Package evaluation to test MoleculeFlow on Julia 1.10.10 (c8be17dcfd*) started at 2026-02-03T03:28:02.642 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.10` Set-up completed after 5.39s ################################################################################ # Installation # Installing MoleculeFlow... Resolving package versions... Installed JpegTurbo_jll ──────────────────── v3.1.4+0 Installed JpegTurbo ──────────────────────── v0.1.6 Installed ImageIO ────────────────────────── v0.6.9 Installed ImageSegmentation ──────────────── v1.10.0 Installed TiledIteration ─────────────────── v0.5.0 Installed AxisArrays ─────────────────────── v0.4.8 Installed OffsetArrays ───────────────────── v1.17.0 Installed TiffImages ─────────────────────── v0.11.6 Installed PNGFiles ───────────────────────── v0.4.4 Installed LERC_jll ───────────────────────── v4.0.1+0 Installed SciMLPublic ────────────────────── v1.0.1 Installed Preferences ────────────────────── v1.5.1 Installed ImageMagick ────────────────────── v1.4.2 Installed FFTW ───────────────────────────── v1.10.0 Installed HistogramThresholding ──────────── v0.3.1 Installed Sixel ──────────────────────────── v0.1.5 Installed RegionTrees ────────────────────── v0.3.2 Installed ProgressMeter ──────────────────── v1.11.0 Installed StaticArrays ───────────────────── v1.9.16 Installed OpenEXR ────────────────────────── v0.3.3 Installed Pidfile ────────────────────────── v1.3.0 Installed ScopedValues ───────────────────── v1.5.0 Installed CEnum ──────────────────────────── v0.5.0 Installed Images ─────────────────────────── v0.26.2 Installed IntelOpenMP_jll ────────────────── v2025.2.0+0 Installed Polynomials ────────────────────── v4.1.0 Installed MetaGraphs ─────────────────────── v0.8.1 Installed NearestNeighbors ───────────────── v0.4.26 Installed Netpbm ─────────────────────────── v1.1.1 Installed UnsafePointers ─────────────────── v1.0.0 Installed Static ─────────────────────────── v1.3.1 Installed FileIO ─────────────────────────── v1.18.0 Installed Xorg_libXau_jll ────────────────── v1.0.13+0 Installed Distances ──────────────────────── v0.10.12 Installed SLEEFPirates ───────────────────── v0.6.43 Installed Missings ───────────────────────── v1.2.0 Installed RealDot ────────────────────────── v0.1.0 Installed SIMDTypes ──────────────────────── v0.1.0 Installed CondaPkg ───────────────────────── v0.2.33 Installed SIMD ───────────────────────────── v3.7.2 Installed IrrationalConstants ────────────── v0.2.6 Installed ColorSchemes ───────────────────── v3.31.0 Installed ArnoldiMethod ──────────────────── v0.4.0 Installed JLD2 ───────────────────────────── v0.6.3 Installed Giflib_jll ─────────────────────── v5.2.3+0 Installed CpuId ──────────────────────────── v0.3.1 Installed PtrArrays ──────────────────────── v1.3.0 Installed Bzip2_jll ──────────────────────── v1.0.9+0 Installed QOI ────────────────────────────── v1.0.2 Installed Clustering ─────────────────────── v0.15.8 Installed MoleculeFlow ───────────────────── v0.6.0 Installed PythonCall ─────────────────────── v0.9.31 Installed IfElse ─────────────────────────── v0.1.1 Installed PkgVersion ─────────────────────── v0.3.3 Installed ChunkCodecLibZstd ──────────────── v1.0.0 Installed StaticArraysCore ───────────────── v1.4.4 Installed XZ_jll ─────────────────────────── v5.8.2+0 Installed NaNMath ────────────────────────── v1.1.3 Installed ThreadingUtilities ─────────────── v0.5.5 Installed micromamba_jll ─────────────────── v1.5.12+0 Installed WebP ───────────────────────────── v0.1.3 Installed ManualMemory ───────────────────── v0.1.8 Installed CustomUnitRanges ───────────────── v1.0.2 Installed Ratios ─────────────────────────── v0.4.5 Installed Graphics ───────────────────────── v1.1.3 Installed DataStructures ─────────────────── v0.19.3 Installed CatIndices ─────────────────────── v0.2.2 Installed Graphs ─────────────────────────── v1.13.4 Installed ComputationalResources ─────────── v0.3.2 Installed ImageMetadata ──────────────────── v0.9.10 Installed Colors ─────────────────────────── v0.13.1 Installed ImageMagick_jll ────────────────── v7.1.2011+0 Installed MappedArrays ───────────────────── v0.4.3 Installed StatsAPI ───────────────────────── v1.8.0 Installed Compat ─────────────────────────── v4.18.1 Installed CommonWorldInvalidations ───────── v1.0.0 Installed PaddedViews ────────────────────── v0.5.12 Installed Xorg_libxcb_jll ────────────────── v1.17.1+0 Installed MosaicViews ────────────────────── v0.3.4 Installed StatsBase ──────────────────────── v0.34.10 Installed LazyModules ────────────────────── v0.3.1 Installed StaticArrayInterface ───────────── v1.8.0 Installed ImageTransformations ───────────── v0.10.2 Installed ColorTypes ─────────────────────── v0.12.1 Installed Scratch ────────────────────────── v1.3.0 Installed libpng_jll ─────────────────────── v1.6.54+0 Installed StructTypes ────────────────────── v1.11.0 Installed ImageCorners ───────────────────── v0.1.3 Installed oneTBB_jll ─────────────────────── v2022.0.0+1 Installed BitTwiddlingConvenienceFunctions ─ v0.1.6 Installed ImageCore ──────────────────────── v0.10.5 Installed ImageFiltering ─────────────────── v0.7.12 Installed LayoutPointers ─────────────────── v0.1.17 Installed Xorg_libXext_jll ───────────────── v1.3.7+0 Installed Zstd_jll ───────────────────────── v1.5.7+1 Installed TableTraits ────────────────────── v1.0.1 Installed TensorCore ─────────────────────── v0.1.1 Installed libzip_jll ─────────────────────── v1.11.3+0 Installed JSON3 ──────────────────────────── v1.14.3 Installed ChunkCodecLibZlib ──────────────── v1.0.0 Installed Inflate ────────────────────────── v0.1.5 Installed Parsers ────────────────────────── v2.8.3 Installed Imath_jll ──────────────────────── v3.2.2+0 Installed ImageShow ──────────────────────── v0.3.8 Installed HashArrayMappedTries ───────────── v0.2.0 Installed ImageQualityIndexes ────────────── v0.3.7 Installed IntegralArrays ─────────────────── v0.1.6 Installed MKL_jll ────────────────────────── v2025.2.0+0 Installed Setfield ───────────────────────── v1.1.2 Installed AbstractFFTs ───────────────────── v1.5.0 Installed Libtiff_jll ────────────────────── v4.7.2+0 Installed JLLWrappers ────────────────────── v1.7.1 Installed ConstructionBase ───────────────── v1.6.0 Installed ImageContrastAdjustment ────────── v0.3.12 Installed DataValueInterfaces ────────────── v1.0.0 Installed LoopVectorization ──────────────── v0.12.173 Installed ColorVectorSpace ───────────────── v0.11.0 Installed ChunkCodecCore ─────────────────── v1.0.1 Installed AbstractTrees ──────────────────── v0.4.5 Installed OrderedCollections ─────────────── v1.8.1 Installed CoordinateTransformations ──────── v0.6.4 Installed PolyesterWeave ─────────────────── v0.2.2 Installed ArrayInterface ─────────────────── v7.22.0 Installed Reexport ───────────────────────── v1.2.2 Installed Ghostscript_jll ────────────────── v9.55.1+0 Installed ChainRulesCore ─────────────────── v1.26.0 Installed LogExpFunctions ────────────────── v0.3.29 Installed Quaternions ────────────────────── v0.7.7 Installed AliasTables ────────────────────── v1.1.3 Installed LittleCMS_jll ──────────────────── v2.17.0+0 Installed StackViews ─────────────────────── v0.1.2 Installed CloseOpenIntervals ─────────────── v0.1.13 Installed MacroTools ─────────────────────── v0.5.16 Installed Interpolations ─────────────────── v0.16.2 Installed RangeArrays ────────────────────── v0.3.2 Installed Rotations ──────────────────────── v1.7.1 Installed UnPack ─────────────────────────── v1.0.2 Installed FFTW_jll ───────────────────────── v3.3.11+0 Installed SimpleTraits ───────────────────── v0.9.5 Installed OpenEXR_jll ────────────────────── v3.4.4+0 Installed DocStringExtensions ────────────── v0.9.5 Installed pixi_jll ───────────────────────── v0.41.3+0 Installed MicroMamba ─────────────────────── v0.1.14 Installed Adapt ──────────────────────────── v4.4.0 Installed IterTools ──────────────────────── v1.10.0 Installed IntervalSets ───────────────────── v0.7.13 Installed ImageBase ──────────────────────── v0.1.7 Installed VectorizationBase ──────────────── v0.21.72 Installed Xorg_xtrans_jll ────────────────── v1.6.0+0 Installed OpenJpeg_jll ───────────────────── v2.5.5+0 Installed OpenSSL_jll ────────────────────── v3.5.5+0 Installed IndirectArrays ─────────────────── v1.0.0 Installed ImageBinarization ──────────────── v0.3.1 Installed Tables ─────────────────────────── v1.12.1 