[INFO] cloning repository https://github.com/wheaton5/molecule_kmers [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/wheaton5/molecule_kmers" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fwheaton5%2Fmolecule_kmers", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fwheaton5%2Fmolecule_kmers'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 9ca991c6fca82ea31e250c5aab9760cf4ac57056 [INFO] testing wheaton5/molecule_kmers against beta-2025-04-13 for beta-1.87-1 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fwheaton5%2Fmolecule_kmers" "/workspace/builds/worker-2-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-2-tc2/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/wheaton5/molecule_kmers on toolchain beta-2025-04-13 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2025-04-13" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/wheaton5/molecule_kmers [INFO] finished tweaking git repo https://github.com/wheaton5/molecule_kmers [INFO] tweaked toml for git repo https://github.com/wheaton5/molecule_kmers written to /workspace/builds/worker-2-tc2/source/Cargo.toml [INFO] crate git repo https://github.com/wheaton5/molecule_kmers 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" "+beta-2025-04-13" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] warning: no edition set: defaulting to the 2015 edition while the latest is 2024 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/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:b0b074c097205a61b89e8ad263052f976b2b332c4dc5f02aef1fe52501660d6e" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-04-13" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 6e4a657dda6c7fa1b607050736589fdd9abc98c318f61625ea8e620515a04d65 [INFO] running `Command { std: "docker" "start" "-a" "6e4a657dda6c7fa1b607050736589fdd9abc98c318f61625ea8e620515a04d65", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "6e4a657dda6c7fa1b607050736589fdd9abc98c318f61625ea8e620515a04d65", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "6e4a657dda6c7fa1b607050736589fdd9abc98c318f61625ea8e620515a04d65", kill_on_drop: false }` [INFO] [stdout] 6e4a657dda6c7fa1b607050736589fdd9abc98c318f61625ea8e620515a04d65 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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:b0b074c097205a61b89e8ad263052f976b2b332c4dc5f02aef1fe52501660d6e" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-04-13" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 8460442f904a7aec1f1cec8206eb67c473b69622a4dea3c3bad2a4adcd4caa9e [INFO] running `Command { std: "docker" "start" "-a" "8460442f904a7aec1f1cec8206eb67c473b69622a4dea3c3bad2a4adcd4caa9e", kill_on_drop: false }` [INFO] [stderr] warning: no edition set: defaulting to the 2015 edition while the latest is 2024 [INFO] [stderr] Compiling autocfg v1.0.1 [INFO] [stderr] Compiling libc v0.2.80 [INFO] [stderr] Compiling cfg-if v1.0.0 [INFO] [stderr] Compiling cc v1.0.66 [INFO] [stderr] Compiling pkg-config v0.3.19 [INFO] [stderr] Compiling lazy_static v1.4.0 [INFO] [stderr] Compiling const_fn v0.4.3 [INFO] [stderr] Compiling rayon-core v1.9.0 [INFO] [stderr] Compiling crc32fast v1.2.1 [INFO] [stderr] Compiling scopeguard v1.1.0 [INFO] [stderr] Compiling memchr v2.3.4 [INFO] [stderr] Compiling adler v0.2.3 [INFO] [stderr] Compiling byteorder v1.3.4 [INFO] [stderr] Compiling crossbeam-utils v0.8.1 [INFO] [stderr] Compiling memoffset v0.6.1 [INFO] [stderr] Compiling miniz_oxide v0.4.3 [INFO] [stderr] Compiling rayon v1.5.0 [INFO] [stderr] Compiling safemem v0.3.3 [INFO] [stderr] Compiling unicode-width v0.1.8 [INFO] [stderr] Compiling either v1.6.1 [INFO] [stderr] Compiling textwrap v0.9.0 [INFO] [stderr] Compiling buf_redux v0.8.4 [INFO] [stderr] Compiling num_cpus v1.13.0 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling yaml-rust v0.3.5 [INFO] [stderr] Compiling bytecount v0.6.2 [INFO] [stderr] Compiling bitflags v0.9.1 [INFO] [stderr] Compiling ansi_term v0.9.0 [INFO] [stderr] Compiling bzip2-sys v0.1.9+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.17 [INFO] [stderr] Compiling crossbeam-epoch v0.9.1 [INFO] [stderr] Compiling crossbeam-channel v0.5.0 [INFO] [stderr] Compiling flate2 v1.0.19 [INFO] [stderr] Compiling strsim v0.6.0 [INFO] [stderr] Compiling crossbeam-deque v0.8.0 [INFO] [stderr] Compiling xz2 v0.1.6 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling scopeguard v0.3.3 [INFO] [stderr] Compiling clap v2.27.1 [INFO] [stderr] Compiling hashbrown v0.1.8 [INFO] [stderr] Compiling itertools v0.9.0 [INFO] [stderr] Compiling fnv v1.0.7 [INFO] [stderr] Compiling bzip2 v0.3.3 [INFO] [stderr] Compiling needletail v0.4.0 [INFO] [stderr] Compiling molecule_kmers v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `HashSet` [INFO] [stdout] --> src/main.rs:22:26 [INFO] [stdout] | [INFO] [stdout] 22 | use hashbrown::{HashMap, HashSet}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `KMER_TYPE` should have an upper camel case name [INFO] [stdout] --> src/main.rs:60:6 [INFO] [stdout] | [INFO] [stdout] 60 | enum KMER_TYPE { [INFO] [stdout] | ^^^^^^^^^ help: convert the identifier to upper camel case: `KmerType` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_camel_case_types)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `PAIRED_HET` should have an upper camel case name [INFO] [stdout] --> src/main.rs:61:5 [INFO] [stdout] | [INFO] [stdout] 61 | PAIRED_HET, [INFO] [stdout] | ^^^^^^^^^^ help: convert the identifier to upper camel case: `PairedHet` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variant `UNPAIRED_HET` should have an upper camel case name [INFO] [stdout] --> src/main.rs:62:5 [INFO] [stdout] | [INFO] [stdout] 62 | UNPAIRED_HET, [INFO] [stdout] | ^^^^^^^^^^^^ help: convert the identifier to upper camel case: `UnpairedHet` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: trait objects without an explicit `dyn` are deprecated [INFO] [stdout] --> src/main.rs:217:46 [INFO] [stdout] | [INFO] [stdout] 217 | fn handle_read(vars: &Vec, writer: &mut Write) { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = warning: this is accepted in the current edition (Rust 2015) but is a hard error in Rust 2021! [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: `#[warn(bare_trait_objects)]` on by default [INFO] [stdout] help: if this is a dyn-compatible trait, use `dyn` [INFO] [stdout] | [INFO] [stdout] 217 | fn handle_read(vars: &Vec, writer: &mut dyn Write) { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `FastxReader` [INFO] [stdout] --> src/main.rs:13:36 [INFO] [stdout] | [INFO] [stdout] 13 | use needletail::{parse_fastx_file, FastxReader, Sequence}; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `first` [INFO] [stdout] --> src/main.rs:104:17 [INFO] [stdout] | [INFO] [stdout] 104 | let first = str::from_utf8(&buf1).unwrap(); [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_first` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `current_readname` [INFO] [stdout] --> src/main.rs:149:13 [INFO] [stdout] | [INFO] [stdout] 149 | let mut current_readname = String::new(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_current_readname` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `linedex` [INFO] [stdout] --> src/main.rs:150:13 [INFO] [stdout] | [INFO] [stdout] 150 | let mut linedex = 0; [INFO] [stdout] | ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_linedex` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/main.rs:149:9 [INFO] [stdout] | [INFO] [stdout] 149 | let mut current_readname = String::new(); [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: variable does not need to be mutable [INFO] [stdout] --> src/main.rs:150:9 [INFO] [stdout] | [INFO] [stdout] 150 | let mut linedex = 0; [INFO] [stdout] | ----^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `kmer_type` [INFO] [stdout] --> src/main.rs:266:47 [INFO] [stdout] | [INFO] [stdout] 266 | if let Some((kmer_id, kmer_type)) = kmer_type.get(kmer) { [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_kmer_type` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `kmer_type` [INFO] [stdout] --> src/main.rs:273:47 [INFO] [stdout] | [INFO] [stdout] 273 | if let Some((kmer_id, kmer_type)) = kmer_type.get(kmer) { [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_kmer_type` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r1` [INFO] [stdout] --> src/main.rs:330:19 [INFO] [stdout] | [INFO] [stdout] 330 | for (filenum, r1, _, r2, _) in to_iterate.iter() { [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_r1` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `r2` [INFO] [stdout] --> src/main.rs:330:26 [INFO] [stdout] | [INFO] [stdout] 330 | for (filenum, r1, _, r2, _) in to_iterate.iter() { [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_r2` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `Kmers` is never constructed [INFO] [stdout] --> src/main.rs:53:8 [INFO] [stdout] | [INFO] [stdout] 53 | struct Kmers { [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `unpaired_kmers` is never read [INFO] [stdout] --> src/main.rs:431:5 [INFO] [stdout] | [INFO] [stdout] 429 | struct Params { [INFO] [stdout] | ------ field in this struct [INFO] [stdout] 430 | paired_kmers: Option, [INFO] [stdout] 431 | unpaired_kmers: Option, [INFO] [stdout] | ^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Params` has a derived impl for the trait `Clone`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `write_1_zero` is never used [INFO] [stdout] --> src/main.rs:555:4 [INFO] [stdout] | [INFO] [stdout] 555 | fn write_1_zero() { [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `write_2_zeros` is never used [INFO] [stdout] --> src/main.rs:561:4 [INFO] [stdout] | [INFO] [stdout] 561 | fn write_2_zeros() { [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: linking with `cc` failed: exit status: 1 [INFO] [stdout] | [INFO] [stdout] = note: "cc" "-m64" "/tmp/rustcPQjNlW/symbols.o" "<10 object files omitted>" "-Wl,--as-needed" "-Wl,-Bstatic" "/opt/rustwide/target/debug/deps/{librayon-6a9a843b464b67b9.rlib,librayon_core-f93987b8a70403ea.rlib,libnum_cpus-7cc642a3e186ac2c.rlib,libcrossbeam_deque-8bb4ebf34a5f76b0.rlib,libcrossbeam_epoch-202ba42836cda77b.rlib,libmemoffset-6debfc62e0fdd714.rlib,libscopeguard-e318caba69bf687f.rlib,libcrossbeam_channel-10f5ff724f93a5bb.rlib,libcrossbeam_utils-c6b7ed69d56a1cfc.rlib,liblazy_static-af860367908b8176.rlib,libneedletail-9569b2e6aa4f1993.rlib,libbytecount-f446dc4c695c44d1.rlib,libbuf_redux-eecb692f7b206b64.rlib,libsafemem-6bde8d6e08a694b2.rlib,libmemchr-edbbdcd29dc31002.rlib,libxz2-7bf8f2e63f046f66.rlib,liblzma_sys-662985474d0445ab.rlib,libbzip2-a482156c872eb381.rlib,libbzip2_sys-c16247d961841afb.rlib,libitertools-ca9b4b17b04314fc.rlib,libeither-ab6c4cd91672d94a.rlib,libhashbrown-627252b8d4041c57.rlib,libscopeguard-f70a82f9723db2c3.rlib,libfnv-79e2cbfbe03dcd16.rlib,libflate2-55ea0222557c74df.rlib,libminiz_oxide-98acebfe287a630d.rlib,libadler-d6881ab7996285c2.rlib,libcrc32fast-bc5cf6667df63cae.rlib,libcfg_if-3e7fc4e38d4a72b5.rlib,libbyteorder-9f385b8d892aa51f.rlib,libclap-514f16ce9dfbea30.rlib,libatty-17733c58a5e1af2f.rlib,liblibc-4469d42dae75cb64.rlib,libtextwrap-0ffe809cf3394939.rlib,libvec_map-75126d96f8392bf4.rlib,libbitflags-ae4318e8fded8832.rlib,libunicode_width-872488d468fe4def.rlib,libyaml_rust-2425132cfe04af2b.rlib,libansi_term-99a8b3070f91b3fc.rlib,libstrsim-34855b8b14397b06.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" "-llzma" "-lgcc_s" "-lutil" "-lrt" "-lpthread" "-lm" "-ldl" "-lc" "-L" "/tmp/rustcPQjNlW/raw-dylibs" "-Wl,--eh-frame-hdr" "-Wl,-z,noexecstack" "-L" "/opt/rustwide/target/debug/build/bzip2-sys-8b99375912759966/out/lib" "-L" "/usr/lib/x86_64-linux-gnu" "-L" "/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-o" "/opt/rustwide/target/debug/deps/molecule_kmers-1e3d59bb688e2448" "-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: /usr/bin/ld: final link failed: No space left on device [INFO] [stdout] collect2: error: ld returned 1 exit status [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `molecule_kmers` (bin "molecule_kmers") due to 1 previous error; 19 warnings emitted [INFO] running `Command { std: "docker" "inspect" "8460442f904a7aec1f1cec8206eb67c473b69622a4dea3c3bad2a4adcd4caa9e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "8460442f904a7aec1f1cec8206eb67c473b69622a4dea3c3bad2a4adcd4caa9e", kill_on_drop: false }` [INFO] [stdout] 8460442f904a7aec1f1cec8206eb67c473b69622a4dea3c3bad2a4adcd4caa9e