[INFO] cloning repository https://github.com/joyliu-q/rust-genomics [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/joyliu-q/rust-genomics" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fjoyliu-q%2Frust-genomics", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fjoyliu-q%2Frust-genomics'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] a62b7e31b41dd1efe396e5ee25b420c4b5bdb887 [INFO] testing joyliu-q/rust-genomics against master#ebf0cf75d368c035f4c7e7246d203bd469ee4a51 for pr-137940 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fjoyliu-q%2Frust-genomics" "/workspace/builds/worker-6-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc1/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/joyliu-q/rust-genomics on toolchain ebf0cf75d368c035f4c7e7246d203bd469ee4a51 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ebf0cf75d368c035f4c7e7246d203bd469ee4a51" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/joyliu-q/rust-genomics [INFO] finished tweaking git repo https://github.com/joyliu-q/rust-genomics [INFO] tweaked toml for git repo https://github.com/joyliu-q/rust-genomics written to /workspace/builds/worker-6-tc1/source/Cargo.toml [INFO] crate git repo https://github.com/joyliu-q/rust-genomics already has a lockfile, it will not be regenerated [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+ebf0cf75d368c035f4c7e7246d203bd469ee4a51" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/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" "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" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:1680c8fbd8dfb46fcd6d22e546df16ab0e007457dc29fcd9e987cdd5077fd1af" "/opt/rustwide/cargo-home/bin/cargo" "+ebf0cf75d368c035f4c7e7246d203bd469ee4a51" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] e8394500386a89b31c90abeee849c66c94886d84c0a2eefdfd8687873203e0fe [INFO] running `Command { std: "docker" "start" "-a" "e8394500386a89b31c90abeee849c66c94886d84c0a2eefdfd8687873203e0fe", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "e8394500386a89b31c90abeee849c66c94886d84c0a2eefdfd8687873203e0fe", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "e8394500386a89b31c90abeee849c66c94886d84c0a2eefdfd8687873203e0fe", kill_on_drop: false }` [INFO] [stdout] e8394500386a89b31c90abeee849c66c94886d84c0a2eefdfd8687873203e0fe [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/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" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:1680c8fbd8dfb46fcd6d22e546df16ab0e007457dc29fcd9e987cdd5077fd1af" "/opt/rustwide/cargo-home/bin/cargo" "+ebf0cf75d368c035f4c7e7246d203bd469ee4a51" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 1b3449668541c99109742495c93e82239aa418a31ae2ed84c41aca3ce7686d08 [INFO] running `Command { std: "docker" "start" "-a" "1b3449668541c99109742495c93e82239aa418a31ae2ed84c41aca3ce7686d08", kill_on_drop: false }` [INFO] [stderr] Compiling autocfg v1.0.1 [INFO] [stderr] Compiling cfg-if v0.1.10 [INFO] [stderr] Compiling libc v0.2.79 [INFO] [stderr] Compiling maybe-uninit v2.0.0 [INFO] [stderr] Compiling lazy_static v1.4.0 [INFO] [stderr] Compiling getrandom v0.1.15 [INFO] [stderr] Compiling rayon-core v1.8.1 [INFO] [stderr] Compiling scopeguard v1.1.0 [INFO] [stderr] Compiling ppv-lite86 v0.2.9 [INFO] [stderr] Compiling either v1.6.1 [INFO] [stderr] Compiling strsim v0.10.0 [INFO] [stderr] Compiling crossbeam-utils v0.7.2 [INFO] [stderr] Compiling memoffset v0.5.6 [INFO] [stderr] Compiling crossbeam-epoch v0.8.2 [INFO] [stderr] Compiling rayon v1.4.1 [INFO] [stderr] Compiling num_cpus v1.13.0 [INFO] [stderr] Compiling rand_core v0.5.1 [INFO] [stderr] Compiling crossbeam-channel v0.4.4 [INFO] [stderr] Compiling rand_chacha v0.2.2 [INFO] [stderr] Compiling rand v0.7.3 [INFO] [stderr] Compiling crossbeam-deque v0.7.3 [INFO] [stderr] Compiling rust-genomics v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused imports: `damerau_levenshtein`, `hamming`, `jaro_winkler`, `jaro`, `levenshtein`, `normalized_damerau_levenshtein`, `osa_distance`, and `sorensen_dice` [INFO] [stdout] --> src/lib.rs:13:14 [INFO] [stdout] | [INFO] [stdout] 13 | use strsim::{hamming, levenshtein, normalized_levenshtein, osa_distance, [INFO] [stdout] | ^^^^^^^ ^^^^^^^^^^^ ^^^^^^^^^^^^ [INFO] [stdout] 14 | damerau_levenshtein, normalized_damerau_levenshtein, jaro, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^ [INFO] [stdout] 15 | jaro_winkler, sorensen_dice}; [INFO] [stdout] | ^^^^^^^^^^^^ ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Write` [INFO] [stdout] --> src/lib.rs:7:15 [INFO] [stdout] | [INFO] [stdout] 7 | use std::io::{Write, BufReader, BufRead}; [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/lib.rs:259:13 [INFO] [stdout] | [INFO] [stdout] 259 | let mut diff = 0; [INFO] [stdout] | ----^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: enum `Nucleotide` is never used [INFO] [stdout] --> src/lib.rs:23:6 [INFO] [stdout] | [INFO] [stdout] 23 | enum Nucleotide { [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated items `to_char` and `index_to_nt` are never used [INFO] [stdout] --> src/lib.rs:30:8 [INFO] [stdout] | [INFO] [stdout] 29 | impl Nucleotide { [INFO] [stdout] | --------------- associated items in this implementation [INFO] [stdout] 30 | fn to_char(&self) -> char { [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 38 | fn index_to_nt(index: usize) -> Result { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `check` is never used [INFO] [stdout] --> src/lib.rs:84:8 [INFO] [stdout] | [INFO] [stdout] 68 | impl Sequence { [INFO] [stdout] | ------------- method in this implementation [INFO] [stdout] ... [INFO] [stdout] 84 | fn check(&self) -> bool { [INFO] [stdout] | ^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/lib.rs:309:9 [INFO] [stdout] | [INFO] [stdout] 309 | write!(f, "File Name: {}\n", self.name); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] = note: `#[warn(unused_must_use)]` on by default [INFO] [stdout] = note: this warning originates in the macro `write` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused `Result` that must be used [INFO] [stdout] --> src/lib.rs:311:13 [INFO] [stdout] | [INFO] [stdout] 311 | write!(f, "Header: {}\nSequence: {}\n\n", record.header, record.sequence); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this `Result` may be an `Err` variant, which should be handled [INFO] [stdout] = note: this warning originates in the macro `write` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Sequence` [INFO] [stdout] --> src/main.rs:1:21 [INFO] [stdout] | [INFO] [stdout] 1 | use rust_genomics::{Sequence, FASTA}; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: linking with `cc` failed: exit status: 1 [INFO] [stdout] | [INFO] [stdout] = note: "cc" "-m64" "/tmp/rustc7EDiyl/symbols.o" "<2 object files omitted>" "-Wl,--as-needed" "-Wl,-Bstatic" "/opt/rustwide/target/debug/deps/{librust_genomics-8f7c588efe22b208.rlib,librayon-2c2fca01d1bed7c2.rlib,librayon_core-c32a65c36c87a8a6.rlib,libnum_cpus-85ff518dea940d12.rlib,libcrossbeam_deque-c117df811d674510.rlib,libcrossbeam_epoch-6d89590bfdc734d8.rlib,libscopeguard-43643e546252cd47.rlib,libmemoffset-12a09adea4f704bd.rlib,libcrossbeam_channel-b82b629e0dc0dd1b.rlib,libmaybe_uninit-dd2e9a8bbd6c23a5.rlib,libcrossbeam_utils-554e8f12bc4a8a4c.rlib,liblazy_static-2bb390fee0230a38.rlib,libeither-9e7e392a8497717b.rlib,librand-6210ce92abd51fd0.rlib,librand_chacha-c59f5ee199434ea7.rlib,libppv_lite86-af6979226c4ae1c7.rlib,librand_core-f70fd797d6fb022d.rlib