[INFO] updating cached repository https://github.com/HopedWall/GFAtoVCF [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "-c" "remote.origin.fetch=refs/heads/*:refs/heads/*" "fetch" "origin" "--force" "--prune", kill_on_drop: false }` [INFO] [stderr] From https://github.com/HopedWall/GFAtoVCF [INFO] [stderr] 96ace73..14bc18c master -> master [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 14bc18c2cd26306e9e2a821e585eb827ac4e6b07 [INFO] testing HopedWall/GFAtoVCF against master#8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e for pr-74409 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FHopedWall%2FGFAtoVCF" "/workspace/builds/worker-11/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-11/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/HopedWall/GFAtoVCF on toolchain 8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e" "read-manifest" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/HopedWall/GFAtoVCF [INFO] finished tweaking git repo https://github.com/HopedWall/GFAtoVCF [INFO] tweaked toml for git repo https://github.com/HopedWall/GFAtoVCF written to /workspace/builds/worker-11/source/Cargo.toml [INFO] crate git repo https://github.com/HopedWall/GFAtoVCF already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=0" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--network" "none" "rustops/crates-build-env@sha256:38e1b949b06cde1964af550a6e548bd9b2b2ea170003ae122f8fc0886596cc07" "/opt/rustwide/cargo-home/bin/cargo" "+8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 9a56e1839bdde6b398de46b9f65710688d28b3f61b99b7a8a5bbb601834202c7 [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] running `Command { std: "docker" "start" "-a" "9a56e1839bdde6b398de46b9f65710688d28b3f61b99b7a8a5bbb601834202c7", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "9a56e1839bdde6b398de46b9f65710688d28b3f61b99b7a8a5bbb601834202c7", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "9a56e1839bdde6b398de46b9f65710688d28b3f61b99b7a8a5bbb601834202c7", kill_on_drop: false }` [INFO] [stdout] 9a56e1839bdde6b398de46b9f65710688d28b3f61b99b7a8a5bbb601834202c7 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=0" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--network" "none" "rustops/crates-build-env@sha256:38e1b949b06cde1964af550a6e548bd9b2b2ea170003ae122f8fc0886596cc07" "/opt/rustwide/cargo-home/bin/cargo" "+8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] [stdout] 616b3c5807c5ad185ebcd1fb105ec82dd280e65ceaba68139c3d823230a204ce [INFO] running `Command { std: "docker" "start" "-a" "616b3c5807c5ad185ebcd1fb105ec82dd280e65ceaba68139c3d823230a204ce", kill_on_drop: false }` [INFO] [stderr] Compiling autocfg v1.0.0 [INFO] [stderr] Compiling memchr v2.3.3 [INFO] [stderr] Compiling libc v0.2.71 [INFO] [stderr] Compiling ryu v1.0.5 [INFO] [stderr] Compiling lexical-core v0.7.4 [INFO] [stderr] Compiling regex-syntax v0.6.18 [INFO] [stderr] Compiling arrayvec v0.5.1 [INFO] [stderr] Compiling strsim v0.8.0 [INFO] [stderr] Compiling fixedbitset v0.2.0 [INFO] [stderr] Compiling ansi_term v0.11.0 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling json v0.12.4 [INFO] [stderr] Compiling nom v5.1.2 [INFO] [stderr] Compiling thread_local v1.0.1 [INFO] [stderr] Compiling num-traits v0.2.12 [INFO] [stderr] Compiling indexmap v1.4.0 [INFO] [stderr] Compiling num-integer v0.1.43 [INFO] [stderr] Compiling priority-queue v1.0.0 [INFO] [stderr] Compiling aho-corasick v0.7.13 [INFO] [stderr] Compiling time v0.1.43 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling petgraph v0.5.1 [INFO] [stderr] Compiling clap v2.33.1 [INFO] [stderr] Compiling chrono v0.4.11 [INFO] [stderr] Compiling regex v1.3.9 [INFO] [stderr] Compiling gfa v0.2.3 [INFO] [stderr] Compiling handlegraph v0.2.0 [INFO] [stderr] Compiling gfa_to_vcf v0.1.