Package evaluation to test LocalAncestry on Julia 1.14.0-DEV.1918 (78a0dc1151*) started at 2026-03-19T19:27:07.762 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.76s ################################################################################ # Installation # Installing LocalAncestry... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [9c717bbe] + LocalAncestry v0.2.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [336ed68f] + CSV v0.10.16 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.18.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [48062228] + FilePathsBase v0.9.24 [92fee26a] + GZip v0.6.2 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [82899510] + IteratorInterfaceExtensions v1.0.0 [b964fa9f] + LaTeXStrings v1.4.0 [9c717bbe] + LocalAncestry v0.2.0 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.2.3 [189a3867] + Reexport v1.2.2 [91c51154] + SentinelArrays v1.4.9 [a2af1166] + SortingAlgorithms v1.2.2 [10745b16] + Statistics v1.11.1 [892a3eda] + StringManipulation v0.4.4 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [6462fe0b] + Sockets v1.11.0 [f489334b] + StyledStrings v1.13.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.30+0 [83775a58] + Zlib_jll v1.3.2+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 5.87s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 17028.1 ms ✓ LocalAncestry 1 dependency successfully precompiled in 19 seconds. 52 already precompiled. Precompilation completed after 37.61s ################################################################################ # Testing # Testing LocalAncestry Status `/tmp/jl_V8C8s0/Project.toml` [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.1 [92fee26a] GZip v0.6.2 [9c717bbe] LocalAncestry v0.2.0 [ade2ca70] Dates v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_V8C8s0/Manifest.toml` [336ed68f] CSV v0.10.16 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.18.1 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [48062228] FilePathsBase v0.9.24 [92fee26a] GZip v0.6.2 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [82899510] IteratorInterfaceExtensions v1.0.0 [b964fa9f] LaTeXStrings v1.4.0 [9c717bbe] LocalAncestry v0.2.0 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.2.3 [189a3867] Reexport v1.2.2 [91c51154] SentinelArrays v1.4.9 [a2af1166] SortingAlgorithms v1.2.2 [10745b16] Statistics v1.11.1 [892a3eda] StringManipulation v0.4.4 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [f489334b] StyledStrings v1.13.0 [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [4536629a] OpenBLAS_jll v0.3.30+0 [83775a58] Zlib_jll v1.3.2+0 [8e850b90] libblastrampoline_jll v5.15.0+0 Testing Running tests... LocalAncestry.jl v0.2.0 Started at 19:30:59 on Mar 19, 2026 Files Reference /home/pkgeval/.julia/packages/LocalAncestry/BzNwI/data/reference.vcf.gz Target /home/pkgeval/.julia/packages/LocalAncestry/BzNwI/data/target.vcf.gz Ancestry /home/pkgeval/.julia/packages/LocalAncestry/BzNwI/data/globalancestries.csv Parameters Chromosome MAF threshold 0.0001 IA threshold 0.66 N threads 1 Reading the locus information Chromosomes chr22 Loci 20129 Loci w. GT field 20129 Reading the reference ancestries Populations AFR, AFRanc, EAS, EASanc, EUR, EURanc, admixed N individuals 10000, 384, 10000, 411, 10000, 323, 10000 Number of haplotypes population N unique omit use ──────────────────────────────────────── EUR 4000 4000 0 4000 EAS 4000 4000 0 4000 AFR 4000 4000 0 4000 Total 12000 12000 0 12000 Subsetting loci Loci on focal chromosome: 20129/20129 Loci with MAF above limit: 10621/20129 Loci for later analysis: 10621/20129 Reading the reference haplotypes Mapping reference ancestries Getting haplotype library Block ranges Block frequencies Genome regions: 180 Reading the target haplotypes Assigning local ancestries ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 16 running 1 of 1 signal (10): User defined signal 1 unknown function (ip: 0x794ac24fcd67) at /lib/x86_64-linux-gnu/libc.so.6 memmove at ./cmem.jl:28 [inlined] unsafe_copyto! at ./genericmemory.jl:139 [inlined] _copyto_impl! at ./array.jl:300 [inlined] copyto! at ./array.jl:291 [inlined] getindex at ./array.jl:996 unknown function (ip: 0x794a88f281d6) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 macro expansion at /home/pkgeval/.julia/packages/LocalAncestry/BzNwI/src/evaluate.jl:24 [inlined] #evaluate##2 at ./threadingconstructs.jl:527 #evaluate##0 at ./threadingconstructs.jl:522 [inlined] #threading_run##0 at ./threadingconstructs.jl:178 unknown function (ip: 0x794a84598289) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [inlined] start_task at /source/src/task.c:1275 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 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:1246 wait_forever at ./task.jl:1168 jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [inlined] start_task at /source/src/task.c:1275 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ┌ 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/v1.14/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007d8d0cd371c0 Total snapshots: 99. Utilization: 0% ╎99 @Base/task.jl:1168 wait_forever() 98╎ 99 @Base/task.jl:1246 wait() [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 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:1246 wait_forever at ./task.jl:1168 jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [inlined] start_task at /source/src/task.c:1275 unknown function (ip: (nil)) at (unknown file) Allocations: 19034621 (Pool: 19033956; Big: 665); GC: 12 [16] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/LocalAncestry/BzNwI/test/runtests.jl:10 unknown function (ip: 0x794ac24fcd57) at /lib/x86_64-linux-gnu/libc.so.6 memmove at ./cmem.jl:28 [inlined] unsafe_copyto! at ./genericmemory.jl:139 [inlined] _copyto_impl! at ./array.jl:300 [inlined] copyto! at ./array.jl:291 [inlined] getindex at ./array.jl:996 unknown function (ip: 0x794a88f281d6) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 macro expansion at /home/pkgeval/.julia/packages/LocalAncestry/BzNwI/src/evaluate.jl:24 [inlined] #evaluate##2 at ./threadingconstructs.jl:527 #evaluate##0 at ./threadingconstructs.jl:522 [inlined] #threading_run##0 at ./threadingconstructs.jl:178 unknown function (ip: 0x794a84598289) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [inlined] start_task at /source/src/task.c:1275 unknown function (ip: (nil)) at (unknown file) Allocations: 101910431 (Pool: 101909636; Big: 795); GC: 4116 PkgEval terminated after 2730.16s: test duration exceeded the time limit