Package evaluation to test BioStructures on Julia 1.14.0-DEV.2593 (15c2b67521*) started at 2026-07-03T21:06:06.551 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.44s ################################################################################ # Installation # Installing BioStructures... Resolving package versions... Installed BioGenerics ──────── v0.1.5 Installed BioSymbols ───────── v5.2.0 Installed RecipesBase ──────── v1.3.4 Installed Format ───────────── v1.3.7 Installed Statistics ───────── v1.11.1 Installed Preferences ──────── v1.5.2 Installed PrecompileTools ──── v1.3.4 Installed CodecZlib ────────── v0.7.8 Installed TranscodingStreams ─ v0.11.3 Installed BioStructures ────── v4.7.1 Updating `~/.julia/environments/v1.14/Project.toml` [de9282ab] + BioStructures v4.7.1 Updating `~/.julia/environments/v1.14/Manifest.toml` [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.7.1 [3c28c6f8] + BioSymbols v5.2.0 [944b1d66] + CodecZlib v0.7.8 [1fa38f19] + Format v1.3.7 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [3cdcf5f2] + RecipesBase v1.3.4 [10745b16] + Statistics v1.11.1 [3bb67fe8] + TranscodingStreams v0.11.3 [0dad84c5] + ArgTools v1.2.0 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [b27032c2] + LibCURL v1.0.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [ca575930] + NetworkOptions v1.3.0 [de0858da] + Printf v1.11.0 [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.5+2 [deac9b47] + LibCURL_jll v8.21.0+0 [29816b5a] + LibSSH2_jll v1.11.101+0 [14a3606d] + MozillaCACerts_jll v2026.5.14 [4536629a] + OpenBLAS_jll v0.3.33+0 [458c3c95] + OpenSSL_jll v3.5.7+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 Installation completed after 4.91s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 9.1 s ✓ TestEnv 1 dependency successfully precompiled in 9 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 4.4 s ✓ MacroTools 319.1 s ✓ InlineStrings 0.6 s ✓ Reexport 1.4 s ✓ Statistics 1.1 s ✓ DataAPI 0.6 s ✓ DataValueInterfaces 1.2 s ✓ StaticArraysCore 151.4 s ✓ OrderedCollections 40.2 s ✓ Format 57.6 s ✓ InvertedIndices 0.7 s ✓ Twiddle 93.7 s ✓ IntervalTrees 1.5 s ✓ Inflate 57.1 s ✓ TranscodingStreams 0.5 s ✓ IteratorInterfaceExtensions 26.7 s ✓ LaTeXStrings 2.6 s ✓ Crayons 2.2 s ✓ MsgPack 182.8 s ✓ SentinelArrays 2.0 s ✓ Compat 31.7 s ✓ Preferences 3.5 s ✓ SimpleTraits 42.1 s ✓ Statistics → SparseArraysExt 56.5 s ✓ Missings 23.3 s ✓ PooledArrays 173.0 s ✓ DataStructures 38.8 s ✓ BioGenerics 20.2 s ✓ CodecZlib 0.7 s ✓ TableTraits 0.9 s ✓ Compat → CompatLinearAlgebraExt 32.4 s ✓ JLLWrappers 31.7 s ✓ PrecompileTools 41.3 s ✓ SortingAlgorithms 20.1 s ✓ MMTF 152.6 s ✓ Tables 49.0 s ✓ Aqua 32.4 s ✓ STRIDE_jll 32.2 s ✓ DSSP_jll 33.9 s ✓ RecipesBase 121.6 s ✓ BioSymbols 367.6 s ✓ StaticArrays 87.8 s ✓ StringManipulation ERROR: LoadError: Creating a new global in closed module `Base` (`##->###0`) breaks incremental compilation because the side effects will not be permanent. Stacktrace:  [1] eval_closure_type(mod::Module, closure_type_name::Symbol, field_names::Core.SimpleVector, field_is_box::Core.SimpleVector)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:96  [2] top-level scope  @ ~/.julia/packages/BioSequences/31amM/src/counting.jl:129  [3] eval(m::Module, e::Any)  @ Core boot.jl:522  [4] _eval(mod::Module, iter::Base.JuliaLowering.LoweringIterator{Dict{Symbol, Dict{Int64, Any}}}; soft_scope::Nothing)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/eval.jl:745  [5] eval(mod::Module, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}; macro_world::UInt64, soft_scope::Nothing, opts::@Kwargs{expr_compat_mode::Bool})  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/eval.jl:718 [inlined]  [6] top-level scope  @ ~/.julia/packages/BioSequences/31amM/src/counting.jl:129  [7] include(mapexpr::Function, mod::Module, _path::String)  @ Base Base.jl:326  [8] top-level scope  @ ~/.julia/packages/BioSequences/31amM/src/BioSequences.jl:225  [9] include(mod::Module, _path::String)  @ Base Base.jl:325  [10] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base loading.jl:3303  [11] top-level scope  @ stdin:5  [12] eval(m::Module, e::Any)  @ Core boot.jl:522  [13] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base loading.jl:3132  [14] include_string(m::Module, txt::String, fname::String)  @ Base loading.jl:3142 [inlined]  [15] exec_options(opts::Base.JLOptions)  @ Base client.jl:353  [16] _start()  @ Base client.jl:596 in expression starting at /home/pkgeval/.julia/packages/BioSequences/31amM/src/counting.jl:129 in expression starting at /home/pkgeval/.julia/packages/BioSequences/31amM/src/BioSequences.jl:8 in expression starting at stdin:5 ✗ BioSequences 119.4 s ✓ BioStructures 36.3 s ✓ StaticArrays → StaticArraysStatisticsExt 39.7 s ✓ ArnoldiMethod  ====================================================================================== 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 313 running 1 of 1  signal (10): User defined signal 1 _ZN4llvm11Instruction12copyMetadataERKS0_NS_8ArrayRefIjEE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZNK4llvm11Instruction5cloneEv at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm15CloneBasicBlockEPKNS_10BasicBlockERNS_8ValueMapIPKNS_5ValueENS_14WeakTrackingVHENS_14ValueMapConfigIS6_NS_3sys10SmartMutexILb0EEEEEEERKNS_5TwineEPNS_8FunctionEPNS_14ClonedCodeInfoEb.constprop.0 at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm21CloneFunctionBodyIntoERNS_8FunctionERKS0_RNS_8ValueMapIPKNS_5ValueENS_14WeakTrackingVHENS_14ValueMapConfigIS7_NS_3sys10SmartMutexILb0EEEEEEENS_10RemapFlagsERNS_15SmallVectorImplIPNS_10ReturnInstEEEPKcPNS_14ClonedCodeInfoEPNS_20ValueMapTypeRemapperEPNS_17ValueMaterializerEPKSt8functionIFbPKNS_8MetadataEEE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm17CloneFunctionIntoEPNS_8FunctionEPKS0_RNS_8ValueMapIPKNS_5ValueENS_14WeakTrackingVHENS_14ValueMapConfigIS7_NS_3sys10SmartMutexILb0EEEEEEENS_23CloneFunctionChangeTypeERNS_15SmallVectorImplIPNS_10ReturnInstEEEPKcPNS_14ClonedCodeInfoEPNS_20ValueMapTypeRemapperEPNS_17ValueMaterializerE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) removeAddrspaces at /source/src/llvm-remove-addrspaces.cpp:357:26 run at /source/src/llvm-remove-addrspaces.cpp:430:37 run at /source/src/llvm-remove-addrspaces.cpp:456:65 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:989:12 operator() at /source/src/jitlayers.cpp:1271:17 operator() at /source/src/jitlayers.cpp:1409:12 [inlined] optimizeModule at /source/src/jitlayers.cpp:2360:18 materialize at /source/src/jitlayers.cpp:876:31 _ZN4llvm3orc19MaterializationTask3runEv at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) dispatch at /source/src/julia-task-dispatcher.h:361:11 _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:2059:14 jl_compile_codeinst_impl at /source/src/jitlayers.cpp:511:39 jl_compile_method_very_internal at /source/src/gf.c:3927:27 _jl_invoke at /source/src/gf.c:4337:16 [inlined] ijl_apply_generic at /source/src/gf.c:4583:12 jl_apply at /source/src/julia.h:2405:12 [inlined] ijl_lower at /source/src/ast.c:1271:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:594:31 jl_eval_module_expr at /source/src/toplevel.c:262:5 [inlined] jl_toplevel_eval_flex at /source/src/toplevel.c:661:27 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:15 jl_toplevel_eval_flex at /source/src/toplevel.c:680:27 ijl_toplevel_eval at /source/src/toplevel.c:778:12 ijl_toplevel_eval_in at /source/src/toplevel.c:823:13 eval at ./boot.jl:522:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 208) _jl_invoke at /source/src/gf.c:4345:23 [inlined] ijl_apply_generic at /source/src/gf.c:4583:12 _include at ./loading.jl:3192:0 (pc: 122) include at ./Base.jl:325:0 (pc: 1) include_package_for_output at ./loading.jl:3303:0 (pc: 848) jfptr_include_package_for_output_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4345:23 [inlined] ijl_apply_generic at /source/src/gf.c:4583:12 jl_apply at /source/src/julia.h:2405:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:259:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:757:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:947:21 ijl_eval_thunk