Package evaluation of PoreMatMod on Julia 1.10.8 (92f03a4775*) started at 2025-02-25T12:54:16.334 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 4.98s ################################################################################ # Installation # Installing PoreMatMod... Resolving package versions... Updating `~/.julia/environments/v1.10/Project.toml` [2de0d7f0] + PoreMatMod v0.2.20 Updating `~/.julia/environments/v1.10/Manifest.toml` [ec485272] + ArnoldiMethod v0.4.0 ⌅ [a963bdd2] + AtomsBase v0.4.2 [99c8bb3a] + Bio3DView v1.0.0 [d1d4a3ce] + BitFlags v0.1.9 [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.16.0 [f0e56b4a] + ConcurrentUtilities v2.5.0 [5218b696] + Configurations v0.17.6 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.20 [e2d170a0] + DataValueInterfaces v1.0.0 [ffbed154] + DocStringExtensions v0.9.3 [460bff9d] + ExceptionUnwrapping v0.1.11 [21656369] + ExpressionExplorer v1.1.1 [55351af7] + ExproniconLite v0.10.14 [5789e2e9] + FileIO v1.16.6 [48062228] + FilePathsBase v0.9.23 [fb4132e2] + FuzzyCompletions v0.5.5 [86223c79] + Graphs v1.12.0 [cd3eb016] + HTTP v1.10.15 [ac1192a8] + HypertextLiteral v0.9.5 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.3 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 ⌅ [033835bb] + JLD2 v0.4.54 [692b3bcd] + JLLWrappers v1.7.0 [b964fa9f] + LaTeXStrings v1.4.0 [0e77f7df] + LazilyInitializedFields v1.3.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e6f89c97] + LoggingExtras v1.1.0 [6c6e2e6c] + MIMEs v1.0.0 [1914dd2f] + MacroTools v0.5.15 [36869731] + Malt v1.1.2 [739be429] + MbedTLS v1.1.9 ⌅ [626554b9] + MetaGraphs v0.7.2 [e1d29d7a] + Missings v1.2.0 [99f44e22] + MsgPack v1.2.1 [4d8831e6] + OpenSSL v1.4.3 [bac558e1] + OrderedCollections v1.8.0 [69de0a69] + Parsers v2.8.1 [7b2266bf] + PeriodicTable v1.2.1 [c3e4b0f8] + Pluto v0.20.4 [72656b73] + PlutoDependencyExplorer v1.2.0 [2dfb63ee] + PooledArrays v1.4.3 [2de0d7f0] + PoreMatMod v0.2.20 [91cefc8d] + PrecompileSignatures v3.0.3 [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [189a3867] + Reexport v1.2.2 [2792f1a3] + RegistryInstances v0.1.0 [05181044] + RelocatableFolders v1.0.1 [ae029012] + Requires v1.3.0 [6c6a2e73] + Scratch v1.2.1 [91c51154] + SentinelArrays v1.4.8 [777ac1f9] + SimpleBufferStream v1.2.0 [699a6c99] + SimpleTraits v0.9.4 [a2af1166] + SortingAlgorithms v1.2.1 [90137ffa] + StaticArrays v1.9.12 [1e83bf80] + StaticArraysCore v1.4.3 [82ae8749] + StatsAPI v1.7.0 ⌅ [2913bbd2] + StatsBase v0.33.21 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [3bb67fe8] + TranscodingStreams v0.11.3 [410a4b4d] + Tricks v0.1.10 [5c2747f8] + URIs v1.5.1 [1986cc42] + Unitful v1.22.0 [a7773ee8] + UnitfulAtomic v1.0.0 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [ede5f01d] + Xtals v0.5.1 [458c3c95] + OpenSSL_jll v3.0.16+0 [0dad84c5] + ArgTools v1.1.1 [56f22d72] + Artifacts [2a0f44e3] + Base64 [ade2ca70] + Dates [8ba89e20] + Distributed [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching [9fa8497b] + Future [b77e0a4c] + InteractiveUtils [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [a63ad114] + Mmap [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.10.0 [de0858da] + Printf [3fa0cd96] + REPL [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [1a1011a3] + SharedArrays [6462fe0b] + Sockets [2f01184e] + SparseArrays v1.10.0 [10745b16] + Statistics v1.10.