[INFO] updating cached repository https://github.com/Helkafen/vcf_pwm [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] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 18924fb3ecec0604db9fa70d1ced6c68aa41e12d [INFO] checking Helkafen/vcf_pwm against master#c724b67e1b474262917a5154d74e7072267593fe for pr-74315 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FHelkafen%2Fvcf_pwm" "/workspace/builds/worker-0/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-0/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/Helkafen/vcf_pwm on toolchain c724b67e1b474262917a5154d74e7072267593fe [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+c724b67e1b474262917a5154d74e7072267593fe" "read-manifest" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/Helkafen/vcf_pwm [INFO] finished tweaking git repo https://github.com/Helkafen/vcf_pwm [INFO] tweaked toml for git repo https://github.com/Helkafen/vcf_pwm written to /workspace/builds/worker-0/source/Cargo.toml [INFO] crate git repo https://github.com/Helkafen/vcf_pwm already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+c724b67e1b474262917a5154d74e7072267593fe" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/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:d9fbb4e2287ab3795bdefaf705efb7541a8875c13bce71e067d6b01dc5ed759b" "/opt/rustwide/cargo-home/bin/cargo" "+c724b67e1b474262917a5154d74e7072267593fe" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] c2ba7fd3f5cecd67587bb9bf62a4e4e82822ff5e2e072ee6f947f27075c3de46 [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" "c2ba7fd3f5cecd67587bb9bf62a4e4e82822ff5e2e072ee6f947f27075c3de46", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "c2ba7fd3f5cecd67587bb9bf62a4e4e82822ff5e2e072ee6f947f27075c3de46", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "c2ba7fd3f5cecd67587bb9bf62a4e4e82822ff5e2e072ee6f947f27075c3de46", kill_on_drop: false }` [INFO] [stdout] c2ba7fd3f5cecd67587bb9bf62a4e4e82822ff5e2e072ee6f947f27075c3de46 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/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:d9fbb4e2287ab3795bdefaf705efb7541a8875c13bce71e067d6b01dc5ed759b" "/opt/rustwide/cargo-home/bin/cargo" "+c724b67e1b474262917a5154d74e7072267593fe" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 6d533f8e506416208d8995223f004ff4e0a7da01d8bd690fe0eaf9e00a642be1 [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" "6d533f8e506416208d8995223f004ff4e0a7da01d8bd690fe0eaf9e00a642be1", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.66 [INFO] [stderr] Compiling proc-macro2 v0.4.30 [INFO] [stderr] Compiling unicode-xid v0.1.0 [INFO] [stderr] Compiling syn v0.15.39 [INFO] [stderr] Compiling memchr v2.2.1 [INFO] [stderr] Compiling serde v1.0.94 [INFO] [stderr] Compiling byteorder v1.3.2 [INFO] [stderr] Checking lazy_static v1.4.0 [INFO] [stderr] Compiling bitflags v1.2.1 [INFO] [stderr] Compiling pkg-config v0.3.14 [INFO] [stderr] Compiling version_check v0.1.5 [INFO] [stderr] Compiling quick-error v1.2.2 [INFO] [stderr] Compiling proc-macro2 v1.0.6 [INFO] [stderr] Compiling unicode-xid v0.2.0 [INFO] [stderr] Compiling cfg-if v0.1.9 [INFO] [stderr] Compiling bindgen v0.51.1 [INFO] [stderr] Checking nodrop v0.1.13 [INFO] [stderr] Compiling ansi_term v0.11.0 [INFO] [stderr] Compiling strsim v0.8.0 [INFO] [stderr] Compiling matrixmultiply v0.1.15 [INFO] [stderr] Compiling doc-comment v0.3.1 [INFO] [stderr] Compiling crc32fast v1.2.0 [INFO] [stderr] Checking memoffset v0.2.1 [INFO] [stderr] Compiling shlex v0.1.1 [INFO] [stderr] Compiling peeking_take_while v0.1.2 [INFO] [stderr] Checking matches v0.1.8 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Checking scopeguard v0.3.3 [INFO] [stderr] Checking rawpointer v0.1.0 [INFO] [stderr] Compiling ndarray v0.12.1 [INFO] [stderr] Checking percent-encoding v2.1.0 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking bit-vec v0.5.1 [INFO] [stderr] Checking owning_ref v0.2.4 [INFO] [stderr] Compiling bio v0.28.2 [INFO] [stderr] Checking bytecount v0.3.2 [INFO] [stderr] Checking cast v0.2.2 [INFO] [stderr] Checking fnv v1.0.6 [INFO] [stderr] Checking smallvec v0.3.4 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking strum v0.13.0 [INFO] [stderr] Compiling backtrace-sys v0.1.30 [INFO] [stderr] Compiling libloading v0.5.2 [INFO] [stderr] Compiling bzip2-sys v0.1.7 [INFO] [stderr] Compiling miniz-sys v0.1.12 [INFO] [stderr] Compiling clang-sys v0.28.0 [INFO] [stderr] Compiling num-complex v0.2.3 [INFO] [stderr] Compiling num-integer v0.1.41 [INFO] [stderr] Checking itertools v0.8.0 [INFO] [stderr] Checking itertools v0.7.11 [INFO] [stderr] Compiling textwrap v0.11.0 [INFO] [stderr] Compiling log v0.4.6 [INFO] [stderr] Checking crossbeam-utils v0.6.5 [INFO] [stderr] Checking thread_local v0.3.6 [INFO] [stderr] Compiling humantime v1.2.0 [INFO] [stderr] Compiling fs-utils v1.1.1 [INFO] [stderr] Checking unicode-bidi v0.3.4 [INFO] [stderr] Compiling nom v4.2.3 [INFO] [stderr] Checking bit-set v0.5.1 [INFO] [stderr] Checking arrayvec v0.4.11 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling bv v0.10.0 [INFO] [stderr] Compiling lzma-sys v0.1.14 [INFO] [stderr] Compiling libz-sys v1.0.25 [INFO] [stderr] Checking crossbeam-queue v0.1.2 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking approx v0.3.2 [INFO] [stderr] Checking ordered-float v1.0.2 [INFO] [stderr] Checking crossbeam-epoch v0.7.1 [INFO] [stderr] Checking idna v0.2.0 [INFO] [stderr] Checking regex-automata v0.1.7 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking rand_xoshiro v0.1.0 [INFO] [stderr] Checking criterion-plot v0.3.1 [INFO] [stderr] Compiling quote v1.0.2 [INFO] [stderr] Compiling rustc-hash v1.0.1 [INFO] [stderr] Compiling quote v0.6.12 [INFO] [stderr] Compiling atty v0.2.11 [INFO] [stderr] Compiling which v3.1.0 [INFO] [stderr] Checking rand v0.4.6 [INFO] [stderr] Checking num_cpus v1.10.1 [INFO] [stderr] Checking thread-id v3.3.0 [INFO] [stderr] Checking time v0.1.42 [INFO] [stderr] Checking rand_os v0.1.3 [INFO] [stderr] Checking subprocess v0.1.18 [INFO] [stderr] Checking crossbeam-deque v0.7.1 [INFO] [stderr] Checking backtrace v0.3.32 [INFO] [stderr] Checking flate2 v1.0.9 [INFO] [stderr] Compiling aho-corasick v0.7.6 [INFO] [stderr] Checking csv-core v0.1.6 [INFO] [stderr] Checking rayon-core v1.6.0 [INFO] [stderr] Checking url v2.1.0 [INFO] [stderr] Checking failure v0.1.5 [INFO] [stderr] Checking which v2.0.1 [INFO] [stderr] Checking bgzip v0.0.3 [INFO] [stderr] Checking rayon v1.2.0 [INFO] [stderr] Checking parking_lot_core v0.2.14 [INFO] [stderr] Checking rand v0.3.23 [INFO] [stderr] Checking statrs v0.9.0 [INFO] [stderr] Checking parking_lot v0.3.8 [INFO] [stderr] Checking regex v1.3.1 [INFO] [stderr] Checking multiqueue v0.3.2 [INFO] [stderr] Compiling cexpr v0.3.5 [INFO] [stderr] Compiling env_logger v0.6.2 [INFO] [stderr] Compiling serde_derive v1.0.94 [INFO] [stderr] Compiling snafu-derive v0.5.0 [INFO] [stderr] Compiling strum_macros v0.13.0 [INFO] [stderr] Checking snafu v0.5.0 [INFO] [stderr] Checking vec_map v0.8.1 [INFO] [stderr] Checking bstr v0.2.1 [INFO] [stderr] Checking bio-types v0.5.1 [INFO] [stderr] Checking multimap v0.4.0 [INFO] [stderr] Checking serde_json v1.0.40 [INFO] [stderr] Checking clap v2.33.0 [INFO] [stderr] Checking csv v1.1.1 [INFO] [stderr] Checking tinytemplate v1.0.2 [INFO] [stderr] Checking criterion v0.2.11 [INFO] [stderr] Compiling rust-htslib v0.26.1 [INFO] [stderr] Checking find-tfbs v1.0.0 (/opt/rustwide/workdir) [INFO] [stdout] error[E0061]: this function takes 16 arguments but 15 arguments were supplied [INFO] [stdout] --> src/main.rs:494:9 [INFO] [stdout] | [INFO] [stdout] 190 | / fn run(chromosome: String, bcf: String, bed_files: Vec<&str>, reference_genome_file: String, wanted_samples: Option<&str>, pwm_file: &str, pwm_threshold_directory: &str, pwm_... [INFO] [stdout] 191 | | wanted_pwms: Vec, output_file: String, forward_only: bool, run_tabix: bool, min_maf: u32, threads: u32, after_position: u64, verbose: bool) { [INFO] [stdout] 192 | | [INFO] [stdout] 193 | | let pwm_list: Vec = parse_pwm_files(pwm_file, pwm_threshold_directory, pwm_threshold, wanted_pwms, !forward_only); [INFO] [stdout] ... | [INFO] [stdout] 337 | | println!("End."); [INFO] [stdout] 338 | | } [INFO] [stdout] | |_- defined here [INFO] [stdout] ... [INFO] [stdout] 494 | run("chr1".to_string(), "test_data/genotypes.bcf".to_string(), vec!