[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] testing SteampunkIslande/rust-hgvs2 against master#d98a5da813da67eb189387b8ccfb73cf481275d8+rustflags=-Copt-level=3 for pr-138759 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FSteampunkIslande%2Frust-hgvs2" "/workspace/builds/worker-0-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc1/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-0-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/SteampunkIslande/rust-hgvs2 on toolchain d98a5da813da67eb189387b8ccfb73cf481275d8 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+d98a5da813da67eb189387b8ccfb73cf481275d8" "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" "+d98a5da813da67eb189387b8ccfb73cf481275d8" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded strum v0.23.0 [INFO] [stderr] Downloaded lazy-regex v3.4.1 [INFO] [stderr] Downloaded lazy-regex-proc_macros v3.4.1 [INFO] [stderr] Downloaded nalgebra-macros v0.1.0 [INFO] [stderr] Downloaded triple_accel v0.4.0 [INFO] [stderr] Downloaded derive-new v0.6.0 [INFO] [stderr] Downloaded enum-map-derive v0.6.0 [INFO] [stderr] Downloaded itertools-num v0.1.3 [INFO] [stderr] Downloaded bio-types v1.0.4 [INFO] [stderr] Downloaded csv-core v0.1.12 [INFO] [stderr] Downloaded enum-map v1.1.1 [INFO] [stderr] Downloaded matrixmultiply v0.3.10 [INFO] [stderr] Downloaded ordered-float v5.0.0 [INFO] [stderr] Downloaded statrs v0.15.0 [INFO] [stderr] Downloaded editdistancek v1.0.2 [INFO] [stderr] Downloaded multimap v0.8.3 [INFO] [stderr] Downloaded bio v2.3.0 [INFO] [stderr] Downloaded nalgebra v0.27.1 [INFO] [stderr] Downloaded semver v0.1.20 [INFO] [stderr] Downloaded rustc_version v0.1.7 [INFO] [stderr] Downloaded bytecount v0.6.9 [INFO] [stderr] Downloaded simba v0.5.1 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded csv v1.3.1 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+d98a5da813da67eb189387b8ccfb73cf481275d8" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 9e8abe263b85373b7fe66595a072bc41014017d68310da5dbdaf777d6cf3272b [INFO] running `Command { std: "docker" "start" "-a" "9e8abe263b85373b7fe66595a072bc41014017d68310da5dbdaf777d6cf3272b", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "9e8abe263b85373b7fe66595a072bc41014017d68310da5dbdaf777d6cf3272b", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "9e8abe263b85373b7fe66595a072bc41014017d68310da5dbdaf777d6cf3272b", kill_on_drop: false }` [INFO] [stdout] 9e8abe263b85373b7fe66595a072bc41014017d68310da5dbdaf777d6cf3272b [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/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 -Copt-level=3" "-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+d98a5da813da67eb189387b8ccfb73cf481275d8" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 8434763b3fb3c97a31734e16f1a712173a2e34d3497bb81cccbe3648eebf4ec1 [INFO] running `Command { std: "docker" "start" "-a" "8434763b3fb3c97a31734e16f1a712173a2e34d3497bb81cccbe3648eebf4ec1", kill_on_drop: false }` [INFO] [stderr] Compiling libm v0.2.15 [INFO] [stderr] Compiling libc v0.2.174 [INFO] [stderr] Compiling memchr v2.7.5 [INFO] [stderr] Compiling zerocopy v0.8.26 [INFO] [stderr] Compiