Package evaluation of PorousMaterials on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T18:45:09.297 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.21s ################################################################################ # Installation # Installing PorousMaterials... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [68953c7c] + PorousMaterials v0.5.0 Updating `~/.julia/environments/v1.11/Manifest.toml` [47edcb42] + ADTypes v1.14.0 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.18.0 ⌅ [a963bdd2] + AtomsBase v0.4.2 [99c8bb3a] + Bio3DView v1.0.0 [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [38540f10] + CommonSolve v0.2.4 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.16.0 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.5.8 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.6.50 [ffbed154] + DocStringExtensions v0.9.4 [4e289a0a] + EnumX v1.0.5 [5789e2e9] + FileIO v1.17.0 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.13.0 [6a86dc24] + FiniteDiff v2.27.0 [f6369f11] + ForwardDiff v1.0.1 [86223c79] + Graphs v1.12.1 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.3 [3587e190] + InverseFunctions v0.1.17 [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 [d3d80556] + LineSearches v7.3.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.15 ⌅ [626554b9] + MetaGraphs v0.7.2 [e1d29d7a] + Missings v1.2.0 [d41bc354] + NLSolversBase v7.9.1 [77ba4419] + NaNMath v1.1.3 [6fe1bfb0] + OffsetArrays v1.16.0 [429524aa] + Optim v1.12.0 [bac558e1] + OrderedCollections v1.8.0 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.1 [7b2266bf] + PeriodicTable v1.2.1 ⌅ [f27b6e38] + Polynomials v3.2.13 [2dfb63ee] + PooledArrays v1.4.3 [68953c7c] + PorousMaterials v0.5.0 [85a6dd25] + PositiveFactorizations v0.2.4 [91cefc8d] + PrecompileSignatures v3.0.3 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [92933f4c] + ProgressMeter v1.10.4 [43287f4e] + PtrArrays v1.3.0 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [f2b01f46] + Roots v2.2.7 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 [699a6c99] + SimpleTraits v0.9.4 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [3bb67fe8] + TranscodingStreams v0.11.3 [3a884ed6] + UnPack v1.0.2 [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 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.11.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [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 4.5s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 87.45s ################################################################################ # Testing # Testing PorousMaterials Status `/tmp/jl_rA6Tnn/Project.toml` [4c88cf16] Aqua v0.8.11 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.7.0 [e30172f5] Documenter v1.10.1 ⌅ [033835bb] JLD2 v0.4.54 [6fe1bfb0] OffsetArrays v1.16.0 [429524aa] Optim v1.12.0 ⌅ [f27b6e38] Polynomials v3.2.13 [68953c7c] PorousMaterials v0.5.0 [10745b16] Statistics v1.11.1 [8ba89e20] Distributed v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_rA6Tnn/Manifest.toml` [47edcb42] ADTypes v1.14.0 [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.11 [ec485272] ArnoldiMethod v0.4.0 [4fba245c] ArrayInterface v7.18.0 ⌅ [a963bdd2] AtomsBase v0.4.2 [99c8bb3a] Bio3DView v1.0.0 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [38540f10] CommonSolve v0.2.4 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.16.0 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.5.8 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [a0c0ee7d] DifferentiationInterface v0.6.50 [ffbed154] DocStringExtensions v0.9.4 [e30172f5] Documenter v1.10.1 [4e289a0a] EnumX v1.0.5 [5789e2e9] FileIO v1.17.0 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [6a86dc24] FiniteDiff v2.27.0 [f6369f11] ForwardDiff v1.0.1 [d7ba0133] Git v1.3.1 [86223c79] Graphs v1.12.1 [b5f81e59] IOCapture v0.2.5 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.3 [3587e190] InverseFunctions v0.1.17 [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 [d3d80556] LineSearches v7.3.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.15 [d0879d2d] MarkdownAST v0.1.2 ⌅ [626554b9] MetaGraphs v0.7.2 [e1d29d7a] Missings v1.2.0 [d41bc354] NLSolversBase v7.9.1 [77ba4419] NaNMath v1.1.3 [6fe1bfb0] OffsetArrays v1.16.0 [429524aa] Optim v1.12.0 [bac558e1] OrderedCollections v1.8.0 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.1 [7b2266bf] PeriodicTable v1.2.1 ⌅ [f27b6e38] Polynomials v3.2.13 [2dfb63ee] PooledArrays v1.4.3 [68953c7c] PorousMaterials v0.5.0 [85a6dd25] PositiveFactorizations v0.2.4 [91cefc8d] PrecompileSignatures v3.0.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [92933f4c] ProgressMeter v1.10.4 [43287f4e] PtrArrays v1.3.0 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [2792f1a3] RegistryInstances 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v1.6.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.11.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.11.0 [f489334b] StyledStrings v1.11.0 [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.6.0+0 [e37daf67] LibGit2_jll v1.7.2+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [05823500] OpenLibm_jll v0.8.5+0 [efcefdf7] PCRE2_jll v10.42.0+1 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 [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... Precompiling PorousMaterials... 11824.6 ms ✓ Roots → RootsForwardDiffExt 97992.7 ms ✓ Xtals 98059.9 ms ✓ PorousMaterials 3 dependencies successfully precompiled in 213 seconds. 149 already precompiled. 1 dependency had output during precompilation: ┌ Xtals │ WARNING: could not import AtomsBase.boundary_conditions into Xtals │ WARNING: could not import AtomsBase.species_type into Xtals └ ________ ___ __ \______________________ _________ __ /_/ / __ \_ ___/ __ \ / / /_ ___/ _ ____// /_/ / / / /_/ / /_/ /_(__ ) /_/ \____//_/ \____/\__,_/ /____/ ______ ___ _____ _____ ______ ___ |/ /_____ __ /_______________(_)_____ ___ /_______ __ /|_/ /_ __ `/ __/ _ \_ ___/_ /_ __ `/_ /__ ___/ _ / / / / /_/ // /_ / __/ / _ / / /_/ /_ / _(__ ) /_/ /_/ \__,_/ \__/ \___//_/ /_/ \__,_/ /_/ /____/ [ Info: Running test/molecule.jl See random_vectors_on_sphere [ Info: see co2s.xyz for dist'n of rotations Test Summary: | Pass Total Time Molecules Tests | 67 67 6m38.3s 473.464268 seconds (941.11 M allocations: 40.035 GiB, 1.86% gc time, 20.59% compilation time: <1% of which was recompilation) [ Info: Running test/gcmc_quick.jl Test Summary: | Pass Total Time GCMC (quick) tests | 6 6 1m58.1s ┌ Warning: GCMC simulations not included in runtests.jl; run gcmc_long.jl to test GCMC simulations (will take hours) └ @ Main ~/.julia/packages/PorousMaterials/EUXh4/test/gcmc_quick.jl:67 118.173592 seconds (14.20 M allocations: 901.548 MiB, 0.71% gc time, 99.92% compilation time) [ Info: Running test/grid.jl See /home/pkgeval/.julia/packages/PorousMaterials/EUXh4/test/data/grids/test_grid.cube Computing energy grid of CH4 in LTA.cif Regular grid (in fractional space) of 4 by 4 by 4 points superimposed over the unit cell. See /home/pkgeval/.julia/packages/PorousMaterials/EUXh4/test/data/grids/CH4_in_LTA_UFF_b4_pocket_blocking.cube See /home/pkgeval/.julia/packages/PorousMaterials/EUXh4/test/data/grids/CH4_in_LTA_UFF_after_pocket_blocking.cube 8 pockets in LTA.cif were found to be inaccessible to CH4 and blocked. Porosity of LTA.cif b4 pocket blocking is 0.137026 Porosity of LTA.cif after