Installed SimpleWeightedGraphs ───────────── v1.5.1 Installed CPUSummary ─────────────────────── v0.2.7 Installed DataAPI ────────────────────────── v1.16.0 Installed FixedPointNumbers ──────────────── v0.8.5 Installed libsixel_jll ───────────────────── v1.10.5+0 Installed IteratorInterfaceExtensions ────── v1.0.0 Installed HostCPUFeatures ────────────────── v0.1.18 Installed Libglvnd_jll ───────────────────── v1.7.1+1 Installed RecipesBase ────────────────────── v1.3.4 Installed AxisAlgorithms ─────────────────── v1.1.0 Installed ImageDistances ─────────────────── v0.2.17 Installed PrecompileTools ────────────────── v1.2.1 Installed Requires ───────────────────────── v1.3.1 Installed Xorg_libX11_jll ────────────────── v1.8.12+0 Installed Xorg_libXdmcp_jll ──────────────── v1.1.6+0 Installed FFTViews ───────────────────────── v0.3.2 Installed Parameters ─────────────────────── v0.12.3 Installed ImageAxes ──────────────────────── v0.6.12 Installed libwebp_jll ────────────────────── v1.6.0+0 Installed WoodburyMatrices ───────────────── v1.1.0 Installed ImageMorphology ────────────────── v0.4.7 Installed SortingAlgorithms ──────────────── v1.2.2 Updating `~/.julia/environments/v1.10/Project.toml` [0907176b] + MoleculeFlow v0.6.0 Updating `~/.julia/environments/v1.10/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.22.0 [13072b0f] + AxisAlgorithms v1.1.0 [39de3d68] + AxisArrays v0.4.8 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [fa961155] + CEnum v0.5.0 [2a0fbf3d] + CPUSummary v0.2.7 [aafaddc9] + CatIndices v0.2.2 [d360d2e6] + ChainRulesCore v1.26.0 [0b6fb165] + ChunkCodecCore v1.0.1 [4c0bbee4] + ChunkCodecLibZlib v1.0.0 [55437552] + ChunkCodecLibZstd v1.0.0 [fb6a15b2] + CloseOpenIntervals v0.1.13 [aaaa29a8] + Clustering v0.15.8 [35d6a980] + ColorSchemes v3.31.0 [3da002f7] + ColorTypes v0.12.1 [c3611d14] + ColorVectorSpace v0.11.0 [5ae59095] + Colors v0.13.1 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [ed09eef8] + ComputationalResources v0.3.2 [992eb4ea] + CondaPkg v0.2.33 [187b0558] + ConstructionBase v1.6.0 [150eb455] + CoordinateTransformations v0.6.4 [adafc99b] + CpuId v0.3.1 [dc8bdbbb] + CustomUnitRanges v1.0.2 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [b4f34e82] + Distances v0.10.12 [ffbed154] + DocStringExtensions v0.9.5 [4f61f5a4] + FFTViews v0.3.2 [7a1cc6ca] + FFTW v1.10.0 [5789e2e9] + FileIO v1.18.0 [53c48c17] + FixedPointNumbers v0.8.5 [a2bd30eb] + Graphics v1.1.3 [86223c79] + Graphs v1.13.4 [076d061b] + HashArrayMappedTries v0.2.0 [2c695a8d] + HistogramThresholding v0.3.1 [3e5b6fbb] + HostCPUFeatures v0.1.18 [615f187c] + IfElse v0.1.1 [2803e5a7] + ImageAxes v0.6.12 [c817782e] + ImageBase v0.1.7 [cbc4b850] + ImageBinarization v0.3.1 [f332f351] + ImageContrastAdjustment v0.3.12 [a09fc81d] + ImageCore v0.10.5 [89d5987c] + ImageCorners v0.1.3 [51556ac3] + ImageDistances v0.2.17 [6a3955dd] + ImageFiltering v0.7.12 [82e4d734] + ImageIO v0.6.9 [6218d12a] + ImageMagick v1.4.2 [bc367c6b] + ImageMetadata v0.9.10 [787d08f9] + ImageMorphology v0.4.7 [2996bd0c] + ImageQualityIndexes v0.3.7 [80713f31] + ImageSegmentation v1.10.0 [4e3cecfd] + ImageShow v0.3.8 [02fcd773] + ImageTransformations v0.10.2 [916415d5] + Images v0.26.2 [9b13fd28] + IndirectArrays v1.0.0 [d25df0c9] + Inflate v0.1.5 [1d092043] + IntegralArrays v0.1.6 [a98d9a8b] + Interpolations v0.16.2 [8197267c] + IntervalSets v0.7.13 [92d709cd] + IrrationalConstants v0.2.6 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [033835bb] + JLD2 v0.6.3 [692b3bcd] + JLLWrappers v1.7.1 [0f8b85d8] + JSON3 v1.14.3 [b835a17e] + JpegTurbo v0.1.6 [10f19ff3] + LayoutPointers v0.1.17 [8cdb02fc] + LazyModules v0.3.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [bdcacae8] + LoopVectorization v0.12.173 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [dbb5928d] + MappedArrays v0.4.3 ⌅ [626554b9] + MetaGraphs v0.8.1 [0b3b1443] + MicroMamba v0.1.14 [e1d29d7a] + Missings v1.2.0 [0907176b] + MoleculeFlow v0.6.0 [e94cdb99] + MosaicViews v0.3.4 [77ba4419] + NaNMath v1.1.3 [b8a86587] + NearestNeighbors v0.4.26 [f09324ee] + Netpbm v1.1.1 [6fe1bfb0] + OffsetArrays v1.17.0 [52e1d378] + OpenEXR v0.3.3 [bac558e1] + OrderedCollections v1.8.1 [f57f5aa1] + PNGFiles v0.4.4 [5432bcbf] + PaddedViews v0.5.12 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [fa939f87] + Pidfile v1.3.0 [eebad327] + PkgVersion v0.3.3 [1d0040c9] + PolyesterWeave v0.2.2 [f27b6e38] + Polynomials v4.1.0 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.5.1 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [6099a3de] + PythonCall v0.9.31 [4b34888f] + QOI v1.0.2 [94ee1d12] + Quaternions v0.7.7 [b3c3ace0] + RangeArrays v0.3.2 [c84ed2f1] + Ratios v0.4.5 [c1ae055f] + RealDot v0.1.0 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [dee08c22] + RegionTrees v0.3.2 [ae029012] + Requires v1.3.1 [6038ab10] + Rotations v1.7.1 [fdea26ae] + SIMD v3.7.2 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.43 [431bcebd] + SciMLPublic v1.0.1 [7e506255] + ScopedValues v1.5.0 [6c6a2e73] + Scratch v1.3.0 [efcf1570] + Setfield v1.1.2 [699a6c99] + SimpleTraits v0.9.5 [47aef6b3] + SimpleWeightedGraphs v1.5.1 [45858cf5] + Sixel v0.1.5 [a2af1166] + SortingAlgorithms v1.2.2 [cae243ae] + StackViews v0.1.2 [aedffcd0] + Static v1.3.1 [0d7ed370] + StaticArrayInterface v1.8.0 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [856f2bd8] + StructTypes v1.11.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [62fd8b95] + TensorCore v0.1.1 [8290d209] + ThreadingUtilities v0.5.5 [731e570b] + TiffImages v0.11.6 [06e1c1a7] + TiledIteration v0.5.0 [3a884ed6] + UnPack v1.0.2 [e17b2a0c] + UnsafePointers v1.0.0 [3d5dd08c] + VectorizationBase v0.21.72 [e3aaa7dc] + WebP v0.1.3 [efce3f68] + WoodburyMatrices v1.1.0 [6e34b625] + Bzip2_jll v1.0.9+0 [f5851436] + FFTW_jll v3.3.11+0 [61579ee1] + Ghostscript_jll v9.55.1+0 [59f7168a] + Giflib_jll v5.2.3+0 [c73af94c] + ImageMagick_jll v7.1.2011+0 [905a6f67] + Imath_jll v3.2.2+0 [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0 [aacddb02] + JpegTurbo_jll v3.1.4+0 [88015f11] + LERC_jll v4.0.1+0 [7e76a0d4] + Libglvnd_jll v1.7.1+1 [89763e89] + Libtiff_jll v4.7.2+0 [d3a379c0] + LittleCMS_jll v2.17.0+0 [856f044c] + MKL_jll v2025.2.0+0 [18a262bb] + OpenEXR_jll v3.4.4+0 [643b3616] + OpenJpeg_jll v2.5.5+0 [458c3c95] + OpenSSL_jll v3.5.5+0 [ffd25f8a] + XZ_jll v5.8.2+0 [4f6342f7] + Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] + Xorg_libXau_jll v1.0.13+0 [a3789734] + Xorg_libXdmcp_jll v1.1.6+0 [1082639a] + Xorg_libXext_jll v1.3.7+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.1+0 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 [3161d3a3] + Zstd_jll v1.5.7+1 [b53b4c65] + libpng_jll v1.6.54+0 [075b6546] + libsixel_jll v1.10.5+0 [c5f90fcd] + libwebp_jll v1.6.0+0 [337d8026] + libzip_jll v1.11.3+0 ⌅ [f8abcde7] + micromamba_jll v1.5.12+0 [1317d2d5] + oneTBB_jll v2022.0.0+1 [4d7b5844] + pixi_jll v0.41.3+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 [4af54fe1] + LazyArtifacts [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 v2.28.1010+0 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.23+5 [05823500] + OpenLibm_jll v0.8.5+0 [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 25.95s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 1199.8 ms ✓ TestEnv 1 dependency successfully precompiled in 4 seconds Precompiling package dependencies... Precompiling packages... 