Package evaluation of VCFTools on Julia 1.13.0-DEV.692 (1ea959a8b1*) started at 2025-06-03T17:53:52.534 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.72s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.13/Manifest.toml` [7d9f7c33] + Accessors v0.1.42 [66dad0bd] + AliasTables v1.1.3 ⌅ [67c07d97] + Automa v0.8.4 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [e1450e63] + BufferedStreams v1.2.2 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.3 [38540f10] + CommonSolve v0.2.4 [34da2185] + Compat v4.16.0 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.5.8 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.4 [1a297f60] + FillArrays v1.13.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.5 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [21216c6a] + Preferences v1.4.3 [92933f4c] + ProgressMeter v1.10.4 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [f2b01f46] + Roots v2.2.7 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [4c63d2b9] + StatsFuns v1.5.0 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.6 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 4.22s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 37.95s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_FLamqs/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.7.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [09f84164] HypothesisTests v0.11.5 [92933f4c] ProgressMeter v1.10.4 [276daf66] SpecialFunctions v2.5.1 [2913bbd2] StatsBase v0.34.5 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.6 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.12.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_FLamqs/Manifest.toml` [7d9f7c33] Accessors v0.1.42 [66dad0bd] AliasTables v1.1.3 ⌅ [67c07d97] Automa v0.8.4 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [e1450e63] BufferedStreams v1.2.2 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.0.3 [38540f10] CommonSolve v0.2.4 [34da2185] Compat v4.16.0 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.5.8 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.4 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.5 [842dd82b] InlineStrings v1.4.3 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [92933f4c] ProgressMeter v1.10.4 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [f2b01f46] Roots v2.2.7 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.5 [4c63d2b9] StatsFuns v1.5.0 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.6 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v0.6.4 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.12.1+1 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.65.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling packages... 6428.7 ms ✓ WeakRefStrings 33469.2 ms ✓ CSV 2 dependencies successfully precompiled in 40 seconds. 37 already precompiled. Precompiling packages... 33245.4 ms ✓ PrettyTables 87510.0 ms ✓ DataFrames 2 dependencies successfully precompiled in 121 seconds. 33 already precompiled. Test Summary: | Pass Total Time H-W test | 1 1 3.9s Test Summary: | Pass Total Time openvcf | 4 4 2.2s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.5s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 2.5s ┌ Warning: `Progress(n::Integer, dt::Real, desc::AbstractString = "Progress: ", barlen = nothing, color::Symbol = :green, output::IO = stderr; offset::Integer = 0)` is deprecated, use `Progress(n; dt = dt, desc = desc, barlen = barlen, color = color, output = output, offset = offset)` instead. │ caller = ip:0x0 └ @ Core :-1 Progress: 0%| | ETA: 0:25:07 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 15.644198 seconds (11.13 M allocations: 682.046 MiB, 4.58% gc time, 91.57% compilation time: 24% of which was recompilation) 1.252149 seconds (2.87 M allocations: 195.928 MiB, 3.53% gc time, 7.44% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:23:26 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 3.576991 seconds (4.42 M allocations: 299.718 MiB, 2.18% gc time, 59.29% compilation time) 1.280572 seconds (2.85 M allocations: 195.278 MiB, 2.60% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 25.7s Test Summary: | Pass Total Time get sampleID | 4 4 0.1s Test Summary: | Pass Total Time Fishers exact HWE test | 20 20 0.0s Test Summary: | Pass Total Time filter_genotype(record) | 9 9 2.1s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.0s Test Summary: | Pass Total Time flip_gt_allele | 4 4 0.9s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 6.2s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:19:31 Progress: 0%|▏ | ETA: 0:18:38 Progress: 0%|▏ | ETA: 0:18:21 Progress: 0%|▏ | ETA: 0:18:11 Progress: 0%|▎ | ETA: 0:18:04 Progress: 1%|▎ | ETA: 0:17:59 Progress: 1%|▎ | ETA: 0:17:53 Progress: 1%|▎ | ETA: 0:17:52 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10%|████▏ | ETA: 0:15:45 Progress: 10%|████▏ | ETA: 0:15:44 Progress: 10%|████▎ | ETA: 0:15:43 Progress: 