Package evaluation to test CrystalNets on Julia 1.14.0-DEV.2275 (3ea3bac2a3*) started at 2026-06-02T21:03:47.913 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 16.43s ################################################################################ # Installation # Installing CrystalNets... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [7952bbbe] + CrystalNets v1.2.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [c7e460c6] + ArgParse v1.2.0 [ec485272] + ArnoldiMethod v0.4.0 [a963bdd2] + AtomsBase v0.5.2 [46823bd8] + Chemfiles v0.10.43 [7952bbbe] + CrystalNets v1.2.0 [864edb3b] + DataStructures v0.19.5 [ffbed154] + DocStringExtensions v0.9.5 [86223c79] + Graphs v1.14.0 [d25df0c9] + Inflate v0.1.5 [692b3bcd] + JLLWrappers v1.8.0 [1914dd2f] + MacroTools v0.5.16 ⌅ [bac558e1] + OrderedCollections v1.8.2 [f305370e] + PeriodicGraphEmbeddings v1.0.2 [72a2d4b8] + PeriodicGraphEquilibriumPlacement v0.2.3 [18c5b727] + PeriodicGraphs v1.0.1 [7b2266bf] + PeriodicTable v1.2.1 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [92933f4c] + ProgressMeter v1.11.0 [ae029012] + Requires v1.3.1 [699a6c99] + SimpleTraits v0.9.6 [90137ffa] + StaticArrays v1.9.18 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [b718987f] + TextWrap v1.0.2 [0796e94c] + Tokenize v0.5.29 [1986cc42] + Unitful v1.28.0 [a7773ee8] + UnitfulAtomic v1.0.0 [78a364fa] + Chemfiles_jll v0.10.4+0 [ac4a9f1e] + spglib_jll v2.7.0+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 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.2+0 [deac9b47] + LibCURL_jll v8.20.0+1 [e37daf67] + LibGit2_jll v1.9.4+0 [29816b5a] + LibSSH2_jll v1.11.101+0 [14a3606d] + MozillaCACerts_jll v2026.5.14 [4536629a] + OpenBLAS_jll v0.3.33+0 [458c3c95] + OpenSSL_jll v3.5.6+0 [efcefdf7] + PCRE2_jll v10.47.0+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 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+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 5.53s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 2.0 s ✓ spglib_jll 77.8 s ✓ PeriodicGraphs 97.1 s ✓ PeriodicGraphEmbeddings 25.4 s ✓ PeriodicGraphEquilibriumPlacement 319.4 s ✓ CrystalNets 5 dependencies successfully precompiled in 522 seconds. 62 already precompiled. Precompilation completed after 550.44s ################################################################################ # Testing # Testing CrystalNets Status `/tmp/jl_ruWWqV/Project.toml` [861a8166] Combinatorics v1.1.0 [7952bbbe] CrystalNets v1.2.0 [86223c79] Graphs v1.14.0 [18c5b727] PeriodicGraphs v1.0.1 [90137ffa] StaticArrays v1.9.18 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_ruWWqV/Manifest.toml` [c7e460c6] ArgParse v1.2.0 [ec485272] ArnoldiMethod v0.4.0 [a963bdd2] AtomsBase v0.5.2 [46823bd8] Chemfiles v0.10.43 [861a8166] Combinatorics v1.1.0 [7952bbbe] CrystalNets v1.2.0 [864edb3b] DataStructures v0.19.5 [ffbed154] DocStringExtensions v0.9.5 [86223c79] Graphs v1.14.0 [d25df0c9] Inflate v0.1.5 [692b3bcd] JLLWrappers v1.8.0 [1914dd2f] MacroTools v0.5.16 ⌅ [bac558e1] OrderedCollections v1.8.2 [f305370e] PeriodicGraphEmbeddings v1.0.2 [72a2d4b8] PeriodicGraphEquilibriumPlacement v0.2.3 [18c5b727] PeriodicGraphs v1.0.1 [7b2266bf] PeriodicTable v1.2.1 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [92933f4c] ProgressMeter v1.11.0 [ae029012] Requires v1.3.1 [699a6c99] SimpleTraits v0.9.6 [90137ffa] StaticArrays v1.9.18 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [b718987f] TextWrap v1.0.2 [0796e94c] Tokenize v0.5.29 [1986cc42] Unitful v1.28.0 [a7773ee8] UnitfulAtomic v1.0.0 [78a364fa] Chemfiles_jll v0.10.4+0 [ac4a9f1e] spglib_jll v2.7.0+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 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.14.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.14.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.13.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.5.2+0 [deac9b47] LibCURL_jll v8.20.0+1 [e37daf67] LibGit2_jll v1.9.4+0 [29816b5a] LibSSH2_jll v1.11.101+0 [14a3606d] MozillaCACerts_jll v2026.5.14 [4536629a] OpenBLAS_jll v0.3.33+0 [458c3c95] OpenSSL_jll v3.5.6+0 [efcefdf7] PCRE2_jll v10.47.0+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 [8e850ede] nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... The following warning about altering performance, the two messages on warning toggling and the three error statements are expected. [ Warning: Warnings may critically alter performance for this operation and were turned off. [ Info: Use CrystalNets.toggle_warning(false) or the --no-warn option to remove this warning [ Info: Use the force_warn option to force printing warnings [ Error: Very suspicious connectivity found for MIL-100. [ Error: Atom ?, used in a bond, has either zero or multiple placements in CIF file MIL-101. This invalidates all bonds from the file, which will thus be discarded. [ Error: Atom ?, used in a bond, has either zero or multiple placements in CIF file MIL-53. This invalidates all bonds from the file, which will thus be discarded. The following warning about symmetry and the three warnings about 0-dimensional structures are expected. [ Warning: Missing _symmetry_equiv_pos_as_xyz and _space_group_symop_operation_xyz