[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] eee01435028349b52326cfa33ac8633da6d33660
[INFO] documenting rodtheo/rs-genomesub against beta-2022-05-20 for beta-1.62-rustdoc-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Frodtheo%2Frs-genomesub" "/workspace/builds/worker-6/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-6/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/rodtheo/rs-genomesub on toolchain beta-2022-05-20
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2022-05-20" "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-6/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" "+beta-2022-05-20" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/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:d190cb871061d98bc6d0581d85cb2ecb09a0f8a142ba5463de30be9999fc3251" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2022-05-20" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 8180cf43a8d0cb0fb5b183916a4aff0d8b5d8445a7f14c0e6ee0e7d5e06839d7
[INFO] running `Command { std: "docker" "start" "-a" "8180cf43a8d0cb0fb5b183916a4aff0d8b5d8445a7f14c0e6ee0e7d5e06839d7", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "8180cf43a8d0cb0fb5b183916a4aff0d8b5d8445a7f14c0e6ee0e7d5e06839d7", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "8180cf43a8d0cb0fb5b183916a4aff0d8b5d8445a7f14c0e6ee0e7d5e06839d7", kill_on_drop: false }`
[INFO] [stdout] 8180cf43a8d0cb0fb5b183916a4aff0d8b5d8445a7f14c0e6ee0e7d5e06839d7
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/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" "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:d190cb871061d98bc6d0581d85cb2ecb09a0f8a142ba5463de30be9999fc3251" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2022-05-20" "doc" "--frozen" "--no-deps" "--document-private-items" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 4fe8e2961c967d58bf9a1f6af6b03032b41045facc7603b8b23381402077b568
[INFO] running `Command { std: "docker" "start" "-a" "4fe8e2961c967d58bf9a1f6af6b03032b41045facc7603b8b23381402077b568", kill_on_drop: false }`
[INFO] [stderr]    Compiling libc v0.2.112
[INFO] [stderr]    Compiling proc-macro2 v1.0.36
[INFO] [stderr]    Compiling syn v1.0.86
[INFO] [stderr]    Compiling libm v0.2.1
[INFO] [stderr]    Compiling crc32fast v1.3.2
[INFO] [stderr]    Compiling cc v1.0.72
[INFO] [stderr]    Compiling crossbeam-utils v0.8.7
[INFO] [stderr]     Checking bit-vec v0.6.3
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]     Checking minimal-lexical v0.2.1
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]     Checking rustc-hash v1.1.0
[INFO] [stderr]    Compiling paste v1.0.6
[INFO] [stderr]    Compiling rayon-core v1.9.1
[INFO] [stderr]     Checking regex-automata v0.1.10
[INFO] [stderr]    Compiling anyhow v1.0.53
[INFO] [stderr]     Checking rle-decode-fast v1.0.3
[INFO] [stderr]     Checking fixedbitset v0.4.1
[INFO] [stderr]     Checking chunked_transfer v1.4.0
[INFO] [stderr]     Checking strsim v0.10.0
[INFO] [stderr]     Checking textwrap v0.15.0
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]     Checking partial-min-max v0.4.0
[INFO] [stderr]     Checking paris v1.5.11
[INFO] [stderr]     Checking bytecount v0.6.2
[INFO] [stderr]     Checking dlv-list v0.3.0
[INFO] [stderr]     Checking adler32 v1.2.0
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[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking protein-translate v0.2.0
[INFO] [stderr]     Checking multipeek v0.1.2
[INFO] [stderr]     Checking dissimilar v1.0.3
[INFO] [stderr]    Compiling num-traits v0.2.14
[INFO] [stderr]    Compiling indexmap v1.8.0
[INFO] [stderr]    Compiling num-integer v0.1.44
[INFO] [stderr]    Compiling memoffset v0.6.5
[INFO] [stderr]    Compiling num-rational v0.4.0
[INFO] [stderr]    Compiling crossbeam-epoch v0.9.8
[INFO] [stderr]    Compiling rayon v1.5.1
[INFO] [stderr]    Compiling serde_derive v1.0.133
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[INFO] [stderr]    Compiling nom v7.1.0
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
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[INFO] [stderr]     Checking noodles-gff v0.5.0
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]    Compiling miniz_oxide v0.4.4
[INFO] [stderr]     Checking matrixmultiply v0.3.2
[INFO] [stderr]     Checking unicode-normalization v0.1.19
[INFO] [stderr]     Checking csv-core v0.1.10
[INFO] [stderr]     Checking os_str_bytes v6.0.0
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[INFO] [stderr]     Checking libflate_lz77 v1.1.0
[INFO] [stderr]     Checking regex v1.5.4
[INFO] [stderr]     Checking min-max v0.1.8
[INFO] [stderr]     Checking bit-set v0.5.2
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking libflate v1.1.2
[INFO] [stderr]     Checking crossbeam-channel v0.5.2
[INFO] [stderr]    Compiling ring v0.16.20
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[INFO] [stderr]     Checking idna v0.2.3
[INFO] [stderr]     Checking getrandom v0.2.4