,libgetrandom-ccda769614ff8fcc.rlib,liblibc-49594ce0bd46ed9f.rlib,libcfg_if-7e9efee4241be1ca.rlib,libstrsim-d620f0ade87b0f1f.rlib}.rlib" "/lib/rustlib/x86_64-unknown-linux-gnu/lib/{libstd-*,libpanic_unwind-*,libobject-*,libmemchr-*,libaddr2line-*,libgimli-*,librustc_demangle-*,libstd_detect-*,libhashbrown-*,librustc_std_workspace_alloc-*,libminiz_oxide-*,libadler2-*,libunwind-*,libcfg_if-*,liblibc-*,liballoc-*,librustc_std_workspace_core-*,libcore-*,libcompiler_builtins-*}.rlib" "-Wl,-Bdynamic" "-lgcc_s" "-lutil" "-lrt" "-lpthread" "-lm" "-ldl" "-lc" "-L" "/tmp/rustc7EDiyl/raw-dylibs" "-B/lib/rustlib/x86_64-unknown-linux-gnu/bin/gcc-ld" "-fuse-ld=lld" "-Wl,-znostart-stop-gc" "-Wl,--eh-frame-hdr" "-Wl,-z,noexecstack" "-L" "/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-o" "/opt/rustwide/target/debug/deps/rust_genomics-04dc942eec7d86d5" "-Wl,--gc-sections" "-pie" "-Wl,-z,relro,-z,now" "-nodefaultlibs" [INFO] [stdout] = note: some arguments are omitted. use `--verbose` to show all linker arguments [INFO] [stdout] = note: PLEASE submit a bug report to https://github.com/llvm/llvm-project/issues/ and include the crash backtrace. [INFO] [stdout] #0 0x00007a0ac50db4f7 llvm::sys::PrintStackTrace(llvm::raw_ostream&, int) (/opt/rustwide/rustup-home/toolchains/ebf0cf75d368c035f4c7e7246d203bd469ee4a51/lib/libLLVM.so.20.1-rust-1.87.0-nightly+0x56db4f7) [INFO] [stdout] #1 0x00007a0ac50db90c SignalHandler(int) (/opt/rustwide/rustup-home/toolchains/ebf0cf75d368c035f4c7e7246d203bd469ee4a51/lib/libLLVM.so.20.1-rust-1.87.0-nightly+0x56db90c) [INFO] [stdout] #2 0x00007a0abf819520 (/lib/x86_64-linux-gnu/libc.so.6+0x42520) [INFO] [stdout] #3 0x00007a0abf977aca (/lib/x86_64-linux-gnu/libc.so.6+0x1a0aca) [INFO] [stdout] #4 0x0000558ace04e184 void lld::elf::InputSection::writeTo >(lld::elf::Ctx&, unsigned char*) (/opt/rustwide/rustup-home/toolchains/ebf0cf75d368c035f4c7e7246d203bd469ee4a51/lib/rustlib/x86_64-unknown-linux-gnu/bin/rust-lld+0x405184) [INFO] [stdout] #5 0x0000558ace0a206b void lld::elf::OutputSection::writeTo >(lld::elf::Ctx&, unsigned char*, llvm::parallel::TaskGroup&)::'lambda'(unsigned long, unsigned long)::operator()(unsigned long, unsigned long) const OutputSections.cpp:0:0 [INFO] [stdout] #6 0x00007a0ac508afe2 std::_Function_handler)::$_0>::_M_invoke(std::_Any_data const&) (/opt/rustwide/rustup-home/toolchains/ebf0cf75d368c035f4c7e7246d203bd469ee4a51/lib/libLLVM.so.20.1-rust-1.87.0-nightly+0x568afe2) [INFO] [stdout] #7 0x00007a0ac508aa4a llvm::parallel::detail::(anonymous namespace)::ThreadPoolExecutor::work(llvm::ThreadPoolStrategy, unsigned int) (/opt/rustwide/rustup-home/toolchains/ebf0cf75d368c035f4c7e7246d203bd469ee4a51/lib/libLLVM.so.20.1-rust-1.87.0-nightly+0x568aa4a) [INFO] [stdout] #8 0x00007a0ac50040d0 execute_native_thread_routine (/opt/rustwide/rustup-home/toolchains/ebf0cf75d368c035f4c7e7246d203bd469ee4a51/lib/libLLVM.so.20.1-rust-1.87.0-nightly+0x56040d0) [INFO] [stdout] #9 0x00007a0abf86bac3 (/lib/x86_64-linux-gnu/libc.so.6+0x94ac3) [INFO] [stdout] #10 0x00007a0abf8fca04 __clone (/lib/x86_64-linux-gnu/libc.so.6+0x125a04) [INFO] [stdout] rust-lld: error: failed to write output '/opt/rustwide/target/debug/deps/rust_genomics-04dc942eec7d86d5': No such file or directory [INFO] [stdout] collect2: error: ld returned 1 exit status [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `rust-genomics` (bin "rust-genomics") due to 1 previous error; 1 warning emitted [INFO] running `Command { std: "docker" "inspect" "1b3449668541c99109742495c93e82239aa418a31ae2ed84c41aca3ce7686d08", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "1b3449668541c99109742495c93e82239aa418a31ae2ed84c41aca3ce7686d08", kill_on_drop: false }` [INFO] [stdout] 1b3449668541c99109742495c93e82239aa418a31ae2ed84c41aca3ce7686d08