Package evaluation to test LineageCollapse on Julia 1.14.0-DEV.1354 (1806b0bc31*) started at 2025-12-14T17:25:19.602 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 10.92s ################################################################################ # Installation # Installing LineageCollapse... Resolving package versions... Installed AliasTables ───────────────── v1.1.3 Installed AbstractTrees ─────────────── v0.4.5 Installed FilePathsBase ─────────────── v0.9.24 Installed InlineStrings ─────────────── v1.4.5 Installed DataStructures ────────────── v0.19.3 Installed StatsBase ─────────────────── v0.34.9 Installed CodecZlib ─────────────────── v0.7.8 Installed OrderedCollections ────────── v1.8.1 Installed Compat ────────────────────── v4.18.1 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed TranscodingStreams ────────── v0.11.3 Installed DataAPI ───────────────────── v1.16.0 Installed Statistics ────────────────── v1.11.1 Installed InvertedIndices ───────────── v1.3.1 Installed StatsAPI ──────────────────── v1.8.0 Installed NearestNeighbors ──────────── v0.4.26 Installed PrecompileTools ───────────── v1.3.3 Installed DataValueInterfaces ───────── v1.0.0 Installed SentinelArrays ────────────── v1.4.8 Installed ProgressMeter ─────────────── v1.11.0 Installed StaticArraysCore ──────────── v1.4.4 Installed Clustering ────────────────── v0.15.8 Installed StaticArrays ──────────────── v1.9.15 Installed IrrationalConstants ───────── v0.2.6 Installed Twiddle ───────────────────── v1.1.2 Installed Distances ─────────────────── v0.10.12 Installed BioSymbols ────────────────── v5.2.0 Installed LogExpFunctions ───────────── v0.3.29 Installed StringManipulation ────────── v0.4.2 Installed Tables ────────────────────── v1.12.1 Installed Parsers ───────────────────── v2.8.3 Installed PtrArrays ─────────────────── v1.3.0 Installed Reexport ──────────────────── v1.2.2 Installed WeakRefStrings ────────────── v1.4.2 Installed PooledArrays ──────────────── v1.4.3 Installed Missings ──────────────────── v1.2.0 Installed Preferences ───────────────── v1.5.0 Installed TableTraits ───────────────── v1.0.1 Installed LaTeXStrings ──────────────── v1.4.0 Installed PrettyTables ──────────────── v3.1.2 Installed SortingAlgorithms ─────────── v1.2.2 Installed Crayons ───────────────────── v4.1.1 Installed StringDistances ───────────── v0.11.3 Installed WorkerUtilities ───────────── v1.6.1 Installed DataFrames ────────────────── v1.8.1 Installed DocStringExtensions ───────── v0.9.5 Installed BioSequences ──────────────── v3.5.0 Installed LineageCollapse ───────────── v0.0.13 Installed CSV ───────────────────────── v0.10.15 Updating `~/.julia/environments/v1.14/Project.toml` [e38bdfdf] + LineageCollapse v0.0.13 Updating `~/.julia/environments/v1.14/Manifest.toml` [1520ce14] + AbstractTrees v0.4.5 [66dad0bd] + AliasTables v1.1.3 [7e6ae17a] + BioSequences v3.5.0 [3c28c6f8] + BioSymbols v5.2.0 [336ed68f] + CSV v0.10.15 [aaaa29a8] + Clustering v0.15.8 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.18.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [b4f34e82] + Distances v0.10.12 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [b964fa9f] + LaTeXStrings v1.4.0 [e38bdfdf] + LineageCollapse v0.0.13 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [b8a86587] + NearestNeighbors v0.4.26 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.2 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [189a3867] + Reexport v1.2.2 [91c51154] + SentinelArrays v1.4.8 [a2af1166] + SortingAlgorithms v1.2.2 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.9 [88034a9c] + StringDistances v0.11.3 [892a3eda] + StringManipulation v0.4.2 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [7200193e] + Twiddle v1.1.2 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 6.61s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 Precompilation failed after 14.93s ################################################################################ # Testing # Testing LineageCollapse Status `/tmp/jl_FGGeGz/Project.toml` [7e6ae17a] BioSequences v3.5.0 [336ed68f] CSV v0.10.15 [aaaa29a8] Clustering v0.15.8 [a93c6f00] DataFrames v1.8.1 [e38bdfdf] LineageCollapse v0.0.13 [92933f4c] ProgressMeter v1.11.0 [88034a9c] StringDistances v0.11.3 [37e2e46d] LinearAlgebra v1.13.0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_FGGeGz/Manifest.toml` [1520ce14] AbstractTrees v0.4.5 [66dad0bd] AliasTables v1.1.3 [7e6ae17a] BioSequences v3.5.0 [3c28c6f8] BioSymbols v5.2.0 [336ed68f] CSV v0.10.15 [aaaa29a8] Clustering v0.15.8 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.18.1 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [b4f34e82] Distances v0.10.12 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [b964fa9f] LaTeXStrings v1.4.0 [e38bdfdf] LineageCollapse v0.0.13 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [b8a86587] NearestNeighbors v0.4.26 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [189a3867] Reexport v1.2.2 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.2 [90137ffa] StaticArrays v1.9.15 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.9 [88034a9c] StringDistances v0.11.3 [892a3eda] StringManipulation v0.4.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [7200193e] Twiddle v1.1.2 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [4536629a] OpenBLAS_jll v0.3.29+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.15.0+0 Testing Running tests... [ Info: Processing 5 rows [ Info: Dropped missing CDR3 rows: 4 [ Info: Dropped stop codons: 3 [ Info: Processing 5 rows [ Info: Dropped missing CDR3 rows: 4 [ Info: Dropped stop codons: 3 [ Info: Dropped short (≤4) D region sequences: 0 [ Info: Processing 5 rows [ Info: Dropped missing CDR3 rows: 4 [ Info: Dropped stop codons: 3 [ Info: Deduplicated using sequence only: 2 [ Info: Processing 5 rows [ Info: Dropped missing CDR3 rows: 4 [ Info: Dropped stop codons: 3 [ Info: Deduplicated using sequence and barcode: 3 [ Info: Processing 2 rows [ Info: Dropped missing CDR3 rows: 2 [ Info: Dropped stop codons: 2 [ Info: Dropped short (≤3) D region sequences: 1 [ Info: Processing 2 rows [ Info: Dropped missing CDR3 rows: 0 [ Info: Dropped stop codons: 0 [ Info: Deduplicated using sequence only: 2 [ Info: Deduplicated using sequence and barcode: 3 [ Info: Deduplicated using sequence only: 2 Process Lineages: Error During Test at /home/pkgeval/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:38 Got exception outside of a @test BoundsError: attempt to access 2×12 DataFrame at index [!, 125393041966272] Stacktrace: [1] getindex @ ~/.julia/packages/DataFrames/b4w9K/src/dataframe/dataframe.jl:551 [inlined] [2] isagg @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/fastaggregates.jl:290 [inlined] [3] (::DataFrames.var"#_combine##0#_combine##1"{GroupedDataFrame{DataFrame}})(x::Pair{Int64, Pair{typeof(length), Symbol}}) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:690 [4] _any(f::DataFrames.var"#_combine##0#_combine##1"{GroupedDataFrame{DataFrame}}, itr::Vector{Any}, ::Colon) @ Base ./anyall.jl:124 [5] any @ ./reducedim.jl:993 [inlined] [6] _combine(gd::GroupedDataFrame{DataFrame}, cs_norm::Vector{Any}, optional_transform::Vector{Bool}, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:690 [7] _combine_prepare_norm(gd::GroupedDataFrame{DataFrame}, cs_vec::Vector{Any}, keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:87 [8] _combine_prepare(gd::GroupedDataFrame{DataFrame}, ::Base.RefValue{Any}; keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:52 [9] _combine_prepare @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:26 [inlined] [10] select(::GroupedDataFrame{DataFrame}, ::Union{Regex, AbstractString, Function, Signed, Symbol, Unsigned, Pair, Type, All, Between, Cols, InvertedIndex, AbstractVecOrMat}, ::Vararg{Union{Regex, AbstractString, Function, Signed, Symbol, Unsigned, Pair, Type, All, Between, Cols, InvertedIndex, AbstractVecOrMat}}; copycols::Bool, keepkeys::Bool, ungroup::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:892 [11] kwcall(::@NamedTuple{copycols::Bool, keepkeys::Bool, ungroup::Bool, renamecols::Bool, threads::Bool}, ::typeof(select), ::GroupedDataFrame{DataFrame}, ::Union{Regex, AbstractString, Function, Signed, Symbol, Unsigned, Pair, Type, All, Between, Cols, InvertedIndex, AbstractVecOrMat}, ::Union{Regex, AbstractString, Function, Signed, Symbol, Unsigned, Pair, Type, All, Between, Cols, InvertedIndex, AbstractVecOrMat}) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:888 [12] transform(gd::GroupedDataFrame{DataFrame}, args::Union{Regex, AbstractString, Function, Signed, Symbol, Unsigned, Pair, Type, All, Between, Cols, InvertedIndex, AbstractVecOrMat}; copycols::Bool, keepkeys::Bool, ungroup::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:917 [13] transform @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:912 [inlined] [14] process_lineages(df::DataFrame; distance_metric::HammingDistance, clustering_method::HierarchicalClustering, linkage::Symbol) @ LineageCollapse ~/.julia/packages/LineageCollapse/klgRo/src/lineage_processing.jl:129 [15] kwcall(::@NamedTuple{distance_metric::HammingDistance, clustering_method::HierarchicalClustering}, ::typeof(process_lineages), df::DataFrame) @ LineageCollapse ~/.julia/packages/LineageCollapse/klgRo/src/lineage_processing.jl:92 [16] top-level scope @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:8 [17] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [18] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:40 [inlined] [19] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [20] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:52 [inlined] [21] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [22] top-level scope @ ~/.julia/packages/LineageCollapse/klgRo/test/runtests.jl:5 [23] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [24] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/runtests.jl:7 [inlined] [25] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [26] top-level scope @ none:6 [27] eval(m::Module, e::Any) @ Core ./boot.jl:489 [28] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [29] _start() @ Base ./client.jl:577 Process Lineages with Levenshtein Distance: Error During Test at /home/pkgeval/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:67 Got exception outside of a @test BoundsError: attempt to access 2×12 DataFrame at index [!, 125393041966272] Stacktrace: [1] getindex @ ~/.julia/packages/DataFrames/b4w9K/src/dataframe/dataframe.jl:551 [inlined] [2] isagg @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/fastaggregates.jl:290 [inlined] [3] (::DataFrames.var"#_combine##0#_combine##1"{GroupedDataFrame{DataFrame}})(x::Pair{Int64, Pair{typeof(length), Symbol}}) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:690 [4] _any(f::DataFrames.var"#_combine##0#_combine##1"{GroupedDataFrame{DataFrame}}, itr::Vector{Any}, ::Colon) @ Base ./anyall.jl:124 [5] any @ ./reducedim.jl:993 [inlined] [6] _combine(gd::GroupedDataFrame{DataFrame}, cs_norm::Vector{Any}, optional_transform::Vector{Bool}, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:690 [7] _combine_prepare_norm(gd::GroupedDataFrame{DataFrame}, cs_vec::Vector{Any}, keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:87 [8] _combine_prepare(gd::GroupedDataFrame{DataFrame}, ::Base.RefValue{Any}; keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:52 [9] _combine_prepare @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:26 [inlined] [10] select(::GroupedDataFrame{DataFrame}, ::Union{Regex, AbstractString, Function, Signed, Symbol, Unsigned, Pair, Type, All, Between, Cols, InvertedIndex, AbstractVecOrMat}, ::Vararg{Union{Regex, AbstractString, Function, Signed, Symbol, Unsigned, Pair, Type, All, Between, Cols, InvertedIndex, AbstractVecOrMat}}; copycols::Bool, keepkeys::Bool, ungroup::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:892 [11] kwcall(::@NamedTuple{copycols::Bool, keepkeys::Bool, ungroup::Bool, renamecols::Bool, threads::Bool}, ::typeof(select), ::GroupedDataFrame{DataFrame}, ::Union{Regex, AbstractString, Function, Signed, Symbol, Unsigned, Pair, Type, All, Between, Cols, InvertedIndex, AbstractVecOrMat}, ::Union{Regex, AbstractString, Function, Signed, Symbol, Unsigned, Pair, Type, All, Between, Cols, InvertedIndex, AbstractVecOrMat}) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:888 [12] transform(gd::GroupedDataFrame{DataFrame}, args::Union{Regex, AbstractString, Function, Signed, Symbol, Unsigned, Pair, Type, All, Between, Cols, InvertedIndex, AbstractVecOrMat}; copycols::Bool, keepkeys::Bool, ungroup::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:917 [13] transform @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:912 [inlined] [14] process_lineages(df::DataFrame; distance_metric::LevenshteinDistance, clustering_method::HierarchicalClustering, linkage::Symbol) @ LineageCollapse ~/.julia/packages/LineageCollapse/klgRo/src/lineage_processing.jl:129 [15] kwcall(::@NamedTuple{distance_metric::LevenshteinDistance, clustering_method::HierarchicalClustering}, ::typeof(process_lineages), df::DataFrame) @ LineageCollapse ~/.julia/packages/LineageCollapse/klgRo/src/lineage_processing.jl:92 [16] top-level scope @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:8 [17] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [18] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:68 [inlined] [19] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [20] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:80 [inlined] [21] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [22] top-level scope @ ~/.julia/packages/LineageCollapse/klgRo/test/runtests.jl:5 [23] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [24] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/runtests.jl:7 [inlined] [25] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [26] top-level scope @ none:6 [27] eval(m::Module, e::Any) @ Core ./boot.jl:489 [28] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [29] _start() @ Base ./client.jl:577 Process Lineages with Normalized Hamming Distance and check grouping: Error During Test at /home/pkgeval/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:86 Got exception outside of a @test BoundsError: attempt to access 10×12 DataFrame at index [!, 125393041966272] Stacktrace: [1] getindex @ ~/.julia/packages/DataFrames/b4w9K/src/dataframe/dataframe.jl:551 [inlined] [2] isagg @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/fastaggregates.jl:290 [inlined] [3] (::DataFrames.var"#_combine##0#_combine##1"{GroupedDataFrame{DataFrame}})(x::Pair{Int64, Pair{typeof(length), Symbol}}) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:690 [4] _any(f::DataFrames.var"#_combine##0#_combine##1"{GroupedDataFrame{DataFrame}}, itr::Vector{Any}, ::Colon) @ Base ./anyall.jl:124 [5] any @ ./reducedim.jl:993 [inlined] [6] _combine(gd::GroupedDataFrame{DataFrame}, cs_norm::Vector{Any}, optional_transform::Vector{Bool}, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:690 [7] _combine_prepare_norm(gd::GroupedDataFrame{DataFrame}, cs_vec::Vector{Any}, keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:87 [8] _combine_prepare(gd::GroupedDataFrame{DataFrame}, ::Base.RefValue{Any}; keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:52 [9] _combine_prepare @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:26 [inlined] [10] select(::GroupedDataFrame{DataFrame}, ::Union{Regex, AbstractString, Function, Signed, Symbol, Unsigned, Pair, Type, All, Between, Cols, InvertedIndex, AbstractVecOrMat}, ::Vararg{Union{Regex, AbstractString, Function, Signed, Symbol, Unsigned, Pair, Type, All, Between, Cols, InvertedIndex, AbstractVecOrMat}}; copycols::Bool, keepkeys::Bool, ungroup::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:892 [11] kwcall(::@NamedTuple{copycols::Bool, keepkeys::Bool, ungroup::Bool, renamecols::Bool, threads::Bool}, ::typeof(select), ::GroupedDataFrame{DataFrame}, ::Union{Regex, AbstractString, Function, Signed, Symbol, Unsigned, Pair, Type, All, Between, Cols, InvertedIndex, AbstractVecOrMat}, ::Union{Regex, AbstractString, Function, Signed, Symbol, Unsigned, Pair, Type, All, Between, Cols, InvertedIndex, AbstractVecOrMat}) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:888 [12] transform(gd::GroupedDataFrame{DataFrame}, args::Union{Regex, AbstractString, Function, Signed, Symbol, Unsigned, Pair, Type, All, Between, Cols, InvertedIndex, AbstractVecOrMat}; copycols::Bool, keepkeys::Bool, ungroup::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:917 [13] transform @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:912 [inlined] [14] process_lineages(df::DataFrame; distance_metric::NormalizedHammingDistance, clustering_method::HierarchicalClustering, linkage::Symbol) @ LineageCollapse ~/.julia/packages/LineageCollapse/klgRo/src/lineage_processing.jl:129 [15] kwcall(::@NamedTuple{distance_metric::NormalizedHammingDistance, clustering_method::HierarchicalClustering}, ::typeof(process_lineages), df::DataFrame) @ LineageCollapse ~/.julia/packages/LineageCollapse/klgRo/src/lineage_processing.jl:92 [16] top-level scope @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:8 [17] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [18] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:87 [inlined] [19] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [20] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:120 [inlined] [21] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [22] top-level scope @ ~/.julia/packages/LineageCollapse/klgRo/test/runtests.jl:5 [23] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [24] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/runtests.jl:7 [inlined] [25] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [26] top-level scope @ none:6 [27] eval(m::Module, e::Any) @ Core ./boot.jl:489 [28] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [29] _start() @ Base ./client.jl:577 Hardest collapse strategy: Error During Test at /home/pkgeval/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:135 Got exception outside of a @test BoundsError: attempt to access 6×6 DataFrame at index [!, 125393199237440] Stacktrace: [1] getindex @ ~/.julia/packages/DataFrames/b4w9K/src/dataframe/dataframe.jl:551 [inlined] [2] isagg @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/fastaggregates.jl:290 [inlined] [3] (::DataFrames.var"#_combine##0#_combine##1"{GroupedDataFrame{DataFrame}})(x::Pair{Int64, Pair{typeof(length), Symbol}}) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:690 [4] _any(f::DataFrames.var"#_combine##0#_combine##1"{GroupedDataFrame{DataFrame}}, itr::Vector{Any}, ::Colon) @ Base ./anyall.jl:124 [5] any @ ./reducedim.jl:993 [inlined] [6] _combine(gd::GroupedDataFrame{DataFrame}, cs_norm::Vector{Any}, optional_transform::Vector{Bool}, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:690 [7] _combine_prepare_norm(gd::GroupedDataFrame{DataFrame}, cs_vec::Vector{Any}, keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:87 [8] _combine_prepare(gd::GroupedDataFrame{DataFrame}, ::Base.RefValue{Any}; keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:52 [9] _combine_prepare @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:26 [inlined] [10] combine @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:857 [inlined] [11] collapse_lineages(df::DataFrame, clone_frequency_threshold::Float64, collapse_strategy::Symbol) @ LineageCollapse ~/.julia/packages/LineageCollapse/klgRo/src/lineage_processing.jl:178 [12] top-level scope @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:8 [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [14] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:126 [inlined] [15] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [16] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:136 [inlined] [17] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [18] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:136 [inlined] [19] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [20] top-level scope @ ~/.julia/packages/LineageCollapse/klgRo/test/runtests.jl:5 [21] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [22] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/runtests.jl:7 [inlined] [23] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [24] top-level scope @ none:6 [25] eval(m::Module, e::Any) @ Core ./boot.jl:489 [26] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [27] _start() @ Base ./client.jl:577 Soft collapse strategy: Error During Test at /home/pkgeval/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:143 Got exception outside of a @test BoundsError: attempt to access 6×6 DataFrame at index [!, 125393199237440] Stacktrace: [1] getindex @ ~/.julia/packages/DataFrames/b4w9K/src/dataframe/dataframe.jl:551 [inlined] [2] isagg @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/fastaggregates.jl:290 [inlined] [3] (::DataFrames.var"#_combine##0#_combine##1"{GroupedDataFrame{DataFrame}})(x::Pair{Int64, Pair{typeof(length), Symbol}}) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:690 [4] _any(f::DataFrames.var"#_combine##0#_combine##1"{GroupedDataFrame{DataFrame}}, itr::Vector{Any}, ::Colon) @ Base ./anyall.jl:124 [5] any @ ./reducedim.jl:993 [inlined] [6] _combine(gd::GroupedDataFrame{DataFrame}, cs_norm::Vector{Any}, optional_transform::Vector{Bool}, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:690 [7] _combine_prepare_norm(gd::GroupedDataFrame{DataFrame}, cs_vec::Vector{Any}, keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:87 [8] _combine_prepare(gd::GroupedDataFrame{DataFrame}, ::Base.RefValue{Any}; keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:52 [9] _combine_prepare @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:26 [inlined] [10] combine @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:857 [inlined] [11] collapse_lineages(df::DataFrame, clone_frequency_threshold::Float64, collapse_strategy::Symbol) @ LineageCollapse ~/.julia/packages/LineageCollapse/klgRo/src/lineage_processing.jl:178 [12] top-level scope @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:8 [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [14] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:126 [inlined] [15] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [16] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:144 [inlined] [17] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [18] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:144 [inlined] [19] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [20] top-level scope @ ~/.julia/packages/LineageCollapse/klgRo/test/runtests.jl:5 [21] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [22] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/runtests.jl:7 [inlined] [23] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [24] top-level scope @ none:6 [25] eval(m::Module, e::Any) @ Core ./boot.jl:489 [26] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [27] _start() @ Base ./client.jl:577 Edge cases: Error During Test at /home/pkgeval/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:159 Got exception outside of a @test BoundsError: attempt to access 2×6 DataFrame at index [!, 125393199237440] Stacktrace: [1] getindex @ ~/.julia/packages/DataFrames/b4w9K/src/dataframe/dataframe.jl:551 [inlined] [2] isagg @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/fastaggregates.jl:290 [inlined] [3] (::DataFrames.var"#_combine##0#_combine##1"{GroupedDataFrame{DataFrame}})(x::Pair{Int64, Pair{typeof(length), Symbol}}) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:690 [4] _any(f::DataFrames.var"#_combine##0#_combine##1"{GroupedDataFrame{DataFrame}}, itr::Vector{Any}, ::Colon) @ Base ./anyall.jl:124 [5] any @ ./reducedim.jl:993 [inlined] [6] _combine(gd::GroupedDataFrame{DataFrame}, cs_norm::Vector{Any}, optional_transform::Vector{Bool}, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:690 [7] _combine_prepare_norm(gd::GroupedDataFrame{DataFrame}, cs_vec::Vector{Any}, keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:87 [8] _combine_prepare(gd::GroupedDataFrame{DataFrame}, ::Base.RefValue{Any}; keepkeys::Bool, ungroup::Bool, copycols::Bool, keeprows::Bool, renamecols::Bool, threads::Bool) @ DataFrames ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:52 [9] _combine_prepare @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:26 [inlined] [10] combine @ ~/.julia/packages/DataFrames/b4w9K/src/groupeddataframe/splitapplycombine.jl:857 [inlined] [11] collapse_lineages(df::DataFrame, clone_frequency_threshold::Float64, collapse_strategy::Symbol) @ LineageCollapse ~/.julia/packages/LineageCollapse/klgRo/src/lineage_processing.jl:178 [12] top-level scope @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:8 [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [14] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:126 [inlined] [15] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [16] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:161 [inlined] [17] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [18] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/test_lineage_processing.jl:169 [inlined] [19] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [20] top-level scope @ ~/.julia/packages/LineageCollapse/klgRo/test/runtests.jl:5 [21] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [22] macro expansion @ ~/.julia/packages/LineageCollapse/klgRo/test/runtests.jl:7 [inlined] [23] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [24] top-level scope @ none:6 [25] eval(m::Module, e::Any) @ Core ./boot.jl:489 [26] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [27] _start() @ Base ./client.jl:577 Test Summary: | Pass Error Total Time LineageCollapse.jl | 50 6 56 2m11.8s Data Loading | 17 17 43.5s Preprocessing | 20 20 16.1s Lineage Processing | 13 6 19 1m10.4s Distance Metrics | 4 4 0.3s Pairwise Distance Computation | 2 2 2.4s Hierarchical Clustering | 3 3 5.5s Process Lineages | 1 1 57.6s Process Lineages with Levenshtein Distance | 1 1 0.8s Process Lineages with Normalized Hamming Distance and check grouping | 1 1 1.6s collapse_lineages function | 4 3 7 2.2s Hardest collapse strategy | 1 1 2.1s Soft collapse strategy | 1 1 0.0s Edge cases | 1 1 0.0s Invalid inputs | 4 4 0.0s RNG of the outermost testset: Random.Xoshiro(0x664448254fc5b68d, 0xd54bfc6cef9ba815, 0xce14173631187d73, 0xca25cb91dc262892, 0x73954278191e3e09) ERROR: LoadError: Some tests did not pass: 50 passed, 0 failed, 6 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/LineageCollapse/klgRo/test/runtests.jl:4 Testing failed after 461.52s ERROR: LoadError: Package LineageCollapse errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3053 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2902 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:572 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:237 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:228 PkgEval failed after 517.31s: package tests unexpectedly errored