Package evaluation to test BioStructures on Julia 1.14.0-DEV.2309 (6e1a27e459*) started at 2026-06-06T10:00:04.718 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 17.42s ################################################################################ # Installation # Installing BioStructures... Resolving package versions... Installed RecipesBase ──────── v1.3.4 Installed Statistics ───────── v1.11.1 Installed Format ───────────── v1.3.7 Installed CodecZlib ────────── v0.7.8 Installed BioGenerics ──────── v0.1.5 Installed TranscodingStreams ─ v0.11.3 Installed PrecompileTools ──── v1.3.4 Installed BioSymbols ───────── v5.2.0 Installed Preferences ──────── v1.5.2 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 v1.1.2 [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 v1.5.2+0 [deac9b47] + LibCURL_jll v8.20.0+1 [29816b5a] + LibSSH2_jll v1.11.101+0 [14a3606d] + MozillaCACerts_jll v2026.5.14 [4536629a] + OpenBLAS_jll v0.3.33+0 [458c3c95] + OpenSSL_jll v3.5.6+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 4.73s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 6.6 s ✓ TestEnv 1 dependency successfully precompiled in 7 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 4.8 s ✓ MacroTools 317.7 s ✓ InlineStrings 0.6 s ✓ Reexport 1.1 s ✓ Statistics 1.1 s ✓ DataAPI 0.5 s ✓ DataValueInterfaces 0.9 s ✓ StaticArraysCore 151.0 s ✓ OrderedCollections 41.8 s ✓ Format 57.1 s ✓ InvertedIndices 0.7 s ✓ Twiddle 90.9 s ✓ IntervalTrees 0.9 s ✓ Inflate 54.1 s ✓ TranscodingStreams 0.5 s ✓ IteratorInterfaceExtensions 41.5 s ✓ LaTeXStrings 2.2 s ✓ Crayons 1.5 s ✓ MsgPack 160.9 s ✓ SentinelArrays 1.6 s ✓ Compat 2.8 s ✓ Preferences 3.3 s ✓ SimpleTraits 42.4 s ✓ Statistics → SparseArraysExt 56.2 s ✓ Missings 23.4 s ✓ PooledArrays 169.5 s ✓ DataStructures 39.6 s ✓ BioGenerics 20.6 s ✓ CodecZlib 0.5 s ✓ TableTraits 0.7 s ✓ Compat → CompatLinearAlgebraExt 3.5 s ✓ JLLWrappers 3.0 s ✓ PrecompileTools 38.6 s ✓ SortingAlgorithms 20.0 s ✓ MMTF 150.9 s ✓ Tables 46.2 s ✓ Aqua 3.9 s ✓ STRIDE_jll 3.8 s ✓ DSSP_jll 5.2 s ✓ RecipesBase 121.3 s ✓ BioSymbols 347.7 s ✓ StaticArrays 76.7 s ✓ StringManipulation 110.4 s ✓ BioSequences 116.4 s ✓ BioStructures 38.3 s ✓ StaticArrays → StaticArraysStatisticsExt 40.7 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 207 running 1 of 1  signal (10): User defined signal 1 _ZN4llvm11ConstantInt3getERNS_11LLVMContextERKNS_5APIntE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm12SelectionDAG11getConstantERKNS_5APIntERKNS_5SDLocENS_3EVTEbb at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm19SelectionDAGBuilder18visitGetElementPtrERKNS_4UserE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm19SelectionDAGBuilder5visitERKNS_11InstructionE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm16SelectionDAGISel16SelectBasicBlockENS_21ilist_iterator_w_bitsINS_12ilist_detail12node_optionsINS_11InstructionELb1ELb0EvLb1ENS_10BasicBlockEEELb0ELb1EEES7_Rb at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm16SelectionDAGISel20SelectAllBasicBlocksERKNS_8FunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm16SelectionDAGISel20runOnMachineFunctionERNS_15MachineFunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm22SelectionDAGISelLegacy20runOnMachineFunctionERNS_15MachineFunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm19MachineFunctionPass13runOnFunctionERNS_8FunctionE.part.0 at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm13FPPassManager13runOnFunctionERNS_8FunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm13FPPassManager11runOnModuleERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm6legacy15PassManagerImpl3runERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) operator() at /source/src/jitlayers.cpp:1414:23 compileModule at /source/src/jitlayers.cpp:2390:79 materialize at /source/src/jitlayers.cpp:906:36 _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 #kw_body#_pretty_table#0 at /home/pkgeval/.julia/packages/PrettyTables/tz31H/src/main.jl:479:0 (pc: 236) _pretty_table at /home/pkgeval/.julia/packages/PrettyTables/tz31H/src/main.jl:212:0 [inlined] #kw_body#pretty_table#3 at /home/pkgeval/.julia/packages/PrettyTables/tz31H/src/main.jl:94:0 [inlined] pretty_table at /home/pkgeval/.julia/packages/PrettyTables/tz31H/src/main.jl:37:0 [inlined] #kw_body#pretty_table#0 at /home/pkgeval/.julia/packages/PrettyTables/tz31H/src/main.jl:11:0 (pc: 31) pretty_table at /home/pkgeval/.julia/packages/PrettyTables/tz31H/src/main.jl:9:0 (pc: 2) unknown function (ip: 0x7d31576b3d26) at (unknown file) _jl_invoke at /source/src/gf.c:4138:23 [inlined] ijl_apply_generic at /source/src/gf.c:4364:12 macro expansion at /home/pkgeval/.julia/packages/PrettyTables/tz31H/src/precompile.jl:224:0 [inlined] macro expansion at /home/pkgeval/.julia/packages/PrettyTables/tz31H/src/precompile.jl:70:0 [inlined] top-level scope at /home/pkgeval/.julia/packages/PrettyTables/tz31H/src/precompile.jl:9:0 (pc: 686) jl_invoke_oneshot at /source/src/gf.c:4173:23 ijl_eval_thunk at /source/src/toplevel.c:760:18 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) _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:327:0 (pc: 1) IncludeInto at ./Base.jl:328:0 (pc: 2) jfptr_IncludeInto_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_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: 0x7d31815fa249) 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 17 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 0x00007e9d809270d0 Total snapshots: 291. Utilization: 0% ╎291 @Base/task.jl:1168 wait_forever() 290╎ 291 @Base/task.jl:1246 wait() │ exception = │ This interactive function requires a stdlib to be loaded, and package code should instead use it directly from that stdlib. │ Stacktrace: │ [1] error(s::String) │ @ Base error.jl:56 │ [2] require_stdlib(package_uuidkey::Base.PkgId, ext::Nothing, from::Module) │ @ Base loading.jl:3024 │ [3] require_stdlib(package_uuidkey::Base.PkgId) │ @ Base loading.jl:3020 [inlined] │ [4] macro expansion │ @ some.jl:157 [inlined] │ [5] profile_printing_listener(cond::Base.AsyncCondition) │ @ Base Base.jl:357 │ [6] (::Base.var"#start_profile_listener##0#start_profile_listener##1"{Base.AsyncCondition})() │ @ Base Base.jl:376 └ @ Base Base.jl:367 212943562713 deps_ns=2000046550 compilation_ns=208992184351 methods=9464 219.4 s ✓ PrettyTables ====================================================================================== 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 0x0000702301a85960 Total snapshots: 365. Utilization: 0% ╎365 @Base/task.jl:1168 wait_forever() 364╎ 365 @Base/task.jl:1246 wait() [17] 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: 15056515 (Pool: 15055731; Big: 784); GC: 16 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) PkgEval terminated after 2730.61s: test duration exceeded the time limit