100%|█████████████████████████████████████████| Time: 0:01:48 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 19:52:44 Progress: 29%|████████████▏ | ETA: 0:04:16 Progress: 58%|████████████████████████ | ETA: 0:01:17 Progress: 83%|█████████████████████████████████▉ | ETA: 0:00:23 Progress: 100%|█████████████████████████████████████████| Time: 0:01:49 [ Info: 0 records are matched 230.477537 seconds (2.19 G allocations: 143.726 GiB, 6.55% gc time, 0.37% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 11m38.9s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:18:38 Progress: 20%|████████▏ | ETA: 0:07:03 Progress: 40%|████████████████▌ | ETA: 0:02:36 Progress: 62%|█████████████████████████▌ | ETA: 0:01:05 Progress: 85%|██████████████████████████████████▊ | ETA: 0:00:19 Progress: 100%|█████████████████████████████████████████| Time: 0:01:47 [ Info: 833 records are matched 118.764173 seconds (1.11 G allocations: 72.817 GiB, 6.42% gc time, 0.47% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:21:35 Progress: 20%|████████ | ETA: 0:07:06 Progress: 39%|████████████████▏ | ETA: 0:02:41 Progress: 61%|█████████████████████████▏ | ETA: 0:01:07 Progress: 83%|██████████████████████████████████▏ | ETA: 0:00:22 Progress: 100%|█████████████████████████████████████████| Time: 0:01:47 [ Info: 493 records are matched 118.625511 seconds (1.11 G allocations: 72.816 GiB, 6.43% gc time, 0.43% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:25:26 Progress: 21%|████████▌ | ETA: 0:06:39 Progress: 42%|█████████████████▍ | ETA: 0:02:23 Progress: 65%|██████████████████████████▌ | ETA: 0:00:58 Progress: 88%|████████████████████████████████████▎ | ETA: 0:00:14 Progress: 100%|█████████████████████████████████████████| Time: 0:01:47 [ Info: 0 records are matched 119.155338 seconds (1.11 G allocations: 72.816 GiB, 6.41% gc time, 0.54% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 5m58.7s 0.950874 seconds (1.34 M allocations: 92.868 MiB, 4.06% gc time, 86.94% compilation time) 0.706707 seconds (1.21 M allocations: 87.965 MiB, 3.65% gc time, 79.48% compilation time) 0.743013 seconds (1.22 M allocations: 87.236 MiB, 84.72% compilation time) 0.400559 seconds (216.34 k allocations: 11.781 MiB, 5.28% gc time, 99.96% compilation time) 0.008155 seconds (6.30 k allocations: 485.055 KiB, 96.92% compilation time) 0.010468 seconds (2.66 k allocations: 248.055 KiB, 96.66% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 7.9s 0.880602 seconds (990.12 k allocations: 75.434 MiB, 3.75% gc time, 83.16% compilation time) 0.725432 seconds (891.39 k allocations: 72.234 MiB, 2.81% gc time, 82.78% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 4.9s Test Summary: | Pass Total Time convert_ds | 5 5 1.2s 0.120648 seconds (525.75 k allocations: 50.463 MiB, 27.30% compilation time) 0.711567 seconds (659.64 k allocations: 57.986 MiB, 6.82% gc time, 78.27% compilation time) ┌ Warning: Reached end of reader; columns 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:72 ┌ Warning: Reached end of reader; rows 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:176 0.071970 seconds (520.43 k allocations: 51.916 MiB) 0.542981 seconds (595.42 k allocations: 56.142 MiB, 3.53% gc time, 83.05% compilation time) ┌ Warning: Reached end of record! Columns 1357-1400 are filled with 0.0s and are NOT haplotypes! └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:414 ┌ Warning: Reached end of record! Rows 1357-1400 are filled with 0.0s and are NOT haplotypes! └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:501 0.119502 seconds (1.56 M allocations: 81.839 MiB, 14.35% gc time, 7.89% compilation time) 0.591286 seconds (1.71 M allocations: 90.584 MiB, 3.21% gc time, 78.56% compilation time) ┌ Warning: Reached end of reader; columns 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:672 ┌ Warning: Reached end of reader; rows 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:787 Test Summary: | Pass Total Time convert to transpose functions | 13 13 6.4s Test Summary: | Pass Total Time record info | 14 14 7.7s Test Summary: | Pass Total Time write VCF | 3 3 4.5s 3.289759 seconds (5.28 M allocations: 379.546 MiB, 17.95% gc time, 33.14% compilation time) 1.647802 seconds (2.86 M allocations: 194.894 MiB, 2.74% gc time, 12.38% compilation time) 1.592414 seconds (4.89 M allocations: 358.124 MiB, 3.76% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 9.0s 1.649977 seconds (626.97 k allocations: 54.540 MiB, 0.97% gc time, 27.67% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 4.4s Test Summary: | Pass Total Time filter_chr | 4 4 1.5s Progress: 0%|▏ | ETA: 0:23:35 Progress: 1%|▍ | ETA: 0:20:39 Progress: 1%|▌ | ETA: 0:18:56 Progress: 2%|▊ | ETA: 0:19:12 Progress: 2%|▉ | ETA: 0:19:22 Progress: 3%|█▏ | ETA: 0:19:28 Progress: 3%|█▎ | ETA: 0:19:29 Progress: 3%|█▍ | ETA: 0:19:10 Progress: 4%|█▋ | ETA: 0:19:08 Progress: 4%|█▊ | ETA: 0:19:12 Progress: 5%|██ | ETA: 0:19:15 Progress: 5%|██▏ | ETA: 