[INFO] cloning repository https://github.com/SteampunkIslande/rust-hgvs2
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/SteampunkIslande/rust-hgvs2" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FSteampunkIslande%2Frust-hgvs2", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FSteampunkIslande%2Frust-hgvs2'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 2cc366012364a61ca9102d9fe441ae2a757af62d
[INFO] checking SteampunkIslande/rust-hgvs2 against try#79452e8441468c5568c20bfca2aa1fe75b645b2d for pr-152210
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FSteampunkIslande%2Frust-hgvs2" "/workspace/builds/worker-5-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/SteampunkIslande/rust-hgvs2
[INFO] finished tweaking git repo https://github.com/SteampunkIslande/rust-hgvs2
[INFO] tweaked toml for git repo https://github.com/SteampunkIslande/rust-hgvs2 written to /workspace/builds/worker-5-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/SteampunkIslande/rust-hgvs2 on toolchain 79452e8441468c5568c20bfca2aa1fe75b645b2d
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+79452e8441468c5568c20bfca2aa1fe75b645b2d" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/SteampunkIslande/rust-hgvs2 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" "+79452e8441468c5568c20bfca2aa1fe75b645b2d" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Blocking waiting for file lock on package cache
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]     Blocking waiting for file lock on package cache
[ERROR] error running command: no output for 300 seconds
[INFO] checking SteampunkIslande/rust-hgvs2 against try#79452e8441468c5568c20bfca2aa1fe75b645b2d for pr-152210
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FSteampunkIslande%2Frust-hgvs2" "/workspace/builds/worker-5-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/SteampunkIslande/rust-hgvs2
[INFO] finished tweaking git repo https://github.com/SteampunkIslande/rust-hgvs2
[INFO] tweaked toml for git repo https://github.com/SteampunkIslande/rust-hgvs2 written to /workspace/builds/worker-5-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/SteampunkIslande/rust-hgvs2 on toolchain 79452e8441468c5568c20bfca2aa1fe75b645b2d
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+79452e8441468c5568c20bfca2aa1fe75b645b2d" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/SteampunkIslande/rust-hgvs2 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" "+79452e8441468c5568c20bfca2aa1fe75b645b2d" "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] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded strum v0.23.0
[INFO] [stderr]   Downloaded enum-map-derive v0.6.0
[INFO] [stderr]   Downloaded itertools-num v0.1.3
[INFO] [stderr]   Downloaded enum-map v1.1.1
[INFO] [stderr]   Downloaded lazy-regex-proc_macros v3.4.1
[INFO] [stderr]   Downloaded newtype_derive v0.1.6
[INFO] [stderr]   Downloaded editdistancek v1.0.2
[INFO] [stderr]   Downloaded triple_accel v0.4.0
[INFO] [stderr]   Downloaded lazy-regex v3.4.1
[INFO] [stderr]   Downloaded derive-new v0.6.0
[INFO] [stderr]   Downloaded bio-types v1.0.4
[INFO] [stderr]   Downloaded bytecount v0.6.9
[INFO] [stderr]   Downloaded bio v2.3.0
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:61361fe0aef631f17e9d025a70c5a647956f8c671dd02950a60ad3f5cc5526d7" "/opt/rustwide/cargo-home/bin/cargo" "+79452e8441468c5568c20bfca2aa1fe75b645b2d" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] f0c54a58e7fcbc53a423d00067f209e57d0c476714c6395ce1d07d703afd8aec
[INFO] running `Command { std: "docker" "start" "-a" "f0c54a58e7fcbc53a423d00067f209e57d0c476714c6395ce1d07d703afd8aec", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "f0c54a58e7fcbc53a423d00067f209e57d0c476714c6395ce1d07d703afd8aec", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "f0c54a58e7fcbc53a423d00067f209e57d0c476714c6395ce1d07d703afd8aec", kill_on_drop: false }`
[INFO] [stdout] f0c54a58e7fcbc53a423d00067f209e57d0c476714c6395ce1d07d703afd8aec