[INFO] [stderr]     Checking flate2 v1.0.22
[INFO] [stderr]     Checking num_cpus v1.13.1
[INFO] [stderr]     Checking time v0.1.44
[INFO] [stderr]     Checking atty v0.2.14
[INFO] [stderr]     Checking ahash v0.7.6
[INFO] [stderr]     Checking rand_core v0.6.3
[INFO] [stderr]     Checking noodles-bgzf v0.10.0
[INFO] [stderr]     Checking rand_chacha v0.3.1
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[INFO] [stderr]     Checking approx v0.5.1
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[INFO] [stderr]     Checking clap v3.1.8
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking simplelog v0.11.2
[INFO] [stderr]     Checking noodles-core v0.5.0
[INFO] [stderr]     Checking noodles-vcf v0.14.1
[INFO] [stderr]     Checking webpki v0.22.0
[INFO] [stderr]     Checking sct v0.7.0
[INFO] [stderr]     Checking rustls v0.20.2
[INFO] [stderr]     Checking webpki-roots v0.22.2
[INFO] [stderr]     Checking noodles v0.20.0
[INFO] [stderr]    Compiling thiserror-impl v1.0.30
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]    Compiling strum_macros v0.23.1
[INFO] [stderr]    Compiling enum-map-derive v0.6.0
[INFO] [stderr]    Compiling getset v0.1.2
[INFO] [stderr]     Checking ureq v2.4.0
[INFO] [stderr]     Checking enum-map v1.1.1
[INFO] [stderr]     Checking nalgebra v0.27.1
[INFO] [stderr]     Checking thiserror v1.0.30
[INFO] [stderr]     Checking bio-types v0.12.1
[INFO] [stderr]     Checking uniprot v0.5.1
[INFO] [stderr]     Checking bstr v0.2.17
[INFO] [stderr]     Checking bv v0.11.1
[INFO] [stderr]     Checking multimap v0.8.3
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking csv v1.1.6
[INFO] [stderr]     Checking statrs v0.15.0
[INFO] [stderr]     Checking bio v0.39.1
[INFO] [stderr]  Documenting rs-genomesub v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Checking rs-genomesub v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unnecessary parentheses around `if` condition
[INFO] [stdout]    --> src/bin/uniref.rs:356:16
[INFO] [stdout]     |
[INFO] [stdout] 356 |             if (s1[0].sseqid == s1[1].sseqid) {
[INFO] [stdout]     |                ^                            ^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_parens)]` on by default
[INFO] [stdout] help: remove these parentheses
[INFO] [stdout]     |
[INFO] [stdout] 356 -             if (s1[0].sseqid == s1[1].sseqid) {
[INFO] [stdout] 356 +             if s1[0].sseqid == s1[1].sseqid {
[INFO] [stdout]     | 
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unnecessary parentheses around `if` condition
[INFO] [stdout]    --> src/bin/uniref.rs:370:12
[INFO] [stdout]     |
[INFO] [stdout] 370 |         if (a_start < b_start) {
[INFO] [stdout]     |            ^                 ^
[INFO] [stdout]     |
[INFO] [stdout] help: remove these parentheses
[INFO] [stdout]     |
[INFO] [stdout] 370 -         if (a_start < b_start) {
[INFO] [stdout] 370 +         if a_start < b_start {
[INFO] [stdout]     | 
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unnecessary parentheses around `if` condition
[INFO] [stdout]    --> src/bin/uniref.rs:372:19
[INFO] [stdout]     |
[INFO] [stdout] 372 |         } else if (a_start == b_start) {
[INFO] [stdout]     |                   ^                  ^
[INFO] [stdout]     |
[INFO] [stdout] help: remove these parentheses
[INFO] [stdout]     |
[INFO] [stdout] 372 -         } else if (a_start == b_start) {
[INFO] [stdout] 372 +         } else if a_start == b_start {
[INFO] [stdout]     | 
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unnecessary parentheses around `if` condition
[INFO] [stdout]    --> src/bin/uniref.rs:649:24
[INFO] [stdout]     |
[INFO] [stdout] 649 |                     if (score_normalized_rev >= 0.95 && score_normalized <= 0.95) {
[INFO] [stdout]     |                        ^                                                        ^
[INFO] [stdout]     |
[INFO] [stdout] help: remove these parentheses
[INFO] [stdout]     |
[INFO] [stdout] 649 -                     if (score_normalized_rev >= 0.95 && score_normalized <= 0.95) {
[INFO] [stdout] 649 +                     if score_normalized_rev >= 0.95 && score_normalized <= 0.95 {
[INFO] [stdout]     | 
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unnecessary parentheses around `if` condition
[INFO] [stdout]    --> src/bin/uniref.rs:655:24
[INFO] [stdout]     |
[INFO] [stdout] 655 |                     if (alignment.ylen > alignment.xlen + 30) {
[INFO] [stdout]     |                        ^                                    ^
[INFO] [stdout]     |
[INFO] [stdout] help: remove these parentheses
[INFO] [stdout]     |
[INFO] [stdout] 655 -                     if (alignment.ylen > alignment.xlen + 30) {
[INFO] [stdout] 655 +                     if alignment.ylen > alignment.xlen + 30 {
[INFO] [stdout]     | 
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unnecessary trailing semicolon
[INFO] [stdout]    --> src/bin/uniref.rs:664:114
[INFO] [stdout]     |