0:19:13 Progress: 6%|██▎ | ETA: 0:19:11 Progress: 6%|██▍ | ETA: 0:19:08 Progress: 6%|██▋ | ETA: 0:19:03 Progress: 7%|██▊ | ETA: 0:18:54 Progress: 7%|███ | ETA: 0:18:49 Progress: 8%|███▏ | ETA: 0:18:46 Progress: 8%|███▎ | ETA: 0:18:40 Progress: 8%|███▌ | ETA: 0:18:35 Progress: 9%|███▋ | ETA: 0:18:30 Progress: 9%|███▊ | ETA: 0:18:27 Progress: 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A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 25 running 1 of 2 signal (10): User defined signal 1 unknown function (ip: 0x793e78515f14) at /lib/x86_64-linux-gnu/libc.so.6 pthread_cond_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv_cond_wait at /workspace/srcdir/libuv/src/unix/thread.c:822 ijl_task_get_next at /source/src/scheduler.c:523 wait at ./task.jl:1213 wait_forever at ./task.jl:1150 jfptr_wait_forever_72271.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 jl_apply at /source/src/julia.h:2339 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) jl_table_assign_bp at /source/src/iddict.c:50 [inlined] ijl_idtable_rehash at /source/src/iddict.c:25 jl_table_assign_bp at /source/src/iddict.c:101 [inlined] ijl_eqtable_put at /source/src/iddict.c:146 setindex! at ./iddict.jl:86 [inlined] deepcopy_internal at ./deepcopy.jl:132 unknown function (ip: 0x793e77025ec6) at (unknown file) _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 _deepcopy_memory_t at ./deepcopy.jl:120 deepcopy_internal at ./deepcopy.jl:104 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 deepcopy at ./deepcopy.jl:34 [inlined] copy at /home/pkgeval/.julia/packages/VariantCallFormat/YgfJC/src/record.jl:309 iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:90 [inlined] iterate at ./iterators.jl:197 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:46 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26 unknown function (ip: 0x793e53359696) at (unknown file) _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.13/Test/src/Test.jl:1833 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_invoke at /source/src/gf.c:3618 jl_toplevel_eval_flex at /source/src/toplevel.c:765 jl_toplevel_eval_flex at /source/src/toplevel.c:716 ijl_toplevel_eval at /source/src/toplevel.c:788 ijl_toplevel_eval_in at /source/src/toplevel.c:833 eval at ./boot.jl:489 include_string at ./loading.jl:2846 _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 _include at ./loading.jl:2906 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_60238.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 jl_apply at /source/src/julia.h:2339 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:776 jl_toplevel_eval_flex at /source/src/toplevel.c:716 ijl_toplevel_eval at /source/src/toplevel.c:788 ijl_toplevel_eval_in at /source/src/toplevel.c:833 eval at ./boot.jl:489 include_string at ./loading.jl:2846 _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 _include at ./loading.jl:2906 include at ./Base.jl:310 Progress: 100%|█████████████████████████████████████████| Time: 0:20:36 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_60238.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 jl_apply at /source/src/julia.h:2339 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:776 jl_toplevel_eval_flex at /source/src/toplevel.c:716 ijl_toplevel_eval at /source/src/toplevel.c:788 ijl_toplevel_eval_in at /source/src/toplevel.c:833 eval at ./boot.jl:489 exec_options at ./client.jl:290 _start at ./client.jl:557 jfptr__start_48840.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 jl_apply at /source/src/julia.h:2339 [inlined] true_main at /source/src/jlapi.c:964 jl_repl_entrypoint at /source/src/jlapi.c:1132 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x793e784b7249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== Test Summary: | Pass Total Time AIM selection | 4 4 21m32.1s ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 2 signal (10): User defined signal 1 unknown function (ip: 0x70fca2efcf14) at /lib/x86_64-linux-gnu/libc.so.6 pthread_cond_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv_cond_wait at /workspace/srcdir/libuv/src/unix/thread.c:822 ijl_task_get_next at /source/src/scheduler.c:523 wait at ./task.jl:1213 wait_forever at ./task.jl:1150 jfptr_wait_forever_72271.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 jl_apply at /source/src/julia.h:2339 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1213 wait_forever at ./task.jl:1150 jfptr_wait_forever_72271.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 jl_apply at /source/src/julia.h:2339 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (interactive) Task 0x000070fc8ca9e2c0 Total snapshots: 1. Utilization: 0% ╎1 @Base/task.jl:1150 wait_forever() ╎ 1 @Base/task.jl:1213 wait() Thread 2 (default) Task 0x000070fc8cbfc100 Total snapshots: 1. Utilization: 0% ╎1 @Base/task.jl:1150 wait_forever() ╎ 1 @Base/task.jl:1213 wait() ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1362 [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 unknown function (ip: 0x70fca2efcf14) at /lib/x86_64-linux-gnu/libc.so.6 pthread_cond_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv_cond_wait at /workspace/srcdir/libuv/src/unix/thread.c:822 ijl_task_get_next at /source/src/scheduler.c:523 [25] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/grm_test.jl:1 unknown function (ip: 0x793e78515f14) at /lib/x86_64-linux-gnu/libc.so.6 pthread_cond_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv_cond_wait at /workspace/srcdir/libuv/src/unix/thread.c:822 ijl_task_get_next at /source/src/scheduler.c:523 wait at ./task.jl:1213 wait at ./task.jl:1213 wait_forever at ./task.jl:1150 wait_forever at ./task.jl:1150 jfptr_wait_forever_72271.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 jl_apply at /source/src/julia.h:2339 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 jfptr_wait_forever_72271.1 at /opt/julia/lib/julia/sys.so (unknown line) uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 jl_apply at /source/src/julia.h:2339 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) wait at ./task.jl:1213 _ZNK4llvm18TargetLoweringBase24isOperationLegalOrCustomEjNS_3EVTEb.constprop.2 at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZNK4llvm14TargetLowering20SimplifyDemandedBitsENS_7SDValueERKNS_5APIntES4_RNS_9KnownBitsERNS0_17TargetLoweringOptEjb at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) wait_forever at ./task.jl:1150 _ZN12_GLOBAL__N_111DAGCombiner20SimplifyDemandedBitsEN4llvm7SDValueERKNS1_5APIntE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) jfptr_wait_forever_72271.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 jl_apply at /source/src/julia.h:2339 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 19138155 (Pool: 19137679; Big: 476); GC: 16 _ZN12_GLOBAL__N_111DAGCombiner20SimplifyDemandedBitsEN4llvm7SDValueE.constprop.0 at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN12_GLOBAL__N_111DAGCombiner12visitADDLikeEPN4llvm6SDNodeE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN12_GLOBAL__N_111DAGCombiner8visitADDEPN4llvm6SDNodeE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN12_GLOBAL__N_111DAGCombiner7combineEPN4llvm6SDNodeE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm12SelectionDAG7CombineENS_12CombineLevelEPNS_14BatchAAResultsENS_15CodeGenOptLevelE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm16SelectionDAGISel17CodeGenAndEmitDAGEv at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm16SelectionDAGISel20SelectAllBasicBlocksERKNS_8FunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm16SelectionDAGISel20runOnMachineFunctionERNS_15MachineFunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm22SelectionDAGISelLegacy20runOnMachineFunctionERNS_15MachineFunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm19MachineFunctionPass13runOnFunctionERNS_8FunctionE.part.0 at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm13FPPassManager13runOnFunctionERNS_8FunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm13FPPassManager11runOnModuleERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm6legacy15PassManagerImpl3runERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm3orc14SimpleCompilerclERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) operator() at /source/src/jitlayers.cpp:1577 addModule at /source/src/jitlayers.cpp:2058 jl_compile_codeinst_now at /source/src/jitlayers.cpp:649 jl_compile_codeinst_impl at /source/src/jitlayers.cpp:840 jl_compile_method_internal at /source/src/gf.c:3131 _jl_invoke at /source/src/gf.c:3603 [inlined] ijl_apply_generic at /source/src/gf.c:3811 jl_apply at /source/src/julia.h:2339 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:708 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:776 jl_toplevel_eval_flex at /source/src/toplevel.c:716 ijl_toplevel_eval at /source/src/toplevel.c:788 ijl_toplevel_eval_in at /source/src/toplevel.c:833 eval at ./boot.jl:489 include_string at ./loading.jl:2846 _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 _include at ./loading.jl:2906 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_60238.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 jl_apply at /source/src/julia.h:2339 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:776 jl_toplevel_eval_flex at /source/src/toplevel.c:716 ijl_toplevel_eval at /source/src/toplevel.c:788 ijl_toplevel_eval_in at /source/src/toplevel.c:833 eval at ./boot.jl:489 include_string at ./loading.jl:2846 _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 _include at ./loading.jl:2906 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_60238.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3611 [inlined] ijl_apply_generic at /source/src/gf.c:3811 jl_apply at /source/src/julia.h:2339 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] PkgEval terminated after 2726.32s: test duration exceeded the time limit