733.7 ms ✓ RangeArrays 1353.7 ms ✓ StructTypes 901.7 ms ✓ AbstractFFTs 621.2 ms ✓ IndirectArrays 563.6 ms ✓ IteratorInterfaceExtensions 680.0 ms ✓ TensorCore 633.4 ms ✓ StatsAPI 748.5 ms ✓ ChunkCodecCore 622.5 ms ✓ CEnum 1372.1 ms ✓ OffsetArrays 621.3 ms ✓ UnPack 963.4 ms ✓ IterTools 866.3 ms ✓ PkgVersion 3246.0 ms ✓ MacroTools 704.9 ms ✓ ManualMemory 856.9 ms ✓ Preferences 862.8 ms ✓ Compat 933.5 ms ✓ OrderedCollections 726.9 ms ✓ Requires 569.8 ms ✓ DataValueInterfaces 572.2 ms ✓ RealDot 601.5 ms ✓ Reexport 585.1 ms ✓ SIMDTypes 876.6 ms ✓ DocStringExtensions 677.0 ms ✓ Pidfile 913.6 ms ✓ AbstractTrees 1664.8 ms ✓ IrrationalConstants 824.8 ms ✓ IntervalSets 640.0 ms ✓ UnsafePointers 564.4 ms ✓ CustomUnitRanges 1340.7 ms ✓ ProgressMeter 591.7 ms ✓ PtrArrays 717.9 ms ✓ HashArrayMappedTries 640.4 ms ✓ LazyModules 739.6 ms ✓ NaNMath 1002.9 ms ✓ CpuId 800.3 ms ✓ Inflate 552.3 ms ✓ IfElse 716.5 ms ✓ ConstructionBase 606.6 ms ✓ CommonWorldInvalidations 690.0 ms ✓ DataAPI 749.9 ms ✓ ComputationalResources 1103.9 ms ✓ Scratch 867.2 ms ✓ SciMLPublic 856.6 ms ✓ StaticArraysCore 1044.3 ms ✓ MappedArrays 1838.0 ms ✓ Statistics 1298.9 ms ✓ WoodburyMatrices 2436.3 ms ✓ AbstractFFTs → AbstractFFTsTestExt 577.1 ms ✓ TableTraits 729.1 ms ✓ ChunkCodecLibZlib 690.6 ms ✓ StackViews 771.2 ms ✓ PaddedViews 1876.4 ms ✓ SimpleTraits 1238.8 ms ✓ ThreadingUtilities 750.0 ms ✓ JLLWrappers 646.5 ms ✓ PrecompileTools 620.1 ms ✓ Compat → CompatLinearAlgebraExt 2944.0 ms ✓ DataStructures 745.5 ms ✓ Parameters 652.8 ms ✓ Ratios 697.1 ms ✓ Adapt 3560.6 ms ✓ FileIO 794.5 ms ✓ Quaternions 1064.0 ms ✓ LogExpFunctions 646.7 ms ✓ IntervalSets → IntervalSetsRandomExt 696.3 ms ✓ CatIndices 747.9 ms ✓ AliasTables 668.7 ms ✓ ScopedValues 615.2 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 715.3 ms ✓ Missings 3649.2 ms ✓ FixedPointNumbers 1624.0 ms ✓ Distances 1153.8 ms ✓ AxisAlgorithms 1281.6 ms ✓ Tables 772.6 ms ✓ MosaicViews 870.2 ms ✓ OpenSSL_jll 844.0 ms ✓ Bzip2_jll 853.1 ms ✓ Xorg_libXau_jll 839.2 ms ✓ libpng_jll 815.9 ms ✓ Imath_jll 844.3 ms ✓ IntelOpenMP_jll 852.5 ms ✓ Giflib_jll 886.8 ms ✓ LERC_jll 919.1 ms ✓ JpegTurbo_jll 911.4 ms ✓ XZ_jll 874.1 ms ✓ oneTBB_jll 866.1 ms ✓ Xorg_libXdmcp_jll 919.5 ms ✓ Zstd_jll 888.3 ms ✓ micromamba_jll 884.2 ms ✓ pixi_jll 733.8 ms ✓ Xorg_xtrans_jll 856.9 ms ✓ FFTW_jll 10672.8 ms ✓ StaticArrays 1806.0 ms ✓ RecipesBase 13119.2 ms ✓ Parsers 12347.2 ms ✓ SIMD 1294.4 ms ✓ Static 1880.2 ms ✓ ChainRulesCore 2162.0 ms ✓ Aqua 807.4 ms ✓ SortingAlgorithms 1088.0 ms ✓ Adapt → AdaptSparseArraysExt 849.8 ms ✓ ArrayInterface 700.5 ms ✓ OffsetArrays → OffsetArraysAdaptExt 1275.2 ms ✓ AxisArrays 1134.5 ms ✓ IntervalSets → IntervalSetsStatisticsExt 2116.6 ms ✓ Setfield 629.4 ms ✓ ConstructionBase → ConstructionBaseIntervalSetsExt 2433.7 ms ✓ ColorTypes 1209.9 ms ✓ Ratios → RatiosFixedPointNumbersExt 1028.3 ms ✓ Distances → DistancesSparseArraysExt 862.0 ms ✓ OpenEXR_jll 951.1 ms ✓ Ghostscript_jll 866.6 ms ✓ libsixel_jll 5570.7 ms ✓ MKL_jll 932.2 ms ✓ Xorg_libxcb_jll 755.1 ms ✓ ChunkCodecLibZstd 874.1 ms ✓ libzip_jll 846.7 ms ✓ Libtiff_jll 1575.0 ms ✓ MicroMamba 2374.2 ms ✓ ArnoldiMethod 1824.7 ms ✓ CoordinateTransformations 2014.6 ms ✓ StaticArrays → StaticArraysStatisticsExt 1377.8 ms ✓ RegionTrees 1257.0 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 1294.8 ms ✓ Adapt → AdaptStaticArraysExt 3626.2 ms ✓ Rotations 1098.1 ms ✓ IntervalSets → IntervalSetsRecipesBaseExt 9965.1 ms ✓ JSON3 731.9 ms ✓ BitTwiddlingConvenienceFunctions 1412.3 ms ✓ CPUSummary 1862.0 ms ✓ ChainRulesCore → ChainRulesCoreSparseArraysExt 710.4 ms ✓ AbstractFFTs → AbstractFFTsChainRulesCoreExt 2643.4 ms ✓ LogExpFunctions → LogExpFunctionsChainRulesCoreExt 1360.1 ms ✓ StaticArrays → StaticArraysChainRulesCoreExt 3779.9 ms ✓ StatsBase 2042.6 ms ✓ StaticArrayInterface 1211.1 ms ✓ ArrayInterface → ArrayInterfaceSparseArraysExt 720.7 ms ✓ ArrayInterface → ArrayInterfaceChainRulesCoreExt 603.9 ms ✓ ArrayInterface → ArrayInterfaceStaticArraysCoreExt 26388.8 ms ✓ Polynomials 1743.6 ms ✓ QOI 1329.6 ms ✓ IntegralArrays 3930.5 ms ✓ ColorVectorSpace 29593.8 ms ✓ TiffImages 6537.8 ms ✓ Colors 4455.3 ms ✓ FFTW 977.1 ms ✓ Xorg_libX11_jll 33283.2 ms ✓ JLD2 894.6 ms ✓ LittleCMS_jll 6602.4 ms ✓ NearestNeighbors 7296.5 ms ✓ Graphs 1541.1 ms ✓ Rotations → RotationsRecipesBaseExt 4810.8 ms ✓ CondaPkg 1369.8 ms ✓ HostCPUFeatures 915.1 ms ✓ PolyesterWeave 1202.5 ms ✓ Distances → DistancesChainRulesCoreExt 3990.5 ms ✓ Interpolations 752.7 ms ✓ StaticArrayInterface → StaticArrayInterfaceOffsetArraysExt 761.5 ms ✓ CloseOpenIntervals 931.1 ms ✓ LayoutPointers 1324.5 ms ✓ StaticArrayInterface → StaticArrayInterfaceStaticArraysExt 2581.4 ms ✓ Polynomials → PolynomialsChainRulesCoreExt 1962.7 ms ✓ Graphics 2156.0 ms ✓ OpenEXR 26717.4 ms ✓ ImageCore 7585.0 ms ✓ ColorSchemes 1072.1 ms ✓ FFTViews 2828.3 ms ✓ Polynomials → PolynomialsFFTWExt 854.7 ms ✓ Xorg_libXext_jll 2254.6 ms ✓ JLD2 → UnPackExt 1456.6 ms ✓ OpenJpeg_jll 3487.3 ms ✓ Clustering 3423.0 ms ✓ MetaGraphs 2453.3 ms ✓ SimpleWeightedGraphs 2293.5 ms ✓ Graphs → GraphsSharedArraysExt 15123.8 ms ✓ PythonCall 879.6 ms ✓ TiledIteration 9695.1 ms ✓ VectorizationBase 4337.1 ms ✓ ImageBase 5615.3 ms ✓ PNGFiles 4088.5 ms ✓ Sixel 4275.3 ms ✓ JpegTurbo 907.4 ms ✓ Libglvnd_jll 1785.9 ms ✓ SLEEFPirates 3343.3 ms ✓ HistogramThresholding 5029.6 ms ✓ ImageAxes 4989.3 ms ✓ ImageTransformations 3555.8 ms ✓ ImageShow 73794.4 ms ✓ ImageFiltering 1036.4 ms ✓ libwebp_jll 24584.3 ms ✓ LoopVectorization 5241.1 ms ✓ ImageBinarization 3603.8 ms ✓ ImageMetadata 6053.2 ms ✓ ImageContrastAdjustment 18583.9 ms ✓ ImageCorners 3977.5 ms ✓ WebP 944.4 ms ✓ ImageMagick_jll 11171.0 ms ✓ ImageMorphology 3772.4 ms ✓ Netpbm 6410.7 ms ✓ ImageMagick 5082.6 ms ✓ ImageDistances 9883.1 ms ✓ ImageSegmentation 935.7 ms ✓ ImageIO 20500.4 ms ✓ ImageQualityIndexes 14121.2 ms ✓ Images 46432.3 ms ✓ MoleculeFlow 207 dependencies successfully precompiled in 724 seconds. 8 already precompiled. 4 dependencies had output during precompilation: ┌ CondaPkg │ Downloading artifact: pixi └ ┌ MicroMamba │ Downloading artifact: micromamba └ ┌ MKL_jll │ Downloading artifact: IntelOpenMP │ Downloading artifact: oneTBB └ ┌ MoleculeFlow │ CondaPkg Found dependencies: /home/pkgeval/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml │ CondaPkg Found dependencies: /home/pkgeval/.julia/packages/MoleculeFlow/5xJwa/CondaPkg.toml │ CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PythonCall/83z4q/CondaPkg.toml │ CondaPkg Resolving changes │ + libstdcxx │ + libstdcxx-ng │ + openssl │ + python │ + rdkit (pip) │ + uv │ CondaPkg Initialising pixi │ │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi │ │ init │ │ --format pixi │ └ /tmp/jl_poU0LM/.CondaPkg │ ✔ Created /tmp/jl_poU0LM/.CondaPkg/pixi.toml │ CondaPkg Wrote /tmp/jl_poU0LM/.CondaPkg/pixi.toml │ │ [dependencies] │ │ openssl = ">=3, <3.6" │ │ libstdcxx = ">=3.4,<14.0" │ │ uv = ">=0.4" │ │ libstdcxx-ng = ">=3.4,<14.0" │ │ │ │ [dependencies.python] │ │ channel = "conda-forge" │ │ build = "*cp*" │ │ version = ">=3.10,!=3.14.0,!=3.14.1,<4" │ │ │ │ [project] │ │ name = ".CondaPkg" │ │ platforms = ["linux-64"] │ │ channels = ["conda-forge"] │ │ channel-priority = "strict" │ │ description = "automatically generated by CondaPkg.jl" │ │ │ │ [pypi-dependencies] │ └ rdkit = "==2025.03.6" │ CondaPkg Installing packages │ │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi │ │ install │ └ --manifest-path /tmp/jl_poU0LM/.CondaPkg/pixi.toml │ ✔ The default environment has been installed. └ Precompilation completed after 728.77s ################################################################################ # Testing # Testing MoleculeFlow Status `/tmp/jl_bGo6OG/Project.toml` [4c88cf16] Aqua v0.8.14 [992eb4ea] CondaPkg v0.2.33 [86223c79] Graphs v1.13.4 [916415d5] Images v0.26.2 [0907176b] MoleculeFlow v0.6.0 [6099a3de] PythonCall v0.9.31 [189a3867] Reexport v1.2.2 [ade2ca70] Dates [8ba89e20] Distributed [37e2e46d] LinearAlgebra [de0858da] Printf [9e88b42a] Serialization [10745b16] Statistics v1.10.0 [8dfed614] Test [c8ffd9c3] MbedTLS_jll v2.28.1010+0 Status `/tmp/jl_bGo6OG/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.14 [ec485272] ArnoldiMethod v0.4.0 [4fba245c] ArrayInterface v7.22.0 [13072b0f] AxisAlgorithms v1.1.0 [39de3d68] AxisArrays v0.4.8 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [fa961155] CEnum v0.5.0 [2a0fbf3d] CPUSummary v0.2.7 [aafaddc9] CatIndices v0.2.2 [d360d2e6] ChainRulesCore v1.26.0 [0b6fb165] ChunkCodecCore v1.0.1 [4c0bbee4] ChunkCodecLibZlib v1.0.0 [55437552] ChunkCodecLibZstd v1.0.0 [fb6a15b2] CloseOpenIntervals v0.1.13 [aaaa29a8] Clustering v0.15.8 [35d6a980] ColorSchemes v3.31.0 [3da002f7] ColorTypes v0.12.1 [c3611d14] ColorVectorSpace v0.11.0 [5ae59095] Colors v0.13.1 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.18.1 [ed09eef8] ComputationalResources v0.3.2 [992eb4ea] CondaPkg v0.2.33 [187b0558] ConstructionBase v1.6.0 [150eb455] CoordinateTransformations v0.6.4 [adafc99b] CpuId v0.3.1 [dc8bdbbb] CustomUnitRanges v1.0.2 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [b4f34e82] Distances v0.10.12 [ffbed154] DocStringExtensions v0.9.5 [4f61f5a4] FFTViews v0.3.2 [7a1cc6ca] FFTW v1.10.0 [5789e2e9] FileIO v1.18.0 [53c48c17] FixedPointNumbers v0.8.5 [a2bd30eb] Graphics v1.1.3 [86223c79] Graphs v1.13.4 [076d061b] HashArrayMappedTries v0.2.0 [2c695a8d] HistogramThresholding v0.3.1 [3e5b6fbb] HostCPUFeatures v0.1.18 [615f187c] IfElse v0.1.1 [2803e5a7] ImageAxes v0.6.12 [c817782e] ImageBase v0.1.7 [cbc4b850] ImageBinarization v0.3.1 [f332f351] ImageContrastAdjustment