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.4.0+0 [e37daf67] + LibGit2_jll v1.6.4+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.2+1 [14a3606d] + MozillaCACerts_jll v2023.1.10 [4536629a] + OpenBLAS_jll v0.3.23+4 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.52.0+1 [3f19e933] + p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 7.21s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 168.95s ################################################################################ # Testing # Testing PoreMatMod Status `/tmp/jl_G7WuzL/Project.toml` [e30172f5] Documenter v1.8.1 [86223c79] Graphs v1.12.0 ⌅ [626554b9] MetaGraphs v0.7.2 [2fc8631c] PlutoSliderServer v1.0.3 [7f904dfe] PlutoUI v0.7.61 [2de0d7f0] PoreMatMod v0.2.20 [b77e0a4c] InteractiveUtils [37e2e46d] LinearAlgebra [d6f4376e] Markdown [44cfe95a] Pkg v1.10.0 [de0858da] Printf [8dfed614] Test Status `/tmp/jl_G7WuzL/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [6e696c72] AbstractPlutoDingetjes v1.3.2 [1520ce14] AbstractTrees v0.4.5 [ec485272] ArnoldiMethod v0.4.0 ⌅ [a963bdd2] AtomsBase v0.4.2 [c9fd44ac] BetterFileWatching v0.1.5 [99c8bb3a] Bio3DView v1.0.0 [d1d4a3ce] BitFlags v0.1.9 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 ⌅ [3da002f7] ColorTypes v0.11.5 [34da2185] Compat v4.16.0 [f0e56b4a] ConcurrentUtilities v2.5.0 [5218b696] Configurations v0.17.6 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.20 [e2d170a0] DataValueInterfaces v1.0.0 [ffbed154] DocStringExtensions v0.9.3 [e30172f5] Documenter v1.8.1 [460bff9d] ExceptionUnwrapping v0.1.11 [21656369] ExpressionExplorer v1.1.1 [55351af7] ExproniconLite v0.10.14 [5789e2e9] FileIO v1.16.6 [48062228] FilePathsBase v0.9.23 [53c48c17] FixedPointNumbers v0.8.5 [ff7dd447] FromFile v0.1.6 [fb4132e2] FuzzyCompletions v0.5.5 [d7ba0133] Git v1.3.1 [6b79fd1a] GitHubActions v0.1.8 [c27321d9] Glob v1.3.1 [86223c79] Graphs v1.12.0 [cd3eb016] HTTP v1.10.15 [47d2ed2b] Hyperscript v0.0.5 [ac1192a8] HypertextLiteral v0.9.5 [b5f81e59] IOCapture v0.2.5 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.3 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 ⌅ [033835bb] JLD2 v0.4.54 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [b964fa9f] LaTeXStrings v1.4.0 [0e77f7df] LazilyInitializedFields v1.3.0 [1d6d02ad] LeftChildRightSiblingTrees v0.2.0 [2ab3a3ac] LogExpFunctions v0.3.29 [e6f89c97] LoggingExtras v1.1.0 [6c6e2e6c] MIMEs v1.0.0 [1914dd2f] MacroTools v0.5.15 [36869731] Malt v1.1.2 [d0879d2d] MarkdownAST v0.1.2 [739be429] MbedTLS v1.1.9 ⌅ [626554b9] MetaGraphs v0.7.2 [e1d29d7a] Missings v1.2.0 [99f44e22] MsgPack v1.2.1 [4d8831e6] OpenSSL v1.4.3 [bac558e1] OrderedCollections v1.8.0 [69de0a69] Parsers v2.8.1 [7b2266bf] PeriodicTable v1.2.1 [c3e4b0f8] Pluto v0.20.4 [72656b73] PlutoDependencyExplorer v1.2.0 [2fc8631c] PlutoSliderServer v1.0.3 [7f904dfe] PlutoUI v0.7.61 [2dfb63ee] PooledArrays v1.4.3 [2de0d7f0] PoreMatMod v0.2.20 [91cefc8d] PrecompileSignatures v3.0.3 [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [33c8b6b6] ProgressLogging v0.1.4 [189a3867] Reexport v1.2.2 [2792f1a3] RegistryInstances v0.1.0 [05181044] RelocatableFolders v1.0.1 [ae029012] Requires v1.3.0 [6c6a2e73] Scratch v1.2.1 [91c51154] SentinelArrays v1.4.8 [777ac1f9] SimpleBufferStream v1.2.0 [699a6c99] SimpleTraits v0.9.4 [a2af1166] SortingAlgorithms v1.2.1 [90137ffa] StaticArrays v1.9.12 [1e83bf80] StaticArraysCore v1.4.3 [82ae8749] StatsAPI v1.7.0 ⌅ [2913bbd2] StatsBase v0.33.21 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [5d786b92] TerminalLoggers v0.1.7 [3bb67fe8] TranscodingStreams v0.11.3 [410a4b4d] Tricks v0.1.10 [5c2747f8] URIs v1.5.1 [1986cc42] Unitful v1.22.0 [a7773ee8] UnitfulAtomic v1.0.0 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [ede5f01d] Xtals v0.5.1 ⌅ [04572ae6] Deno_jll v1.33.4+0 [2e619515] Expat_jll v2.6.5+0 [f8c6e375] Git_jll v2.47.1+0 [94ce4f54] Libiconv_jll v1.18.0+0 [458c3c95] OpenSSL_jll v3.0.16+0 [0dad84c5] ArgTools v1.1.1 [56f22d72] Artifacts [2a0f44e3] Base64 [ade2ca70] Dates [8ba89e20] Distributed [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching [9fa8497b] Future [b77e0a4c] InteractiveUtils [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 [8f399da3] Libdl [37e2e46d] LinearAlgebra [56ddb016] Logging [d6f4376e] Markdown [a63ad114] Mmap [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.10.0 [de0858da] Printf [3fa0cd96] REPL [9a3f8284] Random [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization [1a1011a3] SharedArrays [6462fe0b] Sockets [2f01184e] SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.4.0+0 [e37daf67] LibGit2_jll v1.6.4+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.2+1 [14a3606d] MozillaCACerts_jll v2023.1.10 [4536629a] OpenBLAS_jll v0.3.23+4 [efcefdf7] PCRE2_jll v10.42.0+1 [bea87d4a] SuiteSparse_jll v7.2.1+1 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.52.0+1 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... WARNING: could not import AtomsBase.boundary_conditions into Xtals WARNING: could not import AtomsBase.species_type into Xtals _______ __ __ __ __ __ __ / \ / \ / | / | / \ / | / | $$$$$$$ | ______ ______ ______ $$ \ /$$ | ______ _$$ |_ $$ \ /$$ | ______ ____$$ | $$ |__$$ |/ \ / \ / \ $$$ \ /$$$ | / \ / $$ | $$$ \ /$$$ | / \ / $$ | $$ $$//$$$$$$ |/$$$$$$ |/$$$$$$ |$$$$ /$$$$ | $$$$$$ |$$$$$$/ $$$$ /$$$$ |/$$$$$$ |/$$$$$$$ | $$$$$$$/ $$ | $$ |$$ | $$/ $$ $$ |$$ $$ $$/$$ | / $$ | $$ | __ $$ $$ $$/$$ |$$ | $$ |$$ | $$ | $$ | $$ \__$$ |$$ | $$$$$$$$/ $$ |$$$/ $$ |/$$$$$$$ | $$ |/ |$$ |$$$/ $$ |$$ \__$$ |$$ \__$$ | $$ | $$ $$/ $$ | $$ |$$ | $/ $$ |$$ $$ | $$ $$/ $$ | $/ $$ |$$ $$/ $$ $$ | $$/ $$$$$$/ $$/ $$$$$$$/ $$/ $$/ $$$$$$$/ $$$$/ $$/ $$/ $$$$$$/ $$$$$$$/ [ Info: Running test/moiety.jl Test Summary: | Pass Total Time Moiety Tests | 4 4 12.5s 13.487172 seconds (323.41 k allocations: 17.427 MiB, 99.75% compilation time) [ Info: Running test/ullmann.jl Test Summary: | Pass Total Time Ullmann Tests | 7 7 3.1s 3.094357 seconds (725.93 k allocations: 48.580 MiB, 98.93% compilation time) [ Info: Running test/findreplace.jl Test Summary: | Pass Total Time replacement split across PB | 3 3 25.3s Test Summary: | Pass Total Time split across PB, non-connected replacement | 2 2 0.9s Test Summary: | Pass Total Time replacement spans twice the unit cell | 1 1 0.1s Test Summary: | Pass Total Time substructure_search | 17 17 12.8s Test Summary: | Pass Total Time find_replace | 8 8 42.9s ┌ Warning: atom 1 = C in conglomerate_test.cif is not bonded to any other atom. └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:379 ┌ Warning: atom 2 = C in conglomerate_test.cif is not bonded to any other atom. └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:379 ┌ Warning: atom 5 = C in conglomerate_test.cif is not bonded to any other atom. └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:379 Test Summary: | Pass Total Time conglomerate test | 4 4 0.9s Test Summary: | Pass Total Time remove duplicates | 2 2 0.3s 93.629405 seconds (45.25 M allocations: 19.041 GiB, 2.60% gc time, 40.25% compilation time) [ Info: Running test/examples.jl WARNING: replacing module PoreMatMod_Test. Test Summary: | Pass Total Time correct_missing_Hs | 1 1 17.4s ┌ Warning: carbon atom 1 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 2 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 5 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 14 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 15 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 18 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 24 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 25 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 28 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 34 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 35 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 38 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 44 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 45 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 48 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 49 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 52 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 53 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 56 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 57 