pocket blocking is 0.113703 potential energy barrier used to determine accessibility: 0.000000 kJ_mol See LTAaccessible_inertions.xyz Computing energy grid of CH4 in SOD.cif Regular grid (in fractional space) of 3 by 3 by 3 points superimposed over the unit cell. See /home/pkgeval/.julia/packages/PorousMaterials/EUXh4/test/data/grids/CH4_in_SOD_UFF_b4_pocket_blocking.cube See /home/pkgeval/.julia/packages/PorousMaterials/EUXh4/test/data/grids/CH4_in_SOD_UFF_after_pocket_blocking.cube ┌ Warning: CH4 cannot enter the pores of SOD.cif with 0.000000 K energy tolerance. └ @ PorousMaterials ~/.julia/packages/PorousMaterials/EUXh4/src/grid.jl:881 9 pockets in SOD.cif were found to be inaccessible to CH4 and blocked. Porosity of SOD.cif b4 pocket blocking is 0.074074 Porosity of SOD.cif after pocket blocking is 0.000000 potential energy barrier used to determine accessibility: 0.000000 kJ_mol See /home/pkgeval/.julia/packages/PorousMaterials/EUXh4/test/data/grids/CH4_in_LTA_UFF_b4_pocket_blocking.cube See /home/pkgeval/.julia/packages/PorousMaterials/EUXh4/test/data/grids/CH4_in_LTA_UFF_after_pocket_blocking.cube 8 pockets in LTA.cif were found to be inaccessible to CH4 and blocked. Porosity of LTA.cif b4 pocket blocking is 0.137026 Porosity of LTA.cif after pocket blocking is 0.113703 potential energy barrier used to determine accessibility: 0.000000 kJ_mol See /home/pkgeval/.julia/packages/PorousMaterials/EUXh4/test/data/grids/CH4_in_LTA_UFF_b4_pocket_blocking.cube See /home/pkgeval/.julia/packages/PorousMaterials/EUXh4/test/data/grids/CH4_in_LTA_UFF_after_pocket_blocking.cube 24 pockets in LTA.cif were found to be inaccessible to CH4 and blocked. Porosity of LTA.cif b4 pocket blocking is 0.145171 Porosity of LTA.cif after pocket blocking is 0.131290 potential energy barrier used to determine accessibility: 0.000000 kJ_mol See /home/pkgeval/.julia/packages/PorousMaterials/EUXh4/test/data/grids/CH4_in_SBMOF-1_UFF_b4_pocket_blocking.cube See /home/pkgeval/.julia/packages/PorousMaterials/EUXh4/test/data/grids/CH4_in_SBMOF-1_UFF_after_pocket_blocking.cube See /home/pkgeval/.julia/packages/PorousMaterials/EUXh4/test/data/grids/CH4_in_CAXVII_clean_UFF_b4_pocket_blocking.cube See /home/pkgeval/.julia/packages/PorousMaterials/EUXh4/test/data/grids/CH4_in_CAXVII_clean_UFF_after_pocket_blocking.cube Test Summary: | Pass Total Time Grid Tests | 56 56 1m34.1s required_n_pts | 1 1 0.2s accessibility grid w./o pocket blocking | 8 8 8.0s xf_to_id | 4 4 1.3s update_density! | 5 5 0.4s 94.713749 seconds (68.09 M allocations: 59.757 GiB, 2.58% gc time, 81.39% compilation time) [ Info: Running test/misc.jl Test Summary: | Pass Total Time Misc Tests | 4 4 0.4s 0.416998 seconds (54.03 k allocations: 2.694 MiB, 95.69% compilation time) [ Info: Running test/forcefield.jl ┌ Warning: C missing from bogus force field. └ @ PorousMaterials ~/.julia/packages/PorousMaterials/EUXh4/src/forcefield.jl:203 Test Summary: | Pass Total Time Forcefield Tests | 11 11 1.3s 1.319442 seconds (197.17 k allocations: 6.322 MiB, 96.68% compilation time) [ Info: Running test/vdw_energetics.jl Test Summary: | Pass Total Time VdwEnergetics Tests | 33 33 4.5s 5.932647 seconds (11.96 M allocations: 514.878 MiB, 2.23% gc time, 80.16% compilation time) [ Info: Running test/energy_utilities.jl Test Summary: | Pass Total Time Energetics_Util Tests | 18 18 0.4s 0.469927 seconds (34.18 k allocations: 1.536 MiB, 91.12% compilation time) [ Info: Running test/electrostatics.jl Test Summary: | Pass Total Time ElectrostaticEnergetics Tests | 41 41 2m51.2s 171.276247 seconds (591.47 M allocations: 30.443 GiB, 2.44% gc time, 9.34% compilation time) [ Info: Running test/mc_helpers.jl Test Summary: | Pass Total Time