v0.3.12 [a09fc81d] ImageCore v0.10.5 [89d5987c] ImageCorners v0.1.3 [51556ac3] ImageDistances v0.2.17 [6a3955dd] ImageFiltering v0.7.12 [82e4d734] ImageIO v0.6.9 [6218d12a] ImageMagick v1.4.2 [bc367c6b] ImageMetadata v0.9.10 [787d08f9] ImageMorphology v0.4.7 [2996bd0c] ImageQualityIndexes v0.3.7 [80713f31] ImageSegmentation v1.10.0 [4e3cecfd] ImageShow v0.3.8 [02fcd773] ImageTransformations v0.10.2 [916415d5] Images v0.26.2 [9b13fd28] IndirectArrays v1.0.0 [d25df0c9] Inflate v0.1.5 [1d092043] IntegralArrays v0.1.6 [a98d9a8b] Interpolations v0.16.2 [8197267c] IntervalSets v0.7.13 [92d709cd] IrrationalConstants v0.2.6 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 [033835bb] JLD2 v0.6.3 [692b3bcd] JLLWrappers v1.7.1 [0f8b85d8] JSON3 v1.14.3 [b835a17e] JpegTurbo v0.1.6 [10f19ff3] LayoutPointers v0.1.17 [8cdb02fc] LazyModules v0.3.1 [2ab3a3ac] LogExpFunctions v0.3.29 [bdcacae8] LoopVectorization v0.12.173 [1914dd2f] MacroTools v0.5.16 [d125e4d3] ManualMemory v0.1.8 [dbb5928d] MappedArrays v0.4.3 ⌅ [626554b9] MetaGraphs v0.8.1 [0b3b1443] MicroMamba v0.1.14 [e1d29d7a] Missings v1.2.0 [0907176b] MoleculeFlow v0.6.0 [e94cdb99] MosaicViews v0.3.4 [77ba4419] NaNMath v1.1.3 [b8a86587] NearestNeighbors v0.4.26 [f09324ee] Netpbm v1.1.1 [6fe1bfb0] OffsetArrays v1.17.0 [52e1d378] OpenEXR v0.3.3 [bac558e1] OrderedCollections v1.8.1 [f57f5aa1] PNGFiles v0.4.4 [5432bcbf] PaddedViews v0.5.12 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.3 [fa939f87] Pidfile v1.3.0 [eebad327] PkgVersion v0.3.3 [1d0040c9] PolyesterWeave v0.2.2 [f27b6e38] Polynomials v4.1.0 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.5.1 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [6099a3de] PythonCall v0.9.31 [4b34888f] QOI v1.0.2 [94ee1d12] Quaternions v0.7.7 [b3c3ace0] RangeArrays v0.3.2 [c84ed2f1] Ratios v0.4.5 [c1ae055f] RealDot v0.1.0 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [dee08c22] RegionTrees v0.3.2 [ae029012] Requires v1.3.1 [6038ab10] Rotations v1.7.1 [fdea26ae] SIMD v3.7.2 [94e857df] SIMDTypes v0.1.0 [476501e8] SLEEFPirates v0.6.43 [431bcebd] SciMLPublic v1.0.1 [7e506255] ScopedValues v1.5.0 [6c6a2e73] Scratch v1.3.0 [efcf1570] Setfield v1.1.2 [699a6c99] SimpleTraits v0.9.5 [47aef6b3] SimpleWeightedGraphs v1.5.1 [45858cf5] Sixel v0.1.5 [a2af1166] SortingAlgorithms v1.2.2 [cae243ae] StackViews v0.1.2 [aedffcd0] Static v1.3.1 [0d7ed370] StaticArrayInterface v1.8.0 [90137ffa] StaticArrays v1.9.16 [1e83bf80] StaticArraysCore v1.4.4 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [856f2bd8] StructTypes v1.11.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [62fd8b95] TensorCore v0.1.1 [8290d209] ThreadingUtilities v0.5.5 [731e570b] TiffImages v0.11.6 [06e1c1a7] TiledIteration v0.5.0 [3a884ed6] UnPack v1.0.2 [e17b2a0c] UnsafePointers v1.0.0 [3d5dd08c] VectorizationBase v0.21.72 [e3aaa7dc] WebP v0.1.3 [efce3f68] WoodburyMatrices v1.1.0 [6e34b625] Bzip2_jll v1.0.9+0 [f5851436] FFTW_jll v3.3.11+0 [61579ee1] Ghostscript_jll v9.55.1+0 [59f7168a] Giflib_jll v5.2.3+0 [c73af94c] ImageMagick_jll v7.1.2011+0 [905a6f67] Imath_jll v3.2.2+0 [1d5cc7b8] IntelOpenMP_jll v2025.2.0+0 [aacddb02] JpegTurbo_jll v3.1.4+0 [88015f11] LERC_jll v4.0.1+0 [7e76a0d4] Libglvnd_jll v1.7.1+1 [89763e89] Libtiff_jll v4.7.2+0 [d3a379c0] LittleCMS_jll v2.17.0+0 [856f044c] MKL_jll v2025.2.0+0 [18a262bb] OpenEXR_jll v3.4.4+0 [643b3616] OpenJpeg_jll v2.5.5+0 [458c3c95] OpenSSL_jll v3.5.5+0 [ffd25f8a] XZ_jll v5.8.2+0 [4f6342f7] Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] Xorg_libXau_jll v1.0.13+0 [a3789734] Xorg_libXdmcp_jll v1.1.6+0 [1082639a] Xorg_libXext_jll v1.3.7+0 [c7cfdc94] Xorg_libxcb_jll v1.17.1+0 [c5fb5394] Xorg_xtrans_jll v1.6.0+0 [3161d3a3] Zstd_jll v1.5.7+1 [b53b4c65] libpng_jll v1.6.54+0 [075b6546] libsixel_jll v1.10.5+0 [c5f90fcd] libwebp_jll v1.6.0+0 [337d8026] libzip_jll v1.11.3+0 ⌅ [f8abcde7] micromamba_jll v1.5.12+0 [1317d2d5] oneTBB_jll v2022.0.0+1 [4d7b5844] pixi_jll v0.41.3+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 [4af54fe1] LazyArtifacts [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 v2.28.1010+0 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.23+5 [05823500] OpenLibm_jll v0.8.5+0 [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... CondaPkg Found dependencies: /home/pkgeval/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml CondaPkg Found dependencies: /home/pkgeval/.julia/packages/MoleculeFlow/5xJwa/CondaPkg.toml CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PythonCall/83z4q/CondaPkg.toml CondaPkg Resolving changes + libstdcxx + libstdcxx-ng + openssl + python + rdkit (pip) + uv CondaPkg Initialising pixi │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi │ init │ --format pixi └ /tmp/jl_bGo6OG/.CondaPkg ✔ Created /tmp/jl_bGo6OG/.CondaPkg/pixi.toml CondaPkg Wrote /tmp/jl_bGo6OG/.CondaPkg/pixi.toml │ [dependencies] │ openssl = ">=3, <3.6" │ libstdcxx = ">=3.4,<14.0" │ uv = ">=0.4" │ libstdcxx-ng = ">=3.4,<14.0" │ │ [dependencies.python] │ channel = "conda-forge" │ build = "*cp*" │ version = ">=3.10,!=3.14.0,!=3.14.1,<4" │ │ [project] │ name = ".CondaPkg" │ platforms = ["linux-64"] │ channels = ["conda-forge"] │ channel-priority = "strict" │ description = "automatically generated by CondaPkg.jl" │ │ [pypi-dependencies] └ rdkit = "==2025.03.6" CondaPkg Installing packages │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi │ install └ --manifest-path /tmp/jl_bGo6OG/.CondaPkg/pixi.toml ✔ The default environment has been installed. [03:42:08] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:08] SMILES Parse Error: check for mistakes around position 1: [03:42:08] invalid_smiles [03:42:08] ^ [03:42:08] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:09] SMILES Parse Error: syntax error while parsing: invalid [03:42:09] SMILES Parse Error: check for mistakes around position 1: [03:42:09] invalid [03:42:09] ^ [03:42:09] SMILES Parse Error: Failed parsing SMILES 'invalid' for input: 'invalid' [03:42:13] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:13] SMILES Parse Error: check for mistakes around position 1: [03:42:13] invalid_smiles [03:42:13] ^ [03:42:13] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:13] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:13] SMILES Parse Error: check for mistakes around position 1: [03:42:13] invalid_smiles [03:42:13] ^ [03:42:13] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:13] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:13] SMILES Parse Error: check for mistakes around position 1: [03:42:13] invalid_smiles [03:42:13] ^ [03:42:13] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:13] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:13] SMILES Parse Error: check for mistakes around position 1: [03:42:13] invalid_smiles [03:42:13] ^ [03:42:13] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:14] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:14] SMILES Parse Error: check for mistakes around position 1: [03:42:14] invalid_smiles [03:42:14] ^ [03:42:14] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:14] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:14] SMILES Parse Error: check for mistakes around position 1: [03:42:14] invalid_smiles [03:42:14] ^ [03:42:14] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:14] SMARTS Parse Error: syntax error while parsing: invalid_smarts [03:42:14] SMARTS Parse Error: check for mistakes around position 1: [03:42:14] invalid_smarts [03:42:14] ^ [03:42:14] SMARTS Parse Error: Failed parsing SMARTS 'invalid_smarts' for input: 'invalid_smarts' ┌ Warning: Error deleting substructures: PythonCall.PyException() └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/operations.jl:78 [03:42:16] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:16] SMILES Parse Error: check for mistakes around position 1: [03:42:16] invalid_smiles [03:42:16] ^ [03:42:16] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:16] SMARTS Parse Error: syntax error while parsing: invalid_smarts [03:42:16] SMARTS Parse Error: check for mistakes around position 1: [03:42:16] invalid_smarts [03:42:16] ^ [03:42:16] SMARTS Parse Error: Failed parsing SMARTS 'invalid_smarts' for input: 'invalid_smarts' ┌ Warning: Error replacing substructures: PythonCall.PyException() └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/operations.jl:495 [03:42:16] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:16] SMILES Parse Error: check for mistakes around