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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=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@sha256:61361fe0aef631f17e9d025a70c5a647956f8c671dd02950a60ad3f5cc5526d7" "/opt/rustwide/cargo-home/bin/cargo" "+79452e8441468c5568c20bfca2aa1fe75b645b2d" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 700998a44d214d47901e59f2602618856152fb81654d75dcea0be9bedd337910
[INFO] running `Command { std: "docker" "start" "-a" "700998a44d214d47901e59f2602618856152fb81654d75dcea0be9bedd337910", kill_on_drop: false }`
[INFO] [stderr]    Compiling libm v0.2.15
[INFO] [stderr]    Compiling libc v0.2.174
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]    Compiling serde v1.0.219
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling num-traits v0.2.19
[INFO] [stderr]    Compiling matrixmultiply v0.3.10
[INFO] [stderr]     Checking aho-corasick v1.1.3
[INFO] [stderr]     Checking rawpointer v0.2.1
[INFO] [stderr]    Compiling memchr v2.7.5
[INFO] [stderr]    Compiling regex-syntax v0.8.5
[INFO] [stderr]    Compiling serde_derive v1.0.219
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]     Checking hashbrown v0.15.4
[INFO] [stderr]    Compiling thiserror v2.0.12
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]    Compiling thiserror-impl v2.0.12
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]     Checking csv-core v0.1.12
[INFO] [stderr]     Checking bit-vec v0.8.0
[INFO] [stderr]     Checking fixedbitset v0.4.2
[INFO] [stderr]    Compiling derive_more-impl v2.0.1
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking indexmap v2.10.0
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking strum v0.23.0
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]     Checking bit-set v0.8.0
[INFO] [stderr]     Checking bytecount v0.6.9
[INFO] [stderr]     Checking editdistancek v1.0.2
[INFO] [stderr]     Checking petgraph v0.6.5
[INFO] [stderr]     Checking regex-automata v0.4.9
[INFO] [stderr]     Checking getrandom v0.2.16
[INFO] [stderr]     Checking thiserror v1.0.69
[INFO] [stderr]     Checking rand_core v0.6.4
[INFO] [stderr]     Checking derive_more v2.0.1
[INFO] [stderr]     Checking rand_chacha v0.3.1
[INFO] [stderr]     Checking num-integer v0.1.46
[INFO] [stderr]     Checking num-complex v0.4.6
[INFO] [stderr]     Checking approx v0.5.1
[INFO] [stderr]     Checking ordered-float v5.0.0
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking rand v0.8.5
[INFO] [stderr]     Checking num-rational v0.4.2
[INFO] [stderr]     Checking simba v0.5.1
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking regex v1.11.1
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]    Compiling enum-map-derive v0.6.0
[INFO] [stderr]     Checking bio-types v1.0.4
[INFO] [stderr]     Checking enum-map v1.1.1
[INFO] [stderr]    Compiling lazy-regex-proc_macros v3.4.1
[INFO] [stderr]     Checking lazy-regex v3.4.1
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking bv v0.11.1
[INFO] [stderr]     Checking csv v1.3.1
[INFO] [stderr]     Checking multimap v0.8.3
[INFO] [stderr]     Checking nalgebra v0.27.1
[INFO] [stderr]     Checking statrs v0.15.0
[INFO] [stderr]     Checking bio v2.3.0
[INFO] [stderr]     Checking pyhgvs2 v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused variable: `transcript`
[INFO] [stdout]    --> src/hgvs_name.rs:925:30
[INFO] [stdout]     |
[INFO] [stdout] 925 |     fn get_ref_coords(&self, transcript: Option<&Transcript>) -> Option<(String, i64, i64)> {
[INFO] [stdout]     |                              ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_transcript`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `transcript`
[INFO] [stdout]    --> src/hgvs_name.rs:929:30
[INFO] [stdout]     |
[INFO] [stdout] 929 |     fn get_vcf_coords(&self, transcript: Option<&Transcript>) -> Option<(String, i64, i64)> {
[INFO] [stdout]     |                              ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_transcript`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `coord`
[INFO] [stdout]   --> src/transcript.rs:78:41
[INFO] [stdout]    |
[INFO] [stdout] 78 |     pub fn cdna_to_genomic_coord(&self, coord: &CDNACoord) -> u64 {