fields, will rely on other symmetry indications. [ Warning: Detected 192 structures of dimension 0 in NOTT-112, possibly complex solvent residues. They will be ignored for topology computation. [ Warning: Detected 40 structures of dimension 0 in FOWWAR, possibly complex solvent residues. They will be ignored for topology computation. [ Warning: Detected 2 structures of dimension 0 in CALFIG, possibly complex solvent residues. They will be ignored for topology computation. The following @error about carbon cycle disorder is expected. [ Info: Initial pass found C with invalid number of bonds. [ Error: Found what looks like a disordered carbon ring for CIZPOS: use of disordered input is not advised, please double-check the detected topology or provide a clean input. [ Info: Initial pass found O and C with invalid number of bonds. Test Summary: | Pass Broken Total Time MOF examples | 73 3 76 16m17.3s [ Warning: Guessing bonds with custom algorithm (from Chemfiles and VMD). This may take a while for big structures and may be inexact. [ Info: To avoid guessing bonds, use a file format that contains the bonds. [ Warning: Detected 6 structures of dimension 0 in Clathrate_hydrate, possibly complex solvent residues. They will be ignored for topology computation. [ Warning: Guessing bonds with custom algorithm (from Chemfiles and VMD). This may take a while for big structures and may be inexact. [ Info: To avoid guessing bonds, use a file format that contains the bonds. [ Warning: Detected 6 structures of dimension 0 in Clathrate_hydrate, possibly complex solvent residues. They will be ignored for topology computation. [ Warning: Missing _symmetry_equiv_pos_as_xyz and _space_group_symop_operation_xyz fields, will rely on other symmetry indications. [ Warning: Guessing bonds with custom algorithm (from Chemfiles and VMD). This may take a while for big structures and may be inexact. [ Info: To avoid guessing bonds, use a file format that contains the bonds. Test Summary: | Pass Total Time Other kinds of structures | 4 4 0.8s [ Info: Checking that all known topologies are recognized (this can take a few minutes). [ Info: Use multiple threads to reduce this time Test Summary: | Pass Total Time Archive | 17494 17494 10m12.7s [ Info: Testing pcu [ Info: Testing afy, AFY [ Info: Testing apc, APC [ Info: Testing bam [ Info: Testing bcf [ Info: Testing cdp [ Info: Testing cnd [ Info: Testing ecb [ Info: Testing fiv [ Info: Testing ftd [ Info: Testing ftj [ Info: Testing ins [ Info: Testing kgt [ Info: Testing mot [ Info: Testing moz [ Info: Testing muh [ Info: Testing pbz [ Info: Testing qom [ Info: Testing sig [ Info: Testing sma [ Info: Testing sod-f [ Info: Testing sod-h [ Info: Testing utj [ Info: Testing utp [ Info: Testing nts [ Info: Testing lth [ Info: Testing cys [ Info: Testing llw-z [ Info: Testing nts Test Summary: | Pass Total Time Module | 31 31 1m02.0s Test Summary: | Pass Broken Total Time Executable | 29 1 30 9.1s 1 / 36 .................................................................................................... 2 / 36 .................................................................................................... 3 / 36 .................................................................................................... 4 / 36 .................................................................................................... 5 / 36 .................................................................................................... 6 / 36 .................................................................................................... 7 / 36 .................................................................................................... 8 / 36 .................................................................................................... 9 / 36 .................................................................................................... 10 / 36 .................................................................................................... 11 / 36 .................................................................................................... 12 / 36 .................................................................................................... 13 / 36 .................................................................................................... 14 / 36 .................................................................................................... 15 / 36 .................................................................................................... 16 / 36 .................................................................................................... 17 / 36 .................................................................................................... 18 / 36 .................................................. 19 / 36 .................................................. 20 / 36 .................................................. 21 / 36 .................................................. 22 / 36 .................................................. 23 / 36 .................................................. 24 / 36 .................................................. 