position 1: [03:42:16] invalid_smiles [03:42:16] ^ [03:42:16] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:16] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:16] SMILES Parse Error: check for mistakes around position 1: [03:42:16] invalid_smiles [03:42:16] ^ [03:42:16] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:16] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:16] SMILES Parse Error: check for mistakes around position 1: [03:42:16] invalid_smiles [03:42:16] ^ [03:42:16] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:16] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:16] SMILES Parse Error: check for mistakes around position 1: [03:42:16] invalid_smiles [03:42:16] ^ [03:42:16] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:17] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:17] SMILES Parse Error: check for mistakes around position 1: [03:42:17] invalid_smiles [03:42:17] ^ [03:42:17] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:17] SMARTS Parse Error: syntax error while parsing: invalid_smarts [03:42:17] SMARTS Parse Error: check for mistakes around position 1: [03:42:17] invalid_smarts [03:42:17] ^ [03:42:17] SMARTS Parse Error: Failed parsing SMARTS 'invalid_smarts' for input: 'invalid_smarts' ┌ Warning: Error in SMARTS matching: PythonCall.PyException() └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/operations.jl:629 [03:42:17] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:17] SMILES Parse Error: check for mistakes around position 1: [03:42:17] invalid_smiles [03:42:17] ^ [03:42:17] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:17] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:17] SMILES Parse Error: check for mistakes around position 1: [03:42:17] invalid_smiles [03:42:17] ^ [03:42:17] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' ┌ Warning: Error converting fragment to SMARTS: PythonCall.PyException() └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/operations.jl:232 [03:42:17] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:17] SMILES Parse Error: check for mistakes around position 1: [03:42:17] invalid_smiles [03:42:17] ^ [03:42:17] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:18] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:18] SMILES Parse Error: check for mistakes around position 1: [03:42:18] invalid_smiles [03:42:18] ^ [03:42:18] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:18] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:18] SMILES Parse Error: check for mistakes around position 1: [03:42:18] invalid_smiles [03:42:18] ^ [03:42:18] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:18] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:18] SMILES Parse Error: check for mistakes around position 1: [03:42:18] invalid_smiles [03:42:18] ^ [03:42:18] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:18] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:18] SMILES Parse Error: check for mistakes around position 1: [03:42:18] invalid_smiles [03:42:18] ^ [03:42:18] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:18] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:18] SMILES Parse Error: check for mistakes around position 1: [03:42:18] invalid_smiles [03:42:18] ^ [03:42:18] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:18] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:18] SMILES Parse Error: check for mistakes around position 1: [03:42:18] invalid_smiles [03:42:18] ^ [03:42:18] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:18] Invalid InChI prefix in generating InChI Key [03:42:19] Unable to recognize the number of atoms: cannot convert 'invalid xyz data' to unsigned int on line 0 [03:42:19] Cannot write molecules with no conformers to XYZ block [03:42:19] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:19] SMILES Parse Error: check for mistakes around position 1: [03:42:19] invalid_smiles [03:42:19] ^ [03:42:19] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:19] ethanol: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation. [03:42:19] water: Warning - no explicit hydrogens in mol2 file but needed for formal charge estimation. ┌ Warning: Error reading MOL2 file 'non_existent_file.mol2': PythonCall.PyException() └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/io/read.jl:520 ┌ Warning: Error reading PDB file 'non_existent_file.pdb': PythonCall.PyException() └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/io/read.jl:410 [03:42:21] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:21] SMILES Parse Error: check for mistakes around position 1: [03:42:21] invalid_smiles [03:42:21] ^ [03:42:21] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:21] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:21] SMILES Parse Error: check for mistakes around position 1: [03:42:21] invalid_smiles [03:42:21] ^ [03:42:21] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:21] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:21] SMILES Parse Error: check for mistakes around position 1: [03:42:21] invalid_smiles [03:42:21] ^ [03:42:21] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:22] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:22] SMILES Parse Error: check for mistakes around position 1: [03:42:22] invalid_smiles [03:42:22] ^ [03:42:22] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:22] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:22] SMILES Parse Error: check for mistakes around position 1: [03:42:22] invalid_smiles [03:42:22] ^ [03:42:22] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:23] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:23] SMILES Parse Error: check for mistakes around position 1: [03:42:23] invalid_smiles [03:42:23] ^ [03:42:23] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:24] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:24] SMILES Parse Error: check for mistakes around position 1: [03:42:24] invalid_smiles [03:42:24] ^ [03:42:24] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:24] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:24] SMILES Parse Error: check for mistakes around position 1: [03:42:24] invalid_smiles [03:42:24] ^ [03:42:24] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:24] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:24] SMILES Parse Error: check for mistakes around position 1: [03:42:24] invalid_smiles [03:42:24] ^ [03:42:24] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:24] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:24] SMILES Parse Error: check for mistakes around position 1: [03:42:24] invalid_smiles [03:42:24] ^ [03:42:24] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:24] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:24] SMILES Parse Error: check for mistakes around position 1: [03:42:24] invalid_smiles [03:42:24] ^ [03:42:24] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:24] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:24] SMILES Parse Error: check for mistakes around position 1: [03:42:24] invalid_smiles [03:42:24] ^ [03:42:24] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:24] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:24] SMILES Parse Error: check for mistakes around position 1: [03:42:24] invalid_smiles [03:42:24] ^ [03:42:24] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:25] **** Pre-condition Violation molecule has no conformers Violation occurred on line 208 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** [03:42:25] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:25] SMILES Parse Error: check for mistakes around position 1: [03:42:25] invalid_smiles [03:42:25] ^ [03:42:25] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:25] **** Pre-condition Violation molecule has no conformers Violation occurred on line 165 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** [03:42:25] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:25] SMILES Parse Error: check for mistakes around position 1: [03:42:25] invalid_smiles [03:42:25] ^ [03:42:25] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:25] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:25] **** Pre-condition Violation molecule has no conformers Violation occurred on line 145 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI2: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1820 [03:42:25] **** Pre-condition Violation molecule has no conformers Violation occurred on line 154 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI3: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1836 [03:42:25] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:25] SMILES Parse Error: check for mistakes around position 1: [03:42:25] invalid_smiles [03:42:25] ^ [03:42:25] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:27] **** Pre-condition Violation molecule has no conformers Violation occurred on line 226 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating spherocity index: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1877 [03:42:27] **** Pre-condition Violation molecule has no conformers Violation occurred on line 1226 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/GETAWAY.