[INFO] [stdout]    |                                         ^^^^^ help: if this is intentional, prefix it with an underscore: `_coord`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `transcript`
[INFO] [stdout]    --> src/hgvs_name.rs:925:30
[INFO] [stdout]     |
[INFO] [stdout] 925 |     fn get_ref_coords(&self, transcript: Option<&Transcript>) -> Option<(String, i64, i64)> {
[INFO] [stdout]     |                              ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_transcript`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `transcript`
[INFO] [stdout]    --> src/hgvs_name.rs:929:30
[INFO] [stdout]     |
[INFO] [stdout] 929 |     fn get_vcf_coords(&self, transcript: Option<&Transcript>) -> Option<(String, i64, i64)> {
[INFO] [stdout]     |                              ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_transcript`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `get_raw_coords`, `get_ref_coords`, and `get_vcf_coords` are never used
[INFO] [stdout]    --> src/hgvs_name.rs:904:8
[INFO] [stdout]     |
[INFO] [stdout] 369 | impl HGVSName {
[INFO] [stdout]     | ------------- methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 904 |     fn get_raw_coords(&self, transcript: Option<&Transcript>) -> Option<(String, i64, i64)> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 925 |     fn get_ref_coords(&self, transcript: Option<&Transcript>) -> Option<(String, i64, i64)> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 929 |     fn get_vcf_coords(&self, transcript: Option<&Transcript>) -> Option<(String, i64, i64)> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `start_codon_transcript_pos` and `stop_codon_transcript_pos` are never read
[INFO] [stdout]   --> src/transcript.rs:22:5
[INFO] [stdout]    |
[INFO] [stdout] 14 | pub struct Transcript {
[INFO] [stdout]    |            ---------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 22 |     start_codon_transcript_pos: Option<u64>,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 23 |     stop_codon_transcript_pos: Option<u64>,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `coord`
[INFO] [stdout]   --> src/transcript.rs:78:41
[INFO] [stdout]    |
[INFO] [stdout] 78 |     pub fn cdna_to_genomic_coord(&self, coord: &CDNACoord) -> u64 {
[INFO] [stdout]    |                                         ^^^^^ help: if this is intentional, prefix it with an underscore: `_coord`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `get_raw_coords`, `get_ref_coords`, and `get_vcf_coords` are never used
[INFO] [stdout]    --> src/hgvs_name.rs:904:8
[INFO] [stdout]     |
[INFO] [stdout] 369 | impl HGVSName {
[INFO] [stdout]     | ------------- methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 904 |     fn get_raw_coords(&self, transcript: Option<&Transcript>) -> Option<(String, i64, i64)> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 925 |     fn get_ref_coords(&self, transcript: Option<&Transcript>) -> Option<(String, i64, i64)> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 929 |     fn get_vcf_coords(&self, transcript: Option<&Transcript>) -> Option<(String, i64, i64)> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `start_codon_transcript_pos` and `stop_codon_transcript_pos` are never read
[INFO] [stdout]   --> src/transcript.rs:22:5
[INFO] [stdout]    |
[INFO] [stdout] 14 | pub struct Transcript {
[INFO] [stdout]    |            ---------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 22 |     start_codon_transcript_pos: Option<u64>,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 23 |     stop_codon_transcript_pos: Option<u64>,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 12.51s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.27.1
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1`
[INFO] running `Command { std: "docker" "inspect" "700998a44d214d47901e59f2602618856152fb81654d75dcea0be9bedd337910", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "700998a44d214d47901e59f2602618856152fb81654d75dcea0be9bedd337910", kill_on_drop: false }`
[INFO] [stdout] 700998a44d214d47901e59f2602618856152fb81654d75dcea0be9bedd337910