25 / 36 .................................................. 26 / 36 .................................................. 27 / 36 .................................................. 28 / 36 .................................................. 29 / 36 .................................................. 30 / 36 .................................................. 31 / 36 .................................................. 32 / 36 . ====================================================================================== 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 28 running 1 of 1 signal (10): User defined signal 1 jl_set_typeof at /source/src/julia.h:134:5 [inlined] jl_gc_alloc_ at /source/src/gc-stock.c:813:5 jl_alloc_genericmemory_unchecked at /source/src/genericmemory.c:41:30 GenericMemory at ./boot.jl:654:0 [inlined] Array at ./boot.jl:714:0 [inlined] Array at ./boot.jl:727:0 [inlined] Array at ./boot.jl:735:0 [inlined] similar at ./abstractarray.jl:873:0 [inlined] similar at ./array.jl:414:0 [inlined] similar at ./abstractarray.jl:872:0 [inlined] _array_for_inner at ./array.jl:706:0 [inlined] collect at ./array.jl:838:0 (pc: 192) translation_to_direct_map at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/minimization.jl:699:0 (pc: 1453) find_first_valid_translation_unstable at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/minimization.jl:809:0 (pc: 315) minimize_unstable at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/minimization.jl:287:0 [inlined] minimize at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/minimization.jl:274:0 [inlined] topological_genome at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/query.jl:34:0 (pc: 189) unknown function (ip: 0x75c4264102a3) at (unknown file) _jl_invoke at /source/src/gf.c:4129:23 [inlined] ijl_apply_generic at /source/src/gf.c:4355:12 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/query.jl:153:0 (pc: 765) topological_genome at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/query.jl:87:0 [inlined] #topological_genome#224 at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/query.jl:90:0 [inlined] topological_genome at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/query.jl:90:0 (pc: 3) unknown function (ip: 0x75c44d17747c) at (unknown file) _jl_invoke at /source/src/gf.c:4129:23 [inlined] ijl_apply_generic at /source/src/gf.c:4355:12 jl_apply at /source/src/julia.h:2376:12 [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 eval_body at /source/src/interpreter.c:563:21 eval_body at /source/src/interpreter.c:571:21 eval_body at /source/src/interpreter.c:571:21 eval_body at /source/src/interpreter.c:571:21 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:517:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 207) _jl_invoke at /source/src/gf.c:4129:23 [inlined] ijl_apply_generic at /source/src/gf.c:4355:12 _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:4129:23 [inlined] ijl_apply_generic at /source/src/gf.c:4355:12 jl_apply at /source/src/julia.h:2376:12 [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:517:0 (pc: 1) exec_options at ./client.jl:321:0 (pc: 425) _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:4129:23 [inlined] ijl_apply_generic at /source/src/gf.c:4355:12 jl_apply at /source/src/julia.h:2376:12 [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: 0x75c480793249) 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 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:4129:23 [inlined] ijl_apply_generic at /source/src/gf.c:4355:12 jl_apply at /source/src/julia.h:2376:12 [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 0x000075c4661fc010 Total snapshots: 1. Utilization: 100% ╎1 @Base/client.jl:596 _start() ╎ 1 @Base/client.jl:321 exec_options(opts::Base.JLOptions) ╎ 1 @Base/boot.jl:517 eval(m::Module, e::Any) ╎ 1 @Base/Base.jl:328 (::Base.IncludeInto)(fname::String) ╎ 1 @Base/Base.jl:327 include(mapexpr::Function, mod::Module, _path::Strin… ╎ 1 @Base/loading.jl:3192 _include(mapexpr::Function, mod::Module, _path:… ╎ ╎ 1 @Base/loading.jl:3132 include_string(mapexpr::typeof(identity), mod:… ╎ ╎ 1 @Base/boot.jl:517 eval(m::Module, e::Any) ╎ ╎ 1 @CrystalNets/…query.jl:90 topological_genome(g::PeriodicGraph2D) ╎ ╎ 1 @CrystalNets/…query.jl:90 topological_genome(g::PeriodicGraph2D; … ╎ ╎ 1 @CrystalNets/…uery.jl:87 topological_genome(g::PeriodicGraph2D, … ╎ ╎ ╎ 1 @CrystalNets/…ery.jl:153 topological_genome(group::UnderlyingNe… ╎ ╎ ╎ 1 @CrystalNets/…ery.jl:34 topological_genome(net::CrystalNet2D{R… ╎ ╎ ╎ 1 @CrystalNets/…ion.jl:274 minimize(net::CrystalNet2D{Rational{… ╎ ╎ ╎ 1 @CrystalNets/…on.jl:287 minimize_unstable(shrunk_net::Crysta… ╎ ╎ ╎ 1 @CrystalNets/…on.jl:809 find_first_valid_translation_unstab… ╎ ╎ ╎ ╎ 1 @CrystalNets/…n.jl:677 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ ╎ 1 @Base/task.jl:1071 yield() ╎ ╎ ╎ ╎ 1 @Base/task.jl:1233 wait() ╎ ╎ ╎ ╎ 1 @Base/libuv.jl:133 process_events() ┌ 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 0x000072767f871e10 Total snapshots: 410. Utilization: 0% ╎410 @Base/task.jl:1168 wait_forever() 409╎ 410 @Base/task.jl:1246 wait() PkgEval terminated after 2723.17s: test duration exceeded the time limit