MCHelpers Tests | 31 31 0.8s 7.420098 seconds (5.33 M allocations: 276.003 MiB, 1.40% gc time, 87.93% compilation time) [ Info: Running test/eos.jl Test Summary: | Pass Total Time equation of state (eos.jl) Tests | 13 13 10.8s 10.786779 seconds (1.71 M allocations: 85.527 MiB, 0.36% gc time, 99.61% 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/tbj1p/src/utilities/utilities.jl:660 [ Info: SetupBuildDirectory: setting up build directory. [ Info: Doctest: running doctests. ┌ Error: doctest failure in ../docs/src/box.md:21-36 │ │ ```jldoctest │ a = 26.13173 # Å │ b = 26.13173 │ c = 6.722028 │ α = π / 2 # radians │ β = π / 2 │ γ = 2 * π / 3 │ box = Box(a, b, c, α, β, γ) │ │ # output │ │ Bravais unit cell of a crystal. │ Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000000 deg. │ Unit cell dimensions a = 26.131730 Å. b = 26.131730 Å, c = 6.722028 Å │ Volume of unit cell: 3975.275878 ų │ ``` │ │ Subexpression: │ │ a = 26.13173 # Å │ b = 26.13173 │ c = 6.722028 │ α = π / 2 # radians │ β = π / 2 │ γ = 2 * π / 3 │ box = Box(a, b, c, α, β, γ) │ │ Evaluated output: │ │ Bravais unit cell of a crystal. │ Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000000 deg. │ Unit cell dimensions a = 26.131730 Å. b = 26.131730 Å, c = 6.722028 Å │ Volume of unit cell: 3975.275878 ų │ │ Expected output: │ │ Bravais unit cell of a crystal. │ Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000000 deg. │ Unit cell dimensions a = 26.131730 Å. b = 26.131730 Å, c = 6.722028 Å │ Volume of unit cell: 3975.275878 ų │ │ diff = │ Warning: Diff output requires color. │ Bravais unit cell of a crystal. │ crystal. │ Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000000 deg. │ deg. │ Unit cell dimensions a = 26.131730 Å. b = 26.131730 Å, c = 6.722028 Å │ Å │ Volume of unit cell: 3975.275878 ų └ @ Documenter ~/.julia/packages/PorousMaterials/EUXh4/docs/src/box.md:21 ┌ Error: doctest failure in ../docs/src/box.md:41-50 │ │ ```jldoctest box │ box = Box([26.1317 -13.0659 0; 0 22.6307 0; 0 0 6.72203]) │ │ # output │ │ Bravais unit cell of a crystal. │ Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000113 deg. │ Unit cell dimensions a = 26.131700 Å. b = 26.131711 Å, c = 6.722030 Å │ Volume of unit cell: 3975.265115 ų │ ``` │ │ Subexpression: │ │ box = Box([26.1317 -13.0659 0; 0 22.6307 0; 0 0 6.72203]) │ │ Evaluated output: │ │ Bravais unit cell of a crystal. │ Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000113 deg. │ Unit cell dimensions a = 26.131700 Å. b = 26.131711 Å, c = 6.722030 Å │ Volume of unit cell: 3975.265115 ų │ │ Expected output: │ │ Bravais unit cell of a crystal. │ Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000113 deg. │ Unit cell dimensions a = 26.131700 Å. b = 26.131711 Å, c = 6.722030 Å │ Volume of unit cell: 3975.265115 ų │ │ diff = │ Warning: Diff output requires color. │ Bravais unit cell of a crystal. │ crystal. │ Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000113 deg. │ deg. │ Unit cell dimensions a = 26.131700 Å. b = 26.131711 Å, c = 6.722030 Å │ Å │ Volume of unit cell: 3975.265115 ų └ @ Documenter ~/.julia/packages/PorousMaterials/EUXh4/docs/src/box.md:41 ┌ Error: doctest failure in ../docs/src/box.md:54-63 │ │ ```jldoctest │ unit_cube() │ │ # output │ │ Bravais unit cell of a crystal. │ Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 90.000000 deg. │ Unit cell dimensions a = 1.000000 Å. b = 1.000000 Å, c = 1.000000 Å │ Volume of unit cell: 1.000000 ų │ ``` │ │ Subexpression: │ │ unit_cube() │ │ Evaluated output: │ │ Bravais unit cell of a crystal. │ Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 90.000000 deg. │ Unit cell dimensions a = 1.000000 Å. b = 1.000000 Å, c = 1.000000 Å │ Volume of unit cell: 