["test_data/regions1.bed","test_data/regions2.bed"], "test_data/reference_genome.fa".to_string(... [INFO] [stdout] | ^^^ ------------------ ------------------------------------- ------------------------------------------------------- ------------------------------------------- [INFO] [stdout] | | [INFO] [stdout] | expected 16 arguments [INFO] [stdout] 495 | Some("test_data/samples"), [INFO] [stdout] | ------------------------- [INFO] [stdout] 496 | "test_data/pwm_definitions.txt", [INFO] [stdout] | ------------------------------- [INFO] [stdout] 497 | "test_data", 0.0001, vec!["ACGT".to_string()], "test_data/output1.vcf.gz".to_string(), false, false, 0, 1, 0); [INFO] [stdout] | ----------- ------ ------------------------ -------------------------------------- ----- ----- - - - supplied 15 arguments [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0061]: this function takes 16 arguments but 15 arguments were supplied [INFO] [stdout] --> src/main.rs:505:9 [INFO] [stdout] | [INFO] [stdout] 190 | / fn run(chromosome: String, bcf: String, bed_files: Vec<&str>, reference_genome_file: String, wanted_samples: Option<&str>, pwm_file: &str, pwm_threshold_directory: &str, pwm_t... [INFO] [stdout] 191 | | wanted_pwms: Vec, output_file: String, forward_only: bool, run_tabix: bool, min_maf: u32, threads: u32, after_position: u64, verbose: bool) { [INFO] [stdout] 192 | | [INFO] [stdout] 193 | | let pwm_list: Vec = parse_pwm_files(pwm_file, pwm_threshold_directory, pwm_threshold, wanted_pwms, !forward_only); [INFO] [stdout] ... | [INFO] [stdout] 337 | | println!("End."); [INFO] [stdout] 338 | | } [INFO] [stdout] | |_- defined here [INFO] [stdout] ... [INFO] [stdout] 505 | run("chr1".to_string(), "test_data/genotypes2.bcf".to_string(), vec!["test_data/regions1.bed","test_data/regions2.bed"], "test_data/reference_genome.fa".to_string(... [INFO] [stdout] | ^^^ ------------------ -------------------------------------- ------------------------------------------------------- ------------------------------------------- [INFO] [stdout] | | [INFO] [stdout] | expected 16 arguments [INFO] [stdout] 506 | Some("test_data/samples"), [INFO] [stdout] | ------------------------- [INFO] [stdout] 507 | "test_data/pwm_definitions.txt", [INFO] [stdout] | ------------------------------- [INFO] [stdout] 508 | "test_data", 0.0001, vec!["ACGT".to_string()], "test_data/output2.vcf.gz".to_string(), false, false, 0, 1, 0); [INFO] [stdout] | ----------- ------ ------------------------ -------------------------------------- ----- ----- - - - supplied 15 arguments [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0061]: this function takes 4 arguments but 3 arguments were supplied [INFO] [stdout] --> src/pattern.rs:278:17 [INFO] [stdout] | [INFO] [stdout] 140 | pub fn matches(pattern: &Pattern, haplotype: &Vec, haplotype_ids: Rc>, verbose: bool) -> Vec { [INFO] [stdout] | ----------------------------------------------------------------------------------------------------------------------------------- defined here [INFO] [stdout] ... [INFO] [stdout] 278 | let m = matches(&pwm, &haplotype, haplotype_ids.clone()); [INFO] [stdout] | ^^^^^^^ ---- ---------- --------------------- supplied 3 arguments [INFO] [stdout] | | [INFO] [stdout] | expected 4 arguments [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 3 previous errors [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0061`. [INFO] [stdout] [INFO] [stdout] warning: variant is never constructed: `OtherPattern` [INFO] [stdout] --> src/types.rs:68:6 [INFO] [stdout] | [INFO] [stdout] 68 | OtherPattern { name: String, pattern_id: u16 } [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `find-tfbs`. [INFO] [stderr] [INFO] [stderr] To learn more, run the command again with --verbose. [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" "6d533f8e506416208d8995223f004ff4e0a7da01d8bd690fe0eaf9e00a642be1", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "6d533f8e506416208d8995223f004ff4e0a7da01d8bd690fe0eaf9e00a642be1", kill_on_drop: false }` [INFO] [stdout] 6d533f8e506416208d8995223f004ff4e0a7da01d8bd690fe0eaf9e00a642be1