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating GETAWAY descriptors: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1934 [03:42:27] **** Pre-condition Violation molecule has no conformers Violation occurred on line 382 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/WHIM.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating WHIM descriptors: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1991 [03:42:27] **** Pre-condition Violation molecule has no conformers Violation occurred on line 192 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/RDF.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating RDF descriptors: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:2041 [03:42:27] **** Pre-condition Violation molecule has no conformers Violation occurred on line 172 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/MORSE.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating MORSE descriptors: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:2091 [03:42:27] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:27] SMILES Parse Error: check for mistakes around position 1: [03:42:27] invalid_smiles [03:42:27] ^ [03:42:27] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:29] **** Pre-condition Violation molecule has no conformers Violation occurred on line 226 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating spherocity index: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1877 [03:42:29] **** Pre-condition Violation molecule has no conformers Violation occurred on line 226 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating spherocity index: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1877 [03:42:29] **** Pre-condition Violation molecule has no conformers Violation occurred on line 226 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating spherocity index: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1877 [03:42:30] **** Pre-condition Violation molecule has no conformers Violation occurred on line 1226 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/GETAWAY.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating GETAWAY descriptors: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1934 [03:42:30] **** Pre-condition Violation molecule has no conformers Violation occurred on line 1226 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/GETAWAY.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating GETAWAY descriptors: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1934 [03:42:30] **** Pre-condition Violation molecule has no conformers Violation occurred on line 1226 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/GETAWAY.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating GETAWAY descriptors: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1934 [03:42:30] **** Pre-condition Violation molecule has no conformers Violation occurred on line 382 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/WHIM.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating WHIM descriptors: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1991 [03:42:30] **** Pre-condition Violation molecule has no conformers Violation occurred on line 382 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/WHIM.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating WHIM descriptors: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1991 [03:42:30] **** Pre-condition Violation molecule has no conformers Violation occurred on line 382 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/WHIM.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating WHIM descriptors: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1991 [03:42:31] **** Pre-condition Violation molecule has no conformers Violation occurred on line 192 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/RDF.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating RDF descriptors: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:2041 [03:42:31] **** Pre-condition Violation molecule has no conformers Violation occurred on line 192 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/RDF.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating RDF descriptors: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:2041 [03:42:31] **** Pre-condition Violation molecule has no conformers Violation occurred on line 192 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/RDF.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating RDF descriptors: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:2041 [03:42:31] **** Pre-condition Violation molecule has no conformers Violation occurred on line 172 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/MORSE.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating MORSE descriptors: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:2091 [03:42:31] **** Pre-condition Violation molecule has no conformers Violation occurred on line 172 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/MORSE.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating MORSE descriptors: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:2091 [03:42:31] **** Pre-condition Violation molecule has no conformers Violation occurred on line 172 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/MORSE.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating MORSE descriptors: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:2091 [03:42:31] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:31] SMILES Parse Error: check for mistakes around position 1: [03:42:31] invalid_smiles [03:42:31] ^ [03:42:31] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:35] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:35] SMILES Parse Error: check for mistakes around position 1: [03:42:35] invalid_smiles [03:42:35] ^ [03:42:35] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:36] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:36] SMILES Parse Error: check for mistakes around position 1: [03:42:36] invalid_smiles [03:42:36] ^ [03:42:36] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:36] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:36] SMILES Parse Error: check for mistakes around position 1: [03:42:36] invalid_smiles [03:42:36] ^ [03:42:36] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:37] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:37] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:37] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 145 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI2: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1820 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 154 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI3: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1836 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 145 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI2: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1820 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 154 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI3: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1836 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 145 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI2: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1820 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 154 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI3: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1836 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 145 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI2: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1820 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 