Package evaluation to test BGEN on Julia 1.14.0-DEV.2309 (6e1a27e459*) started at 2026-06-06T15:56:01.859 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 17.56s ################################################################################ # Installation # Installing BGEN... Resolving package versions... Installed AliasTables ───────────────── v1.1.3 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed CodecZlib ─────────────────── v0.7.8 Installed OrderedCollections ────────── v1.8.2 Installed DataStructures ────────────── v0.19.5 Installed StatsBase ─────────────────── v0.34.11 Installed InlineStrings ─────────────── v1.4.5 Installed CodecZstd ─────────────────── v0.8.7 Installed TranscodingStreams ────────── v0.11.3 Installed DataAPI ───────────────────── v1.16.0 Installed DataValueInterfaces ───────── v1.0.0 Installed Statistics ────────────────── v1.11.1 Installed StatsAPI ──────────────────── v1.8.0 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed LogExpFunctions ───────────── v1.0.1 Installed Parsers ───────────────────── v2.8.5 Installed dlfcn_win32_jll ───────────── v1.4.2+0 (no artifacts on this platform) Installed IrrationalConstants ───────── v0.2.6 Installed SIMD ──────────────────────── v3.7.2 Installed PrecompileTools ───────────── v1.3.4 Installed GeneticVariantBase ────────── v0.1.2 Installed Tables ────────────────────── v1.12.1 Installed Missings ──────────────────── v1.2.0 Installed DBInterface ───────────────── v2.6.1 Installed SpecialFunctions ──────────── v2.8.0 Installed TableTraits ───────────────── v1.0.1 Installed PtrArrays ─────────────────── v1.4.0 Installed SortingAlgorithms ─────────── v1.2.2 Installed WeakRefStrings ────────────── v1.4.3 Installed Preferences ───────────────── v1.5.2 Installed SQLite_jll ────────────────── v3.51.2+0 Installed JLLWrappers ───────────────── v1.8.0 Installed DocStringExtensions ───────── v0.9.5 Installed SQLite ────────────────────── v1.8.0 Installed BGEN ──────────────────────── v0.2.2 Installing 2 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact SQLite 1.7 MiB Updating `~/.julia/environments/v1.14/Project.toml` [6db4b851] + BGEN v0.2.2 Updating `~/.julia/environments/v1.14/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [6db4b851] + BGEN v0.2.2 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.5 [e2d170a0] + DataValueInterfaces v1.0.0 [ffbed154] + DocStringExtensions v0.9.5 [2447270c] + GeneticVariantBase v0.1.2 [842dd82b] + InlineStrings v1.4.5 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [2ab3a3ac] + LogExpFunctions v1.0.1 [e1d29d7a] + Missings v1.2.0 ⌅ [bac558e1] + OrderedCollections v1.8.2 [69de0a69] + Parsers v2.8.5 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [43287f4e] + PtrArrays v1.4.0 [fdea26ae] + SIMD v3.7.2 [0aa819cd] + SQLite v1.8.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.8.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.11 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [ea10d353] + WeakRefStrings v1.4.3 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [76ed43ae] + SQLite_jll v3.51.2+0 [c4b69c83] + dlfcn_win32_jll v1.4.2+0 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays v1.13.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.2+0 [4536629a] + OpenBLAS_jll v0.3.33+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+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 8.99s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 6.3 s ✓ TestEnv 1 dependency successfully precompiled in 6 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 313.9 s ✓ InlineStrings 1.1 s ✓ Statistics 1.1 s ✓ DataAPI 2.7 s ✓ IrrationalConstants 0.5 s ✓ DataValueInterfaces 0.6 s ✓ StatsAPI 19.9 s ✓ DBInterface 151.1 s ✓ OrderedCollections 1.2 s ✓ DocStringExtensions 37.8 s ✓ PtrArrays 54.6 s ✓ TranscodingStreams 0.5 s ✓ IteratorInterfaceExtensions 3.0 s ✓ Preferences 42.2 s ✓ Statistics → SparseArraysExt 56.0 s ✓ Missings 169.3 s ✓ DataStructures 1.9 s ✓ LogExpFunctions 40.1 s ✓ AliasTables 21.9 s ✓ CodecZstd 20.7 s ✓ CodecZlib 0.5 s ✓ TableTraits 3.3 s ✓ JLLWrappers 2.9 s ✓ PrecompileTools 38.7 s ✓ SortingAlgorithms 151.9 s ✓ Tables 2.6 s ✓ dlfcn_win32_jll 3.6 s ✓ OpenSpecFun_jll 648.9 s ✓ SIMD 39.2 s ✓ Parsers 172.9 s ✓ StatsBase 3.7 s ✓ SQLite_jll 81.3 s ✓ SpecialFunctions 61.9 s ✓ InlineStrings → ParsersExt 42.4 s ✓ GeneticVariantBase 395.8 s ✓ WeakRefStrings  ====================================================================================== 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 157 running 1 of 1  signal (10): User defined signal 1 _ZN12_GLOBAL__N_18Verifier11visitMDNodeERKN4llvm6MDNodeENS0_19AreDebugLocsAllowedE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN12_GLOBAL__N_18Verifier11visitMDNodeERKN4llvm6MDNodeENS0_19AreDebugLocsAllowedE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN12_GLOBAL__N_18Verifier16visitInstructionERN4llvm11InstructionE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN12_GLOBAL__N_18Verifier6verifyERKN4llvm8FunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm12verifyModuleERKNS_6ModuleEPNS_11raw_ostreamEPb at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) verifyLLVMIR at /source/src/pipeline.cpp:1072:21 run at /source/src/llvm-ptls.cpp:375:5 run at /source/usr/include/llvm/IR/PassManagerInternal.h:91:41 _ZN4llvm11PassManagerINS_6ModuleENS_15AnalysisManagerIS1_JEEEJEE3runERS1_RS3_ at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) run at /source/src/pipeline.cpp:982:12 operator() at /source/src/jitlayers.cpp:1298:17 operator() at /source/src/jitlayers.cpp:1435:12 [inlined] optimizeModule at /source/src/jitlayers.cpp:2382:18 materialize at /source/src/jitlayers.cpp:905:31 _ZN4llvm3orc19MaterializationTask3runEv at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) dispatch at /source/src/julia-task-dispatcher.h:353:11 _ZN4llvm3orc16ExecutionSession22dispatchOutstandingMUsEv at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm3orc16ExecutionSession17OL_completeLookupESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EESt10shared_ptrINS0_23AsynchronousSymbolQueryEESt8functionIFvRKNS_8DenseMapIPNS0_8JITDylibENS_8DenseSetINS0_15SymbolStringPtrENS_12DenseMapInfoISF_vEEEENSG_ISD_vEENS_6detail12DenseMapPairISD_SI_EEEEEE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm3orc25InProgressFullLookupState8completeESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm3orc16ExecutionSession19OL_applyQueryPhase1ESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EENS_5ErrorE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm3orc16ExecutionSession6lookupENS0_10LookupKindERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS8_EENS0_15SymbolLookupSetENS0_11SymbolStateENS_15unique_functionIFvNS_8ExpectedINS_8DenseMapINS0_15SymbolStringPtrENS0_17ExecutorSymbolDefENS_12DenseMapInfoISI_vEENS_6detail12DenseMapPairISI_SJ_EEEEEEEEESt8functionIFvRKNSH_IS6_NS_8DenseSetISI_SL_EENSK_IS6_vEENSN_IS6_SV_EEEEEE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) publishCIs at /source/src/jitlayers.cpp:2085:14 jl_compile_codeinst_impl at /source/src/jitlayers.cpp:510:39 jl_compile_method_internal at /source/src/gf.c:3677:27 _jl_invoke at /source/src/gf.c:4130:16 [inlined] ijl_apply_generic at /source/src/gf.c:4364:12 jl_apply at /source/src/julia.h:2388:12 [inlined] ijl_lower at /source/src/ast.c:1274:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:31 jl_eval_module_expr at /source/src/toplevel.c:263:5 [inlined] jl_toplevel_eval_flex at /source/src/toplevel.c:665:27 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:521:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 207) _jl_invoke at /source/src/gf.c:4138:23 [inlined] ijl_apply_generic at /source/src/gf.c:4364:12 _include at ./loading.jl:3192:0 (pc: 122) include at ./Base.jl:326:0 (pc: 1) include_package_for_output at ./loading.jl:3296:0 (pc: 837) jfptr_include_package_for_output_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4138:23 [inlined] ijl_apply_generic at /source/src/gf.c:4364:12 jl_apply at /source/src/julia.h:2388:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:243:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:706:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:897:21 ijl_eval_thunk at /source/src/toplevel.c:768:18 jl_toplevel_eval_flex at /source/src/toplevel.c:712:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:521:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 207) include_string at ./loading.jl:3142:0 [inlined] exec_options at ./client.jl:353:0 (pc: 841) _start at ./client.jl:596:0 (pc: 294) jfptr__start_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4138:23 [inlined] ijl_apply_generic at /source/src/gf.c:4364:12 jl_apply at /source/src/julia.h:2388:12 [inlined] true_main at /source/src/jlapi.c:971:29 jl_repl_entrypoint at /source/src/jlapi.c:1138:15 main at /source/cli/loader_exe.c:58:15 unknown function (ip: 0x7ac0af741249) 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. 