error: No writable cache directories411 /var/cache/fontconfig412 /homeless-shelter/.cache/fontconfig413414Fontconfig error: No writable cache directories415 /var/cache/fontconfig416 /homeless-shelter/.cache/fontconfig417418Fontconfig error: No writable cache directories419 /var/cache/fontconfig420 /homeless-shelter/.cache/fontconfig421422Fontconfig error: No writable cache directories423 /var/cache/fontconfig424 /homeless-shelter/.cache/fontconfig425426Fontconfig error: No writable cache directories427 /var/cache/fontconfig428 /homeless-shelter/.cache/fontconfigpythonMetadataCheckPhase
429Executing pythonMetadataCheckPhasepytestCheckPhase
430Executing pytestCheckPhase431setting known thread variables to default: 1432 OMP_NUM_THREADS=1 OPENBLAS_NUM_THREADS=1 MKL_NUM_THREADS=1 BLIS_NUM_THREADS=1 VECLIB_MAXIMUM_THREADS=1 NUMBA_NUM_THREADS=1 NUMEXPR_NUM_THREADS=1433pytest flags: -m pytest tests -k not\ \(test_avoid_phage_blast_matches\)\ and\ not\ \(test_avoid_matches_with_phage\)434============================= test session starts ==============================435platform linux -- Python 3.14.7, pytest-9.1.1, pluggy-1.6.0436rootdir: /build/source437configfile: pyproject.toml438collected 149 items / 2 deselected / 147 selected 439440tests/builtin_specifications/test_AllowPrimer.py . [ 0%]441tests/builtin_specifications/test_AvoidBlastMatches.py . [ 1%]442tests/builtin_specifications/test_AvoidChanges.py ..... [ 4%]443tests/builtin_specifications/test_AvoidHairpins.py .. [ 6%]444tests/builtin_specifications/test_AvoidMatches.py . [ 6%]445tests/builtin_specifications/test_AvoidPattern.py ......... [ 12%]446tests/builtin_specifications/test_AvoidRareCodons.py .... [ 15%]447tests/builtin_specifications/test_AvoidStopCodons.py . [ 16%]448tests/builtin_specifications/test_CodonOptimize.py ....... [ 21%]449tests/builtin_specifications/test_EnforceChanges.py ........... [ 28%]450tests/builtin_specifications/test_EnforceChoice.py . [ 29%]451tests/builtin_specifications/test_EnforceGCContent.py .. [ 30%]452tests/builtin_specifications/test_EnforceMeltingTemperature.py . [ 31%]453tests/builtin_specifications/test_EnforcePatternOccurence.py ... [ 33%]454tests/builtin_specifications/test_EnforceRegionsCompatibility.py . [ 34%]455tests/builtin_specifications/test_EnforceSequence.py .. [ 35%]456tests/builtin_specifications/test_EnforceTerminalGCContent.py . [ 36%]457tests/builtin_specifications/test_EnforceTranslation.py ...... [ 40%]458tests/builtin_specifications/test_SequenceLengthBounds.py . [ 40%]459tests/builtin_specifications/test_UniquifyAllKmers.py ...... [ 44%]460tests/test_Location.py ......................................... [ 72%]461tests/test_MutationChoices.py ... [ 74%]462tests/test_NoSolutionError.py ... [ 76%]463tests/test_biotools.py ....... [ 81%]464tests/test_circular_sequences.py .. [ 82%]465tests/test_constraints_reports.py . [ 83%]466tests/test_determinism/test_determinism.py .. [ 85%]467tests/test_features_annotations.py ... [ 87%]468tests/test_io.py .... [ 89%]469tests/test_optimization_with_report.py .... [ 92%]470tests/test_patterns.py ... [ 94%]471tests/test_scenarios/test_primers_collection.py . [ 95%]472tests/test_utils.py . [ 95%]473tests/tests_from_genbanks/test_from_genbanks.py ...... [100%]474475=============================== warnings summary ===============================476tests/builtin_specifications/test_AllowPrimer.py::test_AllowPrimer477tests/builtin_specifications/test_EnforceMeltingTemperature.py::test_enforce_melting_temperature478tests/tests_from_genbanks/test_from_genbanks.py::test_all_shorthands479 /nix/store/15fg2cas1na5408nxy2iwgx21wx2p3cb-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/bindings.py:489: UserWarning: Function deprecated please use "calc_tm" instead480 return THERMO_ANALYSIS.calcTm(seq)481482tests/builtin_specifications/test_AllowPrimer.py::test_AllowPrimer483tests/test_scenarios/test_primers_collection.py::test_primers_collection_example484 /nix/store/15fg2cas1na5408nxy2iwgx21wx2p3cb-python3.14-primer3-py-2.3.1/lib/python3.14/site-packages/primer3/bindings.py:305: UserWarning: Function deprecated please use "calc_heterodimer" instead485 return THERMO_ANALYSIS.calcHeterodimer(486487-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html488================ 147 passed, 2 deselected, 5 warnings in 11.78s ================489Finished executing pytestCheckPhase