at /source/src/toplevel.c:764:18 jl_toplevel_eval_flex at /source/src/toplevel.c:708:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:15 jl_toplevel_eval_flex at /source/src/toplevel.c:680:27 ijl_toplevel_eval at /source/src/toplevel.c:778:12 ijl_toplevel_eval_in at /source/src/toplevel.c:823:13 eval at ./boot.jl:522:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 208) include_string at ./loading.jl:3142:0 [inlined] exec_options at ./client.jl:353:0 (pc: 813) _start at ./client.jl:596:0 (pc: 295) jfptr__start_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4345:23 [inlined] ijl_apply_generic at /source/src/gf.c:4583:12 jl_apply at /source/src/julia.h:2405:12 [inlined] true_main at /source/src/jlapi.c:985:29 jl_repl_entrypoint at /source/src/jlapi.c:1152:15 main at /source/cli/loader_exe.c:58:15 unknown function (ip: 0x7756d4977249) 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 39 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:524:34 wait at ./task.jl:1248:0 (pc: 107) wait_forever at ./task.jl:1170:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4345:23 [inlined] ijl_apply_generic at /source/src/gf.c:4583:12 jl_apply at /source/src/julia.h:2405:12 [inlined] start_task at /source/src/task.c:1276:19 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 0x0000725bee51de10 Total snapshots: 321. Utilization: 0% ╎321 @Base/task.jl:1170 wait_forever() 320╎ 321 @Base/task.jl:1248 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:524:34 wait at ./task.jl:1248:0 (pc: 107) wait_forever at ./task.jl:1170:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4345:23 [inlined] ijl_apply_generic at /source/src/gf.c:4583:12 jl_apply at /source/src/julia.h:2405:12 [inlined] start_task at /source/src/task.c:1276:19 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 0x0000782d0c650f10 Total snapshots: 365. Utilization: 0% ╎365 @Base/task.jl:1170 wait_forever() 364╎ 365 @Base/task.jl:1248 wait() [39] 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:524:34 wait at ./task.jl:1248:0 (pc: 107) wait_forever at ./task.jl:1170:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4345:23 [inlined] ijl_apply_generic at /source/src/gf.c:4583:12 jl_apply at /source/src/julia.h:2405:12 [inlined] start_task at /source/src/task.c:1276:19 unknown function (ip: (nil)) at (unknown file) Allocations: 14975558 (Pool: 14974822; Big: 736); GC: 18 [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:524:34 wait at ./task.jl:1248:0 (pc: 107) wait_forever at ./task.jl:1170:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4345:23 [inlined] ijl_apply_generic at /source/src/gf.c:4583:12 jl_apply at /source/src/julia.h:2405:12 [inlined] start_task at /source/src/task.c:1276:19 unknown function (ip: (nil)) at (unknown file) Allocations: 16063751 (Pool: 16063048; Big: 703); 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#625 at ./task.jl:1053:0 (pc: 71) schedule at ./task.jl:1045:0 [inlined] uv_writecb_task at ./stream.jl:1198:0 (pc: 11) jlcapi_uv_writecb_task_512.1 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:1235:0 (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_129.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4345:23 [inlined] ijl_apply_generic at /source/src/gf.c:4583:12 showerror at ./errorshow.jl:164:0 (pc: 2) unknown function (ip: 0x725bed9bc6f6) at (unknown file) _jl_invoke at /source/src/gf.c:4345:23 [inlined] ijl_apply_generic at /source/src/gf.c:4583:12 _atexit at ./initdefs.jl:544:0 (pc: 211) jfptr__atexit_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4345:23 [inlined] ijl_apply_generic at /source/src/gf.c:4583:12 jl_apply at /source/src/julia.h:2405:12 [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:524:34 wait at ./task.jl:1248:0 (pc: 107) wait_forever at ./task.jl:1170:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4345:23 [inlined] ijl_apply_generic at /source/src/gf.c:4583:12 jl_apply at /source/src/julia.h:2405:12 [inlined] start_task at /source/src/task.c:1276:19 PkgEval terminated after 2732.45s: test duration exceeded the time limit