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 39.41s [INFO] running `Command { std: "docker" "inspect" "616b3c5807c5ad185ebcd1fb105ec82dd280e65ceaba68139c3d823230a204ce", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "616b3c5807c5ad185ebcd1fb105ec82dd280e65ceaba68139c3d823230a204ce", kill_on_drop: false }` [INFO] [stdout] 616b3c5807c5ad185ebcd1fb105ec82dd280e65ceaba68139c3d823230a204ce [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=0" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--network" "none" "rustops/crates-build-env@sha256:38e1b949b06cde1964af550a6e548bd9b2b2ea170003ae122f8fc0886596cc07" "/opt/rustwide/cargo-home/bin/cargo" "+8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] f2d8d80fcb0870c00709381b5071d0385220093d7414ebb5822d014c023d6053 [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] running `Command { std: "docker" "start" "-a" "f2d8d80fcb0870c00709381b5071d0385220093d7414ebb5822d014c023d6053", kill_on_drop: false }` [INFO] [stderr] Compiling gfa_to_vcf v0.1.0 (/opt/rustwide/workdir) [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 4.47s [INFO] running `Command { std: "docker" "inspect" "f2d8d80fcb0870c00709381b5071d0385220093d7414ebb5822d014c023d6053", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f2d8d80fcb0870c00709381b5071d0385220093d7414ebb5822d014c023d6053", kill_on_drop: false }` [INFO] [stdout] f2d8d80fcb0870c00709381b5071d0385220093d7414ebb5822d014c023d6053 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "MAP_USER_ID=0" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--network" "none" "rustops/crates-build-env@sha256:38e1b949b06cde1964af550a6e548bd9b2b2ea170003ae122f8fc0886596cc07" "/opt/rustwide/cargo-home/bin/cargo" "+8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e" "test" "--frozen", kill_on_drop: false }` [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] [stdout] ffd6ccd6d0fa2e6bdeab68c604998b9a3f214a292948a4bb99305651dc823824 [INFO] running `Command { std: "docker" "start" "-a" "ffd6ccd6d0fa2e6bdeab68c604998b9a3f214a292948a4bb99305651dc823824", kill_on_drop: false }` [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 0.15s [INFO] [stderr] Running /opt/rustwide/target/debug/deps/gfa_to_vcf-34a2f9882474969e [INFO] [stdout] [INFO] [stdout] running 12 tests [INFO] [stdout] test tests::find_bfs_paths_2 ... ok [INFO] [stdout] test tests::find_bfs_1 ... ok [INFO] [stdout] test tests::find_all_paths_2 ... ok [INFO] [stdout] test tests::find_all_paths_1 ... ok [INFO] [stdout] test tests::find_bubbles_2 ... ok [INFO] [stdout] test tests::test_bfs_distances ... ok [INFO] [stdout] test tests::test_dist_to_num_nodes ... ok [INFO] [stdout] test tests::test_bubble_detection ... ok [INFO] [stdout] test tests::test_bfs ... ok [INFO] [stdout] test tests::test_path_to_steps ... ok [INFO] [stdout] test tests::test_variant_detection ... ok [INFO] [stderr] error: test failed, to rerun pass '--bin gfa_to_vcf' [INFO] [stdout] test tests::find_bubbles_1 ... FAILED [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] [INFO] [stdout] ---- tests::find_bubbles_1 stdout ---- [INFO] [stdout] thread 'tests::find_bubbles_1' panicked at 'Cannot write json: Os { code: 30, kind: Other, message: "Read-only file system" }', src/main.rs:1382:38 [INFO] [stdout] stack backtrace: [INFO] [stdout] 0: 0x5581c476a245 - backtrace::backtrace::libunwind::trace::hea89dfbbfe67f40d [INFO] [stdout] at /cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.46/src/backtrace/libunwind.rs:86 [INFO] [stdout] 1: 0x5581c476a245 - backtrace::backtrace::trace_unsynchronized::h0513dd713d7644d4 [INFO] [stdout] at /cargo/registry/src/github.com-1ecc6299db9ec823/backtrace-0.3.46/src/backtrace/mod.rs:66 [INFO] [stdout] 2: 0x5581c476a245 - std::sys_common::backtrace::_print_fmt::h040abae64e4a24a9 [INFO] [stdout] at src/libstd/sys_common/backtrace.rs:78 [INFO] [stdout] 3: 0x5581c476a245 - ::fmt::hb4bdb37c3c335733 [INFO] [stdout] at src/libstd/sys_common/backtrace.rs:59 [INFO] [stdout] 4: 0x5581c479221c - core::fmt::write::h540ac4a6a1232abc [INFO] [stdout] at src/libcore/fmt/mod.rs:1076 [INFO] [stdout] 5: 0x5581c46b25a5 - std::io::Write::write_fmt::h4be0daababb55bba [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/libstd/io/mod.rs:1539 [INFO] [stdout] 6: 0x5581c4764911 - std::io::impls::>::write_fmt::h83c1e1aa73f374f5 [INFO] [stdout] at src/libstd/io/impls.rs:176 [INFO] [stdout] 7: 0x5581c476c9a0 - std::sys_common::backtrace::_print::hb55cc635eaf1882e [INFO] [stdout] at src/libstd/sys_common/backtrace.rs:62 [INFO] [stdout] 8: 0x5581c476c9a0 - std::sys_common::backtrace::print::h2b2218fa55714084 [INFO] [stdout] at src/libstd/sys_common/backtrace.rs:49 [INFO] [stdout] 9: 0x5581c476c9a0 - std::panicking::default_hook::{{closure}}::h578517c025765cf3 [INFO] [stdout] at src/libstd/panicking.rs:198 [INFO] [stdout] 10: 0x5581c476c69a - std::panicking::default_hook::h4cafc94c2fc640fb [INFO] [stdout] at src/libstd/panicking.rs:214 [INFO] [stdout] 11: 0x5581c476cfe3 - std::panicking::rust_panic_with_hook::h3eeb5001beeca5c3 [INFO] [stdout] at src/libstd/panicking.rs:526 [INFO] [stdout] 12: 0x5581c476cbdb - rust_begin_unwind [INFO] [stdout] at src/libstd/panicking.rs:437 [INFO] [stdout] 13: 0x5581c4790901 - core::panicking::panic_fmt::h78830ea6a34e7206 [INFO] [stdout] at src/libcore/panicking.rs:85 [INFO] [stdout] 14: 0x5581c4790723 - core::option::expect_none_failed::hf79bbb5ca7e09e08 [INFO] [stdout] at src/libcore/option.rs:1269 [INFO] [stdout] 15: 0x5581c47498af - core::result::Result::expect::hea68707cc33d300f [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/libcore/result.rs:963 [INFO] [stdout] 16: 0x5581c46837af - gfa_to_vcf::tests::find_bubbles_1::hd4c1d7331de8ad28 [INFO] [stdout] at src/main.rs:1382 [INFO] [stdout] 17: 0x5581c468317a - gfa_to_vcf::tests::find_bubbles_1::{{closure}}::h18dbf55af7826ed4 [INFO] [stdout] at src/main.rs:1348 [INFO] [stdout] 18: 0x5581c466d3ce - core::ops::function::FnOnce::call_once::hd1e41f9843bdd243 [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/libcore/ops/function.rs:233 [INFO] [stdout] 19: 0x5581c46d9b1c - as core::ops::function::FnOnce>::call_once::h8340ba6798e0c4ff [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/liballoc/boxed.rs:1081 [INFO] [stdout] 20: 0x5581c46d9b1c - as core::ops::function::FnOnce<()>>::call_once::h5590e98676605094 [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/libstd/panic.rs:318 [INFO] [stdout] 21: 0x5581c46d9b1c - std::panicking::try::do_call::hd8680a2dbb0ed3c4 [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/libstd/panicking.rs:348 [INFO] [stdout] 22: 0x5581c46d9b1c - std::panicking::try::h46b4de2d705e7a8d [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/libstd/panicking.rs:325 [INFO] [stdout] 23: 0x5581c46d9b1c - std::panic::catch_unwind::h059b3f06991e0a9c [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/libstd/panic.rs:394 [INFO] [stdout] 24: 0x5581c46d9b1c - test::run_test_in_process::h5ae08a65430494a4 [INFO] [stdout] at src/libtest/lib.rs:541 [INFO] [stdout] 25: 0x5581c46d9b1c - test::run_test::run_test_inner::{{closure}}::h4b36073838376ae8 [INFO] [stdout] at src/libtest/lib.rs:450 [INFO] [stdout] 26: 0x5581c46b1a96 - std::sys_common::backtrace::__rust_begin_short_backtrace::h0169d0be588b8bf0 [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/libstd/sys_common/backtrace.rs:130 [INFO] [stdout] 27: 0x5581c46b6a85 - std::thread::Builder::spawn_unchecked::{{closure}}::{{closure}}::h71bfc37e887d3973 [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/libstd/thread/mod.rs:475 [INFO] [stdout] 28: 0x5581c46b6a85 - as core::ops::function::FnOnce<()>>::call_once::h36c65072907dc180 [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/libstd/panic.rs:318 [INFO] [stdout] 29: 0x5581c46b6a85 - std::panicking::try::do_call::h4e0f426e17cd216c [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/libstd/panicking.rs:348 [INFO] [stdout] 30: 0x5581c46b6a85 - std::panicking::try::hd05e4ef6b4303d29 [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/libstd/panicking.rs:325 [INFO] [stdout] 31: 0x5581c46b6a85 - std::panic::catch_unwind::h19a1127ec729c5dd [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/libstd/panic.rs:394 [INFO] [stdout] 32: 0x5581c46b6a85 - std::thread::Builder::spawn_unchecked::{{closure}}::h011300735f06b1e2 [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/libstd/thread/mod.rs:474 [INFO] [stdout] 33: 0x5581c46b6a85 - core::ops::function::FnOnce::call_once{{vtable.shim}}::h1e3c55f31f1d122e [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/libcore/ops/function.rs:233 [INFO] [stdout] 34: 0x5581c47731ea - as core::ops::function::FnOnce>::call_once::hc0e15d78a519721e [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/liballoc/boxed.rs:1081 [INFO] [stdout] 35: 0x5581c47731ea - as core::ops::function::FnOnce>::call_once::h211da8fffb09f192 [INFO] [stdout] at /rustc/8534be72fc3b9c5f2f2dc4e4ee7b651a008e9a3e/src/liballoc/boxed.rs:1081 [INFO] [stdout] 36: 0x5581c47731ea - std::sys::unix::thread::Thread::new::thread_start::h29594ddebf23e421 [INFO] [stdout] at src/libstd/sys/unix/thread.rs:87 [INFO] [stdout] 37: 0x7f30b7ab7609 - start_thread [INFO] [stdout] 38: 0x7f30b79c3103 - __clone [INFO] [stdout] 39: 0x0 - [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] tests::find_bubbles_1 [INFO] [stdout] [INFO] [stdout] test result: FAILED. 11 passed; 1 failed; 0 ignored; 0 measured; 0 filtered out [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "ffd6ccd6d0fa2e6bdeab68c604998b9a3f214a292948a4bb99305651dc823824", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "ffd6ccd6d0fa2e6bdeab68c604998b9a3f214a292948a4bb99305651dc823824", kill_on_drop: false }` [INFO] [stdout] ffd6ccd6d0fa2e6bdeab68c604998b9a3f214a292948a4bb99305651dc823824