[INFO] cloning repository https://github.com/rodtheo/rs-genomesub [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/rodtheo/rs-genomesub" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Frodtheo%2Frs-genomesub", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Frodtheo%2Frs-genomesub'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 25a79c0338c934848c6f1285977f0d496a91cfea [INFO] testing rodtheo/rs-genomesub against 1.60.0 for beta-1.61-1 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Frodtheo%2Frs-genomesub" "/workspace/builds/worker-14/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-14/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/rodtheo/rs-genomesub on toolchain 1.60.0 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.60.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/rodtheo/rs-genomesub [INFO] finished tweaking git repo https://github.com/rodtheo/rs-genomesub [INFO] tweaked toml for git repo https://github.com/rodtheo/rs-genomesub written to /workspace/builds/worker-14/source/Cargo.toml [INFO] crate git repo https://github.com/rodtheo/rs-genomesub already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+1.60.0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded nom-unicode v0.3.0 [INFO] [stderr] Downloaded nom-regex v0.2.0 [INFO] [stderr] Downloaded uniprot v0.5.1 [INFO] [stderr] Downloaded ordered-multimap v0.4.2 [INFO] [stderr] Downloaded noodles-gff v0.4.0 [INFO] [stderr] Downloaded protein-translate v0.2.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-14/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-14/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:eaef2f80f755933c374d2ae5edccceec0c1312ceb8a4e0b6404e8ab76561e1e5" "/opt/rustwide/cargo-home/bin/cargo" "+1.60.0" "metadata" "--no-deps" "--format-version=1", 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] f00db49cdb27f52b796d214ef5afcdf66d8ff4be4f2840fb00dbe9e505cecb0f [INFO] running `Command { std: "docker" "start" "-a" "f00db49cdb27f52b796d214ef5afcdf66d8ff4be4f2840fb00dbe9e505cecb0f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "f00db49cdb27f52b796d214ef5afcdf66d8ff4be4f2840fb00dbe9e505cecb0f", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f00db49cdb27f52b796d214ef5afcdf66d8ff4be4f2840fb00dbe9e505cecb0f", kill_on_drop: false }` [INFO] [stdout] f00db49cdb27f52b796d214ef5afcdf66d8ff4be4f2840fb00dbe9e505cecb0f [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-14/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-14/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" "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:eaef2f80f755933c374d2ae5edccceec0c1312ceb8a4e0b6404e8ab76561e1e5" "/opt/rustwide/cargo-home/bin/cargo" "+1.60.0" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] f7192a3f66369c2b381e41d0dbf46caf310aa32dda671f6232916d55d48a9aeb [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" "f7192a3f66369c2b381e41d0dbf46caf310aa32dda671f6232916d55d48a9aeb", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Compiling rustversion v1.0.6 [INFO] [stderr] Compiling paste v1.0.6 [INFO] [stderr] Compiling crossbeam-utils v0.8.7 [INFO] [stderr] Compiling anyhow v1.0.53 [INFO] [stderr] Compiling rle-decode-fast v1.0.3 [INFO] [stderr] Compiling strum v0.23.0 [INFO] [stderr] Compiling dlv-list v0.3.0 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling bytecount v0.6.2 [INFO] [stderr] Compiling triple_accel v0.4.0 [INFO] [stderr] Compiling protein-translate v0.2.0 [INFO] [stderr] Compiling dissimilar v1.0.3 [INFO] [stderr] Compiling ring v0.16.20 [INFO] [stderr] Compiling nom v7.1.0 [INFO] [stderr] Compiling matrixmultiply v0.3.2 [INFO] [stderr] Compiling crc32fast v1.3.2 [INFO] [stderr] Compiling noodles-gff v0.4.0 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling libflate_lz77 v1.1.0 [INFO] [stderr] Compiling getrandom v0.2.4 [INFO] [stderr] Compiling time v0.1.44 [INFO] [stderr] Compiling num_cpus v1.13.1 [INFO] [stderr] Compiling csv-core v0.1.10 [INFO] [stderr] Compiling quick-xml v0.22.0 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Compiling num-complex v0.4.0 [INFO] [stderr] Compiling approx v0.5.1 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling ordered-float v1.1.1 [INFO] [stderr] Compiling flate2 v1.0.22 [INFO] [stderr] Compiling libflate v1.1.2 [INFO] [stderr] Compiling serde_derive v1.0.133 [INFO] [stderr] Compiling thiserror-impl v1.0.30 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling enum-map-derive v0.6.0 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling rand_core v0.6.3 [INFO] [stderr] Compiling ahash v0.7.6 [INFO] [stderr] Compiling num-rational v0.4.0 [INFO] [stderr] Compiling chrono v0.4.19 [INFO] [stderr] Compiling crossbeam-channel v0.5.2 [INFO] [stderr] Compiling simba v0.5.1 [INFO] [stderr] Compiling ndarray v0.15.4 [INFO] [stderr] Compiling rand_chacha v0.3.1 [INFO] [stderr] Compiling hashbrown v0.11.2 [INFO] [stderr] Compiling getset v0.1.2 [INFO] [stderr] Compiling rand v0.8.4 [INFO] [stderr] Compiling enum-map v1.1.1 [INFO] [stderr] Compiling indexmap v1.8.0 [INFO] [stderr] Compiling ordered-multimap v0.4.2 [INFO] [stderr] Compiling strum_macros v0.23.1 [INFO] [stderr] Compiling rand_distr v0.4.3 [INFO] [stderr] Compiling nom-unicode v0.3.0 [INFO] [stderr] Compiling nom-regex v0.2.0 [INFO] [stderr] Compiling petgraph v0.6.0 [INFO] [stderr] Compiling thiserror v1.0.30 [INFO] [stderr] Compiling uniprot v0.5.1 [INFO] [stderr] Compiling webpki v0.22.0 [INFO] [stderr] Compiling sct v0.7.0 [INFO] [stderr] Compiling rustls v0.20.2 [INFO] [stderr] Compiling webpki-roots v0.22.2 [INFO] [stderr] Compiling serde v1.0.133 [INFO] [stderr] Compiling bio-types v0.12.1 [INFO] [stderr] Compiling ureq v2.4.0 [INFO] [stderr] Compiling nalgebra v0.27.1 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling bstr v0.2.17 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling multimap v0.8.3 [INFO] [stderr] Compiling clap v2.34.0 [INFO] [stderr] Compiling csv v1.1.6 [INFO] [stderr] Compiling statrs v0.15.0 [INFO] [stderr] Compiling bio v0.39.1 [INFO] [stderr] Compiling rs-genomesub v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: irrefutable `if let` pattern [INFO] [stdout] --> src/bin/uniref.rs:68:22 [INFO] [stdout] | [INFO] [stdout] 68 | let protseq = if let uniprot::uniref::Member { sequence: seq, .. } = [INFO] [stdout] | ______________________^ [INFO] [stdout] 69 | | entry.unwrap().representative_member [INFO] [stdout] | |____________________________________________^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(irrefutable_let_patterns)]` on by default [INFO] [stdout] = note: this pattern will always match, so the `if let` is useless [INFO] [stdout] = help: consider replacing the `if let` with a `let` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 1 warning emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 2m 07s [INFO] running `Command { std: "docker" "inspect" "f7192a3f66369c2b381e41d0dbf46caf310aa32dda671f6232916d55d48a9aeb", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f7192a3f66369c2b381e41d0dbf46caf310aa32dda671f6232916d55d48a9aeb", kill_on_drop: false }` [INFO] [stdout] f7192a3f66369c2b381e41d0dbf46caf310aa32dda671f6232916d55d48a9aeb [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-14/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-14/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" "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:eaef2f80f755933c374d2ae5edccceec0c1312ceb8a4e0b6404e8ab76561e1e5" "/opt/rustwide/cargo-home/bin/cargo" "+1.60.0" "test" "--frozen" "--no-run" "--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] d5a6e2748df07780906fc8cb391619b3d42ba424802bf899171ade04d249fc77 [INFO] running `Command { std: "docker" "start" "-a" "d5a6e2748df07780906fc8cb391619b3d42ba424802bf899171ade04d249fc77", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Compiling predicates-core v1.0.3 [INFO] [stderr] Compiling termtree v0.2.4 [INFO] [stderr] Compiling difflib v0.4.0 [INFO] [stderr] Compiling wait-timeout v0.2.0 [INFO] [stderr] Compiling float-cmp v0.9.0 [INFO] [stdout] warning: irrefutable `if let` pattern [INFO] [stdout] --> src/bin/uniref.rs:68:22 [INFO] [stdout] | [INFO] [stdout] 68 | let protseq = if let uniprot::uniref::Member { sequence: seq, .. } = [INFO] [stdout] | ______________________^ [INFO] [stdout] 69 | | entry.unwrap().representative_member [INFO] [stdout] | |____________________________________________^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(irrefutable_let_patterns)]` on by default [INFO] [stdout] = note: this pattern will always match, so the `if let` is useless [INFO] [stdout] = help: consider replacing the `if let` with a `let` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 1 warning emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Compiling predicates-tree v1.0.5 [INFO] [stderr] Compiling predicates v2.1.1 [INFO] [stderr] Compiling assert_cmd v1.0.8 [INFO] [stderr] Compiling rs-genomesub v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] error: couldn't read src/../out_diamond.txt: No such file or directory (os error 2) [INFO] [stdout] --> src/blast_tabular.rs:118:25 [INFO] [stdout] | [INFO] [stdout] 118 | let fblastout = include_str!("../out_diamond.txt"); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this error originates in the macro `include_str` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: couldn't read src/../gc2.prt: No such file or directory (os error 2) [INFO] [stdout] --> src/prot_utils.rs:161:25 [INFO] [stdout] | [INFO] [stdout] 161 | let fblastout = include_str!("../gc2.prt"); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this error originates in the macro `include_str` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: irrefutable `if let` pattern [INFO] [stdout] --> src/bin/uniref.rs:68:22 [INFO] [stdout] | [INFO] [stdout] 68 | let protseq = if let uniprot::uniref::Member { sequence: seq, .. } = [INFO] [stdout] | ______________________^ [INFO] [stdout] 69 | | entry.unwrap().representative_member [INFO] [stdout] | |____________________________________________^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(irrefutable_let_patterns)]` on by default [INFO] [stdout] = note: this pattern will always match, so the `if let` is useless [INFO] [stdout] = help: consider replacing the `if let` with a `let` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 2 previous errors [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `rs-genomesub` due to 3 previous errors [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stdout] warning: 1 warning emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: build failed [INFO] running `Command { std: "docker" "inspect" "d5a6e2748df07780906fc8cb391619b3d42ba424802bf899171ade04d249fc77", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "d5a6e2748df07780906fc8cb391619b3d42ba424802bf899171ade04d249fc77", kill_on_drop: false }` [INFO] [stdout] d5a6e2748df07780906fc8cb391619b3d42ba424802bf899171ade04d249fc77