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 44 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:1404:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430:0 ijl_task_get_next at /source/src/scheduler.c:457:34 wait at ./task.jl:1246:0 (pc: 107) wait_forever at ./task.jl:1168:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4138:23 [inlined] ijl_apply_generic at /source/src/gf.c:4364:12 jl_apply at /source/src/julia.h:2388:12 [inlined] start_task at /source/src/task.c:1275:19 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 0x00007385452c1d20 Total snapshots: 373. Utilization: 0% ╎373 @Base/task.jl:1168 wait_forever() 372╎ 373 @Base/task.jl:1246 wait() ====================================================================================== 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:1404:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430:0 ijl_task_get_next at /source/src/scheduler.c:457:34 wait at ./task.jl:1246:0 (pc: 107) wait_forever at ./task.jl:1168:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4138:23 [inlined] ijl_apply_generic at /source/src/gf.c:4364:12 jl_apply at /source/src/julia.h:2388:12 [inlined] start_task at /source/src/task.c:1275:19 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 0x0000728f93116680 Total snapshots: 398. Utilization: 0% ╎398 @Base/task.jl:1168 wait_forever() 397╎ 398 @Base/task.jl:1246 wait() [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:156 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430:0 ijl_task_get_next at /source/src/scheduler.c:457:34 wait at ./task.jl:1246:0 (pc: 107) wait_forever at ./task.jl:1168:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4138:23 [inlined] [44] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/precompile.jl:34 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430:0 ijl_task_get_next at /source/src/scheduler.c:457:34 wait at ./task.jl:1246:0 (pc: 107) wait_forever at ./task.jl:1168:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4138:23 [inlined] ijl_apply_generic at /source/src/gf.c:4364:12 jl_apply at /source/src/julia.h:2388:12 [inlined] start_task at /source/src/task.c:1275:19 unknown function (ip: (nil)) at (unknown file) Allocations: 12711332 (Pool: 12710682; Big: 650); GC: 12 ijl_apply_generic at /source/src/gf.c:4364:12 jl_apply at /source/src/julia.h:2388:12 [inlined] start_task at /source/src/task.c:1275:19 unknown function (ip: (nil)) at (unknown file) Allocations: 18609577 (Pool: 18608848; Big: 729); GC: 15 val already in a list atexit hook threw an error: ErrorException("schedule: Task not runnable") error at ./error.jl:56:0 (pc: 6) #schedule#623 at ./task.jl:1051:0 (pc: 71) schedule at ./task.jl:1043:0 [inlined] uv_writecb_task at ./stream.jl:1198:0 (pc: 11) jlcapi_uv_writecb_task_643.1 at /opt/julia/lib/julia/sys.so (unknown line) uv__write_callbacks at /workspace/srcdir/libuv/src/unix/stream.c:926:0 uv__stream_io at /workspace/srcdir/libuv/src/unix/stream.c:1227:0 uv__run_pending at /workspace/srcdir/libuv/src/unix/core.c:824:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:420:0 ijl_process_events at /source/src/jl_uv.c:397:21 process_events at ./libuv.jl:133:0 [inlined] wait at ./task.jl:1233:0 (pc: 15) uv_write at ./stream.jl:1079:0 (pc: 11) unsafe_write at ./stream.jl:1152:0 (pc: 55) write at ./strings/io.jl:237:0 [inlined] print at ./strings/io.jl:239:0 (pc: 5) jfptr_print_138.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4138:23 [inlined] ijl_apply_generic at /source/src/gf.c:4364:12 showerror at ./errorshow.jl:164:0 (pc: 2) unknown function (ip: 0x73854337c966) at (unknown file) _jl_invoke at /source/src/gf.c:4138:23 [inlined] ijl_apply_generic at /source/src/gf.c:4364:12 _atexit at ./initdefs.jl:543:0 (pc: 210) jfptr__atexit_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4138:23 [inlined] ijl_apply_generic at /source/src/gf.c:4364:12 jl_apply at /source/src/julia.h:2388:12 [inlined] ijl_atexit_hook at /source/src/init.c:264:17 jl_exit_thread0_cb at /source/src/signals-unix.c:678:5 jl_fake_signal_return at /opt/julia/bin/../lib/julia/libjulia-internal.so.1.14 (unknown line) epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430:0 ijl_task_get_next at /source/src/scheduler.c:457:34 wait at ./task.jl:1246:0 (pc: 107) wait_forever at ./task.jl:1168:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4138:23 [inlined] ijl_apply_generic at /source/src/gf.c:4364:12 jl_apply at /source/src/julia.h:2388:12 [inlined] start_task at /source/src/task.c:1275:19 PkgEval terminated after 2731.39s: test duration exceeded the time limit