154 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI3: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1836 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 145 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI2: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1820 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 154 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI3: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1836 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 145 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI2: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1820 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 154 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI3: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1836 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 145 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI2: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1820 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 154 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI3: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1836 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 145 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI2: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1820 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 154 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI3: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1836 [03:42:38] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:38] SMILES Parse Error: check for mistakes around position 1: [03:42:38] invalid_smiles [03:42:38] ^ [03:42:38] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:38] **** Pre-condition Violation molecule has no conformers Violation occurred on line 136 in file /project/build/temp.linux-x86_64-cpython-313/rdkit/Code/GraphMol/Descriptors/PMI.cpp Failed Expression: mol.getNumConformers() >= 1 ---------- Stacktrace: ---------- **** ┌ Warning: Error calculating PMI1: PythonCall.PyException(= 1\n\tRDKIT: 2025.03.6\n\tBOOST: 1_85\n')>) └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/descriptors.jl:1804 [03:42:39] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:39] SMILES Parse Error: check for mistakes around position 1: [03:42:39] invalid_smiles [03:42:39] ^ [03:42:39] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:41] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:41] SMILES Parse Error: check for mistakes around position 1: [03:42:41] invalid_smiles [03:42:41] ^ [03:42:41] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:41] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:41] SMILES Parse Error: check for mistakes around position 1: [03:42:41] invalid_smiles [03:42:41] ^ [03:42:41] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:42] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:42] SMILES Parse Error: check for mistakes around position 1: [03:42:42] invalid_smiles [03:42:42] ^ [03:42:42] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:48] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:48] SMILES Parse Error: check for mistakes around position 1: [03:42:48] invalid_smiles [03:42:48] ^ [03:42:48] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' Drawing Functions: Error During Test at /home/pkgeval/.julia/packages/MoleculeFlow/5xJwa/test/test_drawing.jl:4 Got exception outside of a @test Python: ImportError: libXrender.so.1: cannot open shared object file: No such file or directory Python stacktrace: [1] @ /tmp/jl_bGo6OG/.CondaPkg/.pixi/envs/default/lib/python3.13/site-packages/rdkit/Chem/Draw/__init__.py:21 Stacktrace: [1] pythrow() @ PythonCall.Core ~/.julia/packages/PythonCall/83z4q/src/Core/err.jl:77 [2] errcheck(val::Ptr{PythonCall.C.PyObject}) @ PythonCall.Core ~/.julia/packages/PythonCall/83z4q/src/Core/err.jl:10 [3] pyimport(m::String) @ PythonCall.Core ~/.julia/packages/PythonCall/83z4q/src/Core/builtins.jl:1458 [4] _mol_to_image(mol::PythonCall.Py; kwargs::@Kwargs{size::Tuple{Int64, Int64}, kekulize::Bool, wedgeBonds::Bool, highlightAtoms::Nothing, highlightBonds::Nothing, highlightAtomColors::Nothing, highlightBondColors::Nothing}) @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/rdkit.jl:755 [5] _mol_to_image @ ~/.julia/packages/MoleculeFlow/5xJwa/src/rdkit.jl:754 [inlined] [6] mol_to_image(mol::Molecule; size::Tuple{Int64, Int64}, kekulize::Bool, wedge_bonds::Bool, highlight_atoms::Nothing, highlight_bonds::Nothing, highlight_atom_colors::Nothing, highlight_bond_colors::Nothing, use_svg::Bool) @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/draw/draw.jl:95 [7] mol_to_image(mol::Molecule) @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/draw/draw.jl:36 [8] macro expansion @ ~/.julia/packages/MoleculeFlow/5xJwa/test/test_drawing.jl:7 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [10] top-level scope @ ~/.julia/packages/MoleculeFlow/5xJwa/test/test_drawing.jl:5 [11] include(fname::String) @ Base.MainInclude ./client.jl:487 [12] macro expansion @ ~/.julia/packages/MoleculeFlow/5xJwa/test/runtests.jl:18 [inlined] [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [14] top-level scope @ ~/.julia/packages/MoleculeFlow/5xJwa/test/runtests.jl:6 [15] include(fname::String) @ Base.MainInclude ./client.jl:487 [16] top-level scope @ none:6 [03:42:53] SMILES Parse Error: syntax error while parsing: invalid [03:42:53] SMILES Parse Error: check for mistakes around position 1: [03:42:53] invalid [03:42:53] ^ [03:42:53] SMILES Parse Error: Failed parsing SMILES 'invalid' for input: 'invalid' [03:42:53] SMILES Parse Error: syntax error while parsing: invalid [03:42:53] SMILES Parse Error: check for mistakes around position 1: [03:42:53] invalid [03:42:53] ^ [03:42:53] SMILES Parse Error: Failed parsing SMILES 'invalid' for input: 'invalid' [03:42:53] SMILES Parse Error: syntax error while parsing: invalid [03:42:53] SMILES Parse Error: check for mistakes around position 1: [03:42:53] invalid [03:42:53] ^ [03:42:53] SMILES Parse Error: Failed parsing SMILES 'invalid' for input: 'invalid' [03:42:53] SMILES Parse Error: syntax error while parsing: invalid [03:42:53] SMILES Parse Error: check for mistakes around position 1: [03:42:53] invalid [03:42:53] ^ [03:42:53] SMILES Parse Error: Failed parsing SMILES 'invalid' for input: 'invalid' [03:42:53] SMILES Parse Error: syntax error while parsing: invalid [03:42:53] SMILES Parse Error: check for mistakes around position 1: [03:42:53] invalid [03:42:53] ^ [03:42:53] SMILES Parse Error: Failed parsing SMILES 'invalid' for input: 'invalid' [03:42:53] SMILES Parse Error: syntax error while parsing: invalid [03:42:53] SMILES Parse Error: check for mistakes around position 1: [03:42:53] invalid [03:42:53] ^ [03:42:53] SMILES Parse Error: Failed parsing SMILES 'invalid' for input: 'invalid' [03:42:57] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:57] SMILES Parse Error: check for mistakes around position 1: [03:42:57] invalid_smiles [03:42:57] ^ [03:42:57] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' [03:42:57] SMILES Parse Error: syntax error while parsing: invalid_smiles [03:42:57] SMILES Parse Error: check for mistakes around position 1: [03:42:57] invalid_smiles [03:42:57] ^ [03:42:57] SMILES Parse Error: Failed parsing SMILES 'invalid_smiles' for input: 'invalid_smiles' ┌ Warning: Error in align_mol: PythonCall.PyException() └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/alignment.jl:107 [03:43:02] Molecule does not have explicit Hs. Consider calling AddHs() [03:43:02] Molecule does not have explicit Hs. Consider calling AddHs() [03:43:02] Molecule does not have explicit Hs. Consider calling AddHs() [03:43:02] Molecule does not have explicit Hs. Consider calling AddHs() [03:43:03] Molecule does not have explicit Hs. Consider calling AddHs() [03:43:03] Molecule does not have explicit Hs. Consider calling AddHs() [03:43:03] SMILES Parse Error: syntax error while parsing: INVALID_SMILES [03:43:03] SMILES Parse Error: check for mistakes around position 3: [03:43:03] INVALID_SMILES [03:43:03] ~~^ [03:43:03] SMILES Parse Error: Failed parsing SMILES 'INVALID_SMILES' for input: 'INVALID_SMILES' ┌ Warning: Error in align_mol: PythonCall.PyException() └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/alignment.jl:107 ┌ Warning: Error in calc_rms: PythonCall.PyException() └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/alignment.jl:204 ┌ Warning: Error in get_alignment_transform: PythonCall.PyException() └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/alignment.jl:385 ┌ Warning: Error in align_mol: PythonCall.PyException() └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/alignment.jl:107 ┌ Warning: Error in align_mol: PythonCall.PyException() └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/alignment.jl:107 ┌ Warning: Error in align_mol: PythonCall.PyException() └ @ MoleculeFlow ~/.julia/packages/MoleculeFlow/5xJwa/src/molecule/alignment.jl:107 [03:43:03] SMILES Parse Error: syntax error while parsing: invalid [03:43:03] SMILES Parse Error: check for mistakes around position 1: [03:43:03] invalid [03:43:03] ^ [03:43:03] SMILES Parse Error: Failed parsing SMILES 'invalid' for input: 'invalid' [03:43:04] Found a SCD/SED line with missing/empty SDT specification at line 39 [03:43:04] Found a SCD/SED line with missing/empty SDT specification at line 54 [03:43:04] mapped atoms in the reactants were not mapped in the products. unmapped numbers are: 2 [03:43:04] mapped atoms in the reactants were not mapped in the products. unmapped numbers are: 2 [03:43:07] mapped atoms in the reactants were not mapped in the products. unmapped numbers are: 2 [03:43:07] mapped atoms in the reactants were not mapped in the products. unmapped numbers are: 2 [03:43:07] mapped atoms in the reactants were not mapped in the products. unmapped numbers are: 2 [03:43:08] mapped atoms in the reactants were not mapped in the products. unmapped numbers are: 4 WARNING: both ImageMetadata and ImageAxes export "data"; uses of it in module Images must be qualified WARNING: using deprecated binding ImageMorphology.morphogradient in Images. , use mgradient instead. WARNING: Images.morphogradient is deprecated, use ImageMorphology.mgradient instead. likely near none:8 WARNING: using deprecated binding ImageMorphology.morpholaplace in Images. , use mlaplacian instead. WARNING: Images.morpholaplace is deprecated, use ImageMorphology.mlaplacian instead. likely near none:8 WARNING: using deprecated binding ImageCore.permuteddimsview in ImageAxes. , use PermutedDimsArray instead. WARNING: using deprecated binding ImageCore.permuteddimsview in ImageBase. , use PermutedDimsArray instead. WARNING: using deprecated binding ImageAxes.permuteddimsview in Images. , use Base.PermutedDimsArrays.PermutedDimsArray{T, N, perm, iperm, AA} where AA<:(AbstractArray{T, N} where N where T) where iperm where perm where N where T instead. WARNING: Images.permuteddimsview is deprecated, use Base.PermutedDimsArrays.PermutedDimsArray{T, N, perm, iperm, AA} where AA<:(AbstractArray{T, N} where N where T) where iperm where perm where N where T instead. likely near none:8 WARNING: both ImageMetadata and ImageAxes export "data"; uses of it in module Images must be qualified WARNING: using deprecated binding ImageMorphology.morphogradient in Images. , use mgradient instead. WARNING: Images.morphogradient is deprecated, use ImageMorphology.mgradient instead. likely near /home/pkgeval/.julia/packages/MoleculeFlow/5xJwa/test/test_aqua.jl:5 WARNING: using deprecated binding ImageMorphology.morpholaplace in Images. , use mlaplacian instead. WARNING: Images.morpholaplace is deprecated, use ImageMorphology.mlaplacian instead. likely near /home/pkgeval/.julia/packages/MoleculeFlow/5xJwa/test/test_aqua.jl:5 WARNING: using deprecated binding ImageCore.permuteddimsview in ImageAxes. , use PermutedDimsArray instead. WARNING: using deprecated binding ImageCore.permuteddimsview in ImageBase. , use PermutedDimsArray instead. WARNING: using deprecated binding ImageAxes.permuteddimsview in Images. , use Base.PermutedDimsArrays.PermutedDimsArray{T, N, perm, iperm, AA} where AA<:(AbstractArray{T, N} where N where T) where iperm where perm where N where T instead. WARNING: Images.permuteddimsview is deprecated, use Base.PermutedDimsArrays.PermutedDimsArray{T, N, perm, iperm, AA} where AA<:(AbstractArray{T, N} where N where T) where iperm where perm where N where T instead. likely near /home/pkgeval/.julia/packages/MoleculeFlow/5xJwa/test/test_aqua.jl:5 Stale dependencies: Test Failed at /home/pkgeval/.julia/packages/Aqua/MCcFg/src/stale_deps.jl:31 Expression: isempty(stale_deps) Evaluated: isempty(Base.PkgId[Distributed [8ba89e20-285c-5b6f-9357-94700520ee1b]]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:673 [inlined] [2] test_stale_deps(pkg::Base.PkgId; kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/MCcFg/src/stale_deps.jl:31 [3] test_stale_deps @ ~/.julia/packages/Aqua/MCcFg/src/stale_deps.jl:29 [inlined] [4] #test_stale_deps#34 @ ~/.julia/packages/Aqua/MCcFg/src/stale_deps.jl:35 [inlined] [5] test_stale_deps @ ~/.julia/packages/Aqua/MCcFg/src/stale_deps.jl:34 [inlined] [6] macro expansion @ ~/.julia/packages/Aqua/MCcFg/src/Aqua.jl:94 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [8] test_all(testtarget::Module; ambiguities::Bool, unbound_args::Bool, undefined_exports::Bool, project_extras::Bool, stale_deps::Bool, deps_compat::Bool, piracies::Bool, persistent_tasks::Bool, undocumented_names::Bool) @ Aqua ~/.julia/packages/Aqua/MCcFg/src/Aqua.jl:94 Test Summary: | Pass Fail Error Total Time MoleculeFlow.jl Tests | 2060 1 1 2062 2m46.6s Basic Molecule Operations | 9 9 9.8s Vectorized Operations | 10 10 3.5s Hydrogen Manipulation | 10 10 0.4s Extended File I/O | 12 12 0.4s Molecular Editing and Manipulation | 14 14 2.0s Stereochemistry Operations | 5 5 0.6s Ring Analysis | 6 6 0.4s Pattern Matching | 11 11 0.5s Advanced Ring Analysis | 7 7 0.5s Molecular Editing Operations | 15 15 0.5s Error Handling and Edge Cases | 4 4 0.0s XYZ Format Support | 12 12 0.8s MOL2 Format Support | 17 17 0.1s Format Integration Tests | 10 10 0.3s Molecular Descriptors | 10 10 0.6s Additional Molecular Descriptors | 65 65 2.5s Advanced Drug-like and ADMET Descriptors | 30 30 0.9s Advanced Ring and Structure Counts | 19 19 0.1s 3D Descriptors | 41 41 2.7s Vectorized Operations for New Descriptors | 20 20 3.6s Error Handling and Edge Cases | 7 7 0.0s VSA Descriptors | 184 184 3.6s BCUT Descriptors | 28 28 0.9s Additional Structure Count Descriptors | 29 29 0.5s Additional E-State Descriptors | 5 5 0.1s Vectorized Operations for New Descriptors | 12 12 0.8s New Wrappers Integration Tests | 872 872 0.7s Backward Compatibility | 13 13 0.7s Fingerprints | 12 12 0.0s Similarity Calculations | 17 17 2.5s Atom Operations | 13 13 0.1s Bond Operations | 9 9 0.2s Substructure Search | 9 9 0.3s Basic Functional Groups | 13 13 0.0s Sulfur-Containing Groups | 7 7 0.0s Phosphorus-Containing Groups | 4 4 0.0s Halogen-Containing Groups | 5 5 0.0s Advanced Nitrogen Groups | 6 6 0.0s Advanced Oxygen Groups | 3 3 0.0s Carbon-Carbon Multiple Bonds | 3 3 0.0s 5-Membered Aromatic Heterocycles | 7 7 0.0s 6-Membered Aromatic Heterocycles | 4 4 0.0s Fused Aromatic Systems | 5 5 0.0s Saturated Heterocycles | 4 4 0.0s Reactive Groups | 4 4 0.0s Protecting Groups | 4 4 0.0s Drug-like Molecules | 9 9 0.0s FUNCTIONAL_GROUPS Dictionary | 41 41 0.0s Ring Analysis | 5 5 0.1s Graph Operations | 19 19 4.8s Graph Operations - Complex Molecules | 16 16 0.0s Graph Operations - Edge Cases | 9 9 0.0s Graph Operations - Disconnected Molecules | 4 4 0.0s Drawing Functions | 1 1 4.7s Molecular Standardization | 56 56 0.8s Conformer Generation | 44 44 0.1s Molecular Alignment Functions | 182 182 5.5s Error Handling | 7 7 0.0s Basic Reaction Creation | 5 5 0.2s Reaction File I/O | 3 3 0.1s Reaction Validation | 4 4 0.0s Run Reaction | 5 5 0.4s Reaction Templates | 4 4 0.1s Substructure Matching | 3 3 0.1s Reaction Fingerprinting | 5 5 1.3s Reaction Similarity | 5 5 1.4s Atom Mapping | 3 3 0.2s Reaction Preprocessing | 3 3 0.1s Reaction Analysis | 9 9 0.1s Reaction Library Enumeration | 1 1 0.3s Reaction Database Search | 2 2 0.9s Aqua.jl Quality Checks | 10 1 11 1m36.7s Method ambiguity | 1 1 25.4s Unbound type parameters | 1 1 0.3s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.0s Stale dependencies | 1 1 28.3s Compat bounds | 4 4 0.4s Piracy | 1 1 0.2s Persistent tasks | 1 1 34.1s ERROR: LoadError: Some tests did not pass: 2060 passed, 1 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/MoleculeFlow/5xJwa/test/runtests.jl:5 Testing failed after 210.0s ERROR: LoadError: Package MoleculeFlow 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:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1012.08s: package requires a missing binary dependency