1.000000 ų │ │ Expected output: │ │ Bravais unit cell of a crystal. │ Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 90.000000 deg. │ Unit cell dimensions a = 1.000000 Å. b = 1.000000 Å, c = 1.000000 Å │ Volume of unit cell: 1.000000 ų │ │ diff = │ Warning: Diff output requires color. │ Bravais unit cell of a crystal. │ crystal. │ Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 90.000000 deg. │ deg. │ Unit cell dimensions a = 1.000000 Å. b = 1.000000 Å, c = 1.000000 Å │ Å │ Volume of unit cell: 1.000000 ų └ @ Documenter ~/.julia/packages/PorousMaterials/EUXh4/docs/src/box.md:54 ┌ Error: doctest failure in ../docs/src/box.md:84-93 │ │ ```jldoctest box │ replicated_box = replicate(box, (2, 2, 2)) │ │ # output │ │ Bravais unit cell of a crystal. │ Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000113 deg. │ Unit cell dimensions a = 52.263400 Å. b = 52.263422 Å, c = 13.444060 Å │ Volume of unit cell: 31802.120923 ų │ ``` │ │ Subexpression: │ │ replicated_box = replicate(box, (2, 2, 2)) │ │ Evaluated output: │ │ Bravais unit cell of a crystal. │ Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000113 deg. │ Unit cell dimensions a = 52.263400 Å. b = 52.263422 Å, c = 13.444060 Å │ Volume of unit cell: 31802.120923 ų │ │ Expected output: │ │ Bravais unit cell of a crystal. │ Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000113 deg. │ Unit cell dimensions a = 52.263400 Å. b = 52.263422 Å, c = 13.444060 Å │ Volume of unit cell: 31802.120923 ų │ │ diff = │ Warning: Diff output requires color. │ Bravais unit cell of a crystal. │ crystal. │ Unit cell angles α = 90.000000 deg. β = 90.000000 deg. γ = 120.000113 deg. │ deg. │ Unit cell dimensions a = 52.263400 Å. b = 52.263422 Å, c = 13.444060 Å │ Å │ Volume of unit cell: 31802.120923 ų └ @ Documenter ~/.julia/packages/PorousMaterials/EUXh4/docs/src/box.md:84 ┌ Error: Doctesting failed │ exception = │ MethodError: no method matching atomic_number(::Atoms{Frac}) │ The function `atomic_number` exists, but no method is defined for this combination of argument types. │ │ 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:678 [inlined] │ [3] _broadcast_getindex │ @ ./broadcast.jl:651 [inlined] │ [4] getindex │ @ ./broadcast.jl:610 [inlined] │ [5] copy │ @ ./broadcast.jl:911 [inlined] │ [6] materialize │ @ ./broadcast.jl:872 [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:1055 [inlined] │ [14] invokelatest │ @ ./essentials.jl:1052 [inlined] │ [15] result_to_string │ @ ~/.julia/packages/Documenter/tbj1p/src/doctests.jl:460 [inlined] │ [16] checkresult(sandbox::Module, result::Documenter.Result, meta::Dict{Symbol, Any}, doc::Documenter.Document; prefix::Documenter.MutablePrefix) │ @ Documenter ~/.julia/packages/Documenter/tbj1p/src/doctests.jl:380 │ [17] checkresult │ @ ~/.julia/packages/Documenter/tbj1p/src/doctests.jl:330 [inlined] │ [18] eval_script(block::Documenter.MutableMD2CodeBlock, sandbox::Module, meta::Dict{Symbol, Any}, doc::Documenter.Document, page::String) │ @ Documenter ~/.julia/packages/Documenter/tbj1p/src/doctests.jl:306 │ [19] _doctest(ctx::Documenter.DocTestContext, block_immutable::MarkdownAST.CodeBlock) │ @ Documenter ~/.julia/packages/Documenter/tbj1p/src/doctests.jl:183 │ [20] _doctest(ctx::Documenter.DocTestContext, mdast::MarkdownAST.Node{Nothing}) │ @ Documenter ~/.julia/packages/Documenter/tbj1p/src/doctests.jl:103 │ [21] _doctest │ @ ~/.julia/packages/Documenter/tbj1p/src/doctests.jl:64 [inlined] │ [22] _doctest(blueprint::Documenter.DocumentBlueprint, doc::Documenter.Document) │ @ Documenter ~/.julia/packages/Documenter/tbj1p/src/doctests.jl:37 │ [23] runner(::Type{Documenter.Builder.Doctest}, doc::Documenter.Document) │ @ Documenter ~/.julia/packages/Documenter/tbj1p/src/builder_pipeline.jl:210 │ [24] dispatch(::Type{Documenter.Builder.DocumentPipeline}, x::Documenter.Document) │ @ Documenter.Selectors ~/.julia/packages/Documenter/tbj1p/src/utilities/Selectors.jl:170 │ [25] #90 │ @ ~/.julia/packages/Documenter/tbj1p/src/makedocs.jl:275 [inlined] │ [26] withenv(::Documenter.var"#90#92"{Documenter.Document}, ::Pair{String, Nothing}, ::Vararg{Pair{String, Nothing}}) │ @ Base ./env.jl:265 │ [27] #89 │ @ ~/.julia/packages/Documenter/tbj1p/src/makedocs.jl:274 [inlined] │ [28] cd(f::Documenter.var"#89#91"{Documenter.Document}, dir::String) │ @ Base.Filesystem ./file.jl:112 │ [29] makedocs(; debug::Bool, format::Documenter.HTMLWriter.HTML, kwargs::@Kwargs{root::String, source::String, sitename::String, doctest::Symbol, modules::Vector{Module}, doctestfilters::Vector{Regex}, remotes::Nothing, plugins::Vector{Documenter.Plugin}}) │ @ Documenter ~/.julia/packages/Documenter/tbj1p/src/makedocs.jl:273 │ [30] (::Documenter.var"#all_doctests#135"{Bool, Vector{Regex}, Vector{Documenter.Plugin}, Vector{Module}})() │ @ Documenter ~/.julia/packages/Documenter/tbj1p/src/doctest.jl:85 │ [31] macro expansion │ @ ~/.julia/packages/Documenter/tbj1p/src/doctest.jl:110 [inlined] │ [32] macro expansion │ @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined] │ [33] macro expansion │ @ ~/.julia/packages/Documenter/tbj1p/src/doctest.jl:110 [inlined] │ [34] macro expansion │ @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] │ [35] doctest(source::String, modules::Vector{Module}; fix::Bool, testset::String, doctestfilters::Vector{Regex}, plugins::Vector{Documenter.Plugin}) │ @ Documenter ~/.julia/packages/Documenter/tbj1p/src/doctest.jl:110 │ [36] doctest │ @ ~/.julia/packages/Documenter/tbj1p/src/doctest.jl:69 [inlined] │ [37] doctest(package::Module; manual::Bool, testset::Nothing, kwargs::@Kwargs{}) │ @ Documenter ~/.julia/packages/Documenter/tbj1p/src/doctest.jl:37 │ [38] doctest(package::Module) │ @ Documenter ~/.julia/packages/Documenter/tbj1p/src/doctest.jl:20 │ [39] top-level scope │ @ ~/.julia/packages/PorousMaterials/EUXh4/test/runtests.jl:23 │ [40] include(fname::String) │ @ Main ./sysimg.jl:38 │ [41] top-level scope │ @ none:6 │ [42] eval │ @ ./boot.jl:430 [inlined] │ [43] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:296 │ [44] _start() │ @ Base ./client.jl:531 └ @ Documenter ~/.julia/packages/Documenter/tbj1p/src/doctest.jl:99 Doctests: PorousMaterials: Test Failed at /home/pkgeval/.julia/packages/Documenter/tbj1p/src/doctest.jl:110 Expression: all_doctests() Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:679 [inlined] [2] macro expansion @ ~/.julia/packages/Documenter/tbj1p/src/doctest.jl:110 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [4] doctest(source::String, modules::Vector{Module}; fix::Bool, testset::String, doctestfilters::Vector{Regex}, plugins::Vector{Documenter.Plugin}) @ Documenter ~/.julia/packages/Documenter/tbj1p/src/doctest.jl:110 Test Summary: | Fail Total Time Doctests: PorousMaterials | 1 1 1m24.6s ERROR: LoadError: Some tests did not pass: 0 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/PorousMaterials/EUXh4/test/runtests.jl:23 Testing failed after 1226.83s ERROR: LoadError: Package PorousMaterials errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68 [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/v1.11/Pkg/src/Operations.jl:2124 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [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::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:481 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/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 1347.76s: package has test failures