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 60 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 61 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 67 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 68 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 73 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 74 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 79 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 80 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 85 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 86 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 89 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 90 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 93 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 94 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 97 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 98 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 101 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 102 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 105 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 114 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 115 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 118 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 124 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 125 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 128 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 134 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 135 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 138 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 144 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 145 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 148 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 149 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 152 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 153 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 156 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 157 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 160 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 161 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 167 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 168 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 173 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 174 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 179 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 180 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 185 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 186 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 189 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 190 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 193 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 194 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 197 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 198 in SIFSIX-2-Cu-i.cif is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 6 in disordered_ligand!.xyz is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 8 in disordered_ligand!.xyz is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 11 in disordered_ligand!.xyz is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 12 in disordered_ligand!.xyz is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 1 in disordered_ligand!.xyz is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 2 in disordered_ligand!.xyz is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 3 in disordered_ligand!.xyz is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 4 in disordered_ligand!.xyz is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 6 in disordered_ligand!.xyz is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 8 in disordered_ligand!.xyz is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 11 in disordered_ligand!.xyz is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 12 in disordered_ligand!.xyz is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 1 in disordered_ligand!.xyz is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 2 in disordered_ligand!.xyz is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 3 in disordered_ligand!.xyz is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 ┌ Warning: carbon atom 4 in disordered_ligand!.xyz is bonded to more than four atoms! └ @ Xtals ~/.julia/packages/Xtals/paV65/src/bonds.jl:389 Test Summary: | Pass Total Time disorder_and_guests | 1 1 3.5s Test Summary: | Pass Total Time make_hypothetical_MOF | 1 1 10.9s ┌ Warning: Dropping charges from parent. └ @ PoreMatMod ~/.julia/packages/PoreMatMod/R2OKZ/src/replace.jl:424 Test Summary: | Pass Total Time missing_linker_defect | 1 1 1m10.4s Test Summary: | Pass Total Time replacement_modes | 1 1 11.3s 113.687111 seconds (55.60 M allocations: 25.264 GiB, 1.87% gc time, 12.86% compilation time) ┌ Warning: Unable to determine HTML(edit_link = ...) from remote HEAD branch, defaulting to "master". │ Calling `git remote` failed with an exception. Set JULIA_DEBUG=Documenter to see the error. │ Unless this is due to a configuration error, the relevant variable should be set explicitly. └ @ Documenter ~/.julia/packages/Documenter/iwb7N/src/utilities/utilities.jl:651 [ Info: SetupBuildDirectory: setting up build directory. [ Info: Doctest: running doctests. ┌ Error: Doctesting failed │ exception = │ MethodError: no method matching atomic_number(::Atoms{Frac}) │ │ Closest candidates are: │ atomic_number(!Matched::Crystal) │ @ Xtals ~/.julia/packages/Xtals/paV65/src/crystal.jl:1362 │ atomic_number(!Matched::Symbol) │ @ AtomsBase ~/.julia/packages/AtomsBase/pcOuK/src/utils/chemspecies.jl:143 │ atomic_number(!Matched::AtomsBase.ChemicalSpecies) │ @ AtomsBase ~/.julia/packages/AtomsBase/pcOuK/src/utils/chemspecies.jl:139 │ ... │ │ Stacktrace: │ [1] element_symbol(species::Atoms{Frac}) │ @ AtomsBase ~/.julia/packages/AtomsBase/pcOuK/src/utils/chemspecies.jl:190 │ [2] _broadcast_getindex_evalf │ @ ./broadcast.jl:709 [inlined] │ [3] _broadcast_getindex │ @ ./broadcast.jl:682 [inlined] │ [4] getindex │ @ ./broadcast.jl:636 [inlined] │ [5] copy │ @ ./broadcast.jl:942 [inlined] │ [6] materialize │ @ ./broadcast.jl:903 [inlined] │ [7] element_symbol │ @ ~/.julia/packages/AtomsBase/pcOuK/src/utils/chemspecies.jl:187 [inlined] │ [8] chemical_formula(system::Crystal) │ @ AtomsBase ~/.julia/packages/AtomsBase/pcOuK/src/utils/properties.jl:20 │ [9] chemical_formula(crystal::Crystal) │ @ Xtals ~/.julia/packages/Xtals/paV65/src/crystal.jl:1389 │ [10] show(io::IOContext{IOBuffer}, crystal::Crystal) │ @ Xtals ~/.julia/packages/Xtals/paV65/src/crystal.jl:1230 │ [11] print(io::IOContext{IOBuffer}, xtal::Crystal) │ @ Xtals ~/.julia/packages/Xtals/paV65/src/crystal.jl:1207 │ [12] show(io::IOContext{IOBuffer}, mime::MIME{Symbol("text/plain")}, system::Crystal) │ @ Xtals ~/.julia/packages/Xtals/paV65/src/crystal.jl:1202 │ [13] #invokelatest#2 │ @ ./essentials.jl:892 [inlined] │ [14] invokelatest │ @ ./essentials.jl:889 [inlined] │ [15] result_to_string │ @ ~/.julia/packages/Documenter/iwb7N/src/doctests.jl:441 [inlined] │ [16] checkresult(sandbox::Module, result::Documenter.Result, meta::Dict{Symbol, Any}, doc::Documenter.Document; prefix::Documenter.MutablePrefix) │ @ Documenter ~/.julia/packages/Documenter/iwb7N/src/doctests.jl:361 │ [17] checkresult │ @ ~/.julia/packages/Documenter/iwb7N/src/doctests.jl:317 [inlined] │ [18] eval_script(block::Documenter.MutableMD2CodeBlock, sandbox::Module, meta::Dict{Symbol, Any}, doc::Documenter.Document, page::String) │ @ Documenter ~/.julia/packages/Documenter/iwb7N/src/doctests.jl:293 │ [19] _doctest(ctx::Documenter.DocTestContext, block_immutable::MarkdownAST.CodeBlock) │ @ Documenter ~/.julia/packages/Documenter/iwb7N/src/doctests.jl:183 │ [20] _doctest(ctx::Documenter.DocTestContext, mdast::MarkdownAST.Node{Nothing}) │ @ Documenter ~/.julia/packages/Documenter/iwb7N/src/doctests.jl:103 │ [21] _doctest │ @ ~/.julia/packages/Documenter/iwb7N/src/doctests.jl:64 [inlined] │ [22] _doctest(blueprint::Documenter.DocumentBlueprint, doc::Documenter.Document) │ @ Documenter ~/.julia/packages/Documenter/iwb7N/src/doctests.jl:37 │ [23] runner(::Type{Documenter.Builder.Doctest}, doc::Documenter.Document) │ @ Documenter ~/.julia/packages/Documenter/iwb7N/src/builder_pipeline.jl:210 │ [24] dispatch(::Type{Documenter.Builder.DocumentPipeline}, x::Documenter.Document) │ @ Documenter.Selectors ~/.julia/packages/Documenter/iwb7N/src/utilities/Selectors.jl:170 │ [25] #89 │ @ ~/.julia/packages/Documenter/iwb7N/src/makedocs.jl:273 [inlined] │ [26] withenv(::Documenter.var"#89#91"{Documenter.Document}, ::Pair{String, Nothing}, ::Vararg{Pair{String, Nothing}}) │ @ Base ./env.jl:257 │ [27] #88 │ @ ~/.julia/packages/Documenter/iwb7N/src/makedocs.jl:272 [inlined] │ [28] cd(f::Documenter.var"#88#90"{Documenter.Document}, dir::String) │ @ Base.Filesystem ./file.jl:112 │ [29] #makedocs#87 │ @ ~/.julia/packages/Documenter/iwb7N/src/makedocs.jl:271 [inlined] │ [30] (::Documenter.var"#all_doctests#134"{Bool, Vector{Regex}, Vector{Documenter.Plugin}, Vector{Module}})() │ @ Documenter ~/.julia/packages/Documenter/iwb7N/src/doctest.jl:85 │ [31] macro expansion │ @ ~/.julia/packages/Documenter/iwb7N/src/doctest.jl:110 [inlined] │ [32] macro expansion │ @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:669 [inlined] │ [33] macro expansion │ @ ~/.julia/packages/Documenter/iwb7N/src/doctest.jl:110 [inlined] │ [34] macro expansion │ @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined] │ [35] doctest(source::String, modules::Vector{Module}; fix::Bool, testset::String, doctestfilters::Vector{Regex}, plugins::Vector{Documenter.Plugin}) │ @ Documenter ~/.julia/packages/Documenter/iwb7N/src/doctest.jl:110 │ [36] doctest │ @ ~/.julia/packages/Documenter/iwb7N/src/doctest.jl:69 [inlined] │ [37] doctest(package::Module; manual::Bool, testset::Nothing, kwargs::@Kwargs{}) │ @ Documenter ~/.julia/packages/Documenter/iwb7N/src/doctest.jl:37 │ [38] doctest │ @ ~/.julia/packages/Documenter/iwb7N/src/doctest.jl:20 [inlined] │ [39] macro expansion │ @ ./timing.jl:279 [inlined] │ [40] top-level scope │ @ ~/.julia/packages/PoreMatMod/R2OKZ/test/runtests.jl:20 │ [41] include(fname::String) │ @ Base.MainInclude ./client.jl:494 │ [42] top-level scope │ @ none:6 │ [43] eval │ @ ./boot.jl:385 [inlined] │ [44] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:296 │ [45] _start() │ @ Base ./client.jl:557 └ @ Documenter ~/.julia/packages/Documenter/iwb7N/src/doctest.jl:99 Doctests: PoreMatMod: Test Failed at /home/pkgeval/.julia/packages/Documenter/iwb7N/src/doctest.jl:110 Expression: all_doctests() Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:672 [inlined] [2] macro expansion @ ~/.julia/packages/Documenter/iwb7N/src/doctest.jl:110 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined] [4] doctest(source::String, modules::Vector{Module}; fix::Bool, testset::String, doctestfilters::Vector{Regex}, plugins::Vector{Documenter.Plugin}) @ Documenter ~/.julia/packages/Documenter/iwb7N/src/doctest.jl:110 Test Summary: | Fail Total Time Doctests: PoreMatMod | 1 1 28.4s ERROR: LoadError: Some tests did not pass: 0 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/PoreMatMod/R2OKZ/test/runtests.jl:19 Testing failed after 439.58s ERROR: LoadError: Package PoreMatMod errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.10/Pkg/src/Operations.jl:2034 [3] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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::Base.PipeEndpoint}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 629.04s: package has test failures