[INFO] [stdout] 664 | ...                   boundary_seq_start = boundary_seq_start - ((alignment.yend - alignment.xend) as u64);;
[INFO] [stdout]     |                                                                                                            ^ help: remove this semicolon
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(redundant_semicolons)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unnecessary parentheses around `if` condition
[INFO] [stdout]    --> src/bin/uniref.rs:703:24
[INFO] [stdout]     |
[INFO] [stdout] 703 |                     if (score_normalized >= 0.95 || score_normalized_rev >= 0.95) {
[INFO] [stdout]     |                        ^                                                        ^
[INFO] [stdout]     |
[INFO] [stdout] help: remove these parentheses
[INFO] [stdout]     |
[INFO] [stdout] 703 -                     if (score_normalized >= 0.95 || score_normalized_rev >= 0.95) {
[INFO] [stdout] 703 +                     if score_normalized >= 0.95 || score_normalized_rev >= 0.95 {
[INFO] [stdout]     | 
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: 7 warnings emitted
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished dev [unoptimized + debuginfo] target(s) in 52.06s
[INFO] running `Command { std: "docker" "inspect" "4fe8e2961c967d58bf9a1f6af6b03032b41045facc7603b8b23381402077b568", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "4fe8e2961c967d58bf9a1f6af6b03032b41045facc7603b8b23381402077b568", kill_on_drop: false }`
[INFO] [stdout] 4fe8e2961c967d58bf9a1f6af6b03032b41045facc7603b8b23381402077b568
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/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" "RUSTC_BOOTSTRAP=1" "-e" "DOCS_RS=1" "-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:d190cb871061d98bc6d0581d85cb2ecb09a0f8a142ba5463de30be9999fc3251" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2022-05-20" "rustdoc" "--lib" "-Zrustdoc-map" "--frozen" "--message-format=json" "--" "-Z" "unstable-options" "--document-private-items", kill_on_drop: false }`
[INFO] [stdout] 2559a9fa58b54ed877663c56cf3575f8dec7a8b0517be8a988a36537c0ac0e12
[INFO] running `Command { std: "docker" "start" "-a" "2559a9fa58b54ed877663c56cf3575f8dec7a8b0517be8a988a36537c0ac0e12", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]    Compiling autocfg v1.0.1
[INFO] [stderr]    Compiling libc v0.2.112
[INFO] [stderr]     Checking cfg-if v1.0.0
[INFO] [stderr]    Compiling proc-macro2 v1.0.36
[INFO] [stderr]    Compiling version_check v0.9.4
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[INFO] [stderr]    Compiling syn v1.0.86
[INFO] [stderr]    Compiling memchr v2.4.1
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[INFO] [stderr]     Checking lazy_static v1.4.0
[INFO] [stderr]     Checking adler v1.0.2
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[INFO] [stderr]    Compiling serde_derive v1.0.133
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[INFO] [stderr]     Checking dlv-list v0.3.0
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[INFO] [stdout] error[E0277]: the trait bound `proc_macro2::Span: From<proc_macro::Span>` is not satisfied
[INFO] [stdout]    --> /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/proc-macro-error-1.0.4/src/lib.rs:549:37
[INFO] [stdout]     |
[INFO] [stdout] 549 |                 first: self.clone().into(),
[INFO] [stdout]     |                                     ^^^^ the trait `From<proc_macro::Span>` is not implemented for `proc_macro2::Span`
[INFO] [stdout]     |
[INFO] [stdout]     = note: required because of the requirements on the impl of `Into<proc_macro2::Span>` for `proc_macro::Span`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error[E0277]: the trait bound `proc_macro2::Span: From<proc_macro::Span>` is not satisfied
[INFO] [stdout]    --> /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/proc-macro-error-1.0.4/src/lib.rs:550:36
[INFO] [stdout]     |
[INFO] [stdout] 550 |                 last: self.clone().into(),
[INFO] [stdout]     |                                    ^^^^ the trait `From<proc_macro::Span>` is not implemented for `proc_macro2::Span`
[INFO] [stdout]     |
[INFO] [stdout]     = note: required because of the requirements on the impl of `Into<proc_macro2::Span>` for `proc_macro::Span`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error: aborting due to 2 previous errors
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] For more information about this error, try `rustc --explain E0277`.
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `proc-macro-error` due to 3 previous errors
[INFO] [stderr] warning: build failed, waiting for other jobs to finish...
[INFO] running `Command { std: "docker" "inspect" "2559a9fa58b54ed877663c56cf3575f8dec7a8b0517be8a988a36537c0ac0e12", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "2559a9fa58b54ed877663c56cf3575f8dec7a8b0517be8a988a36537c0ac0e12", kill_on_drop: false }`
[INFO] [stdout] 2559a9fa58b54ed877663c56cf3575f8dec7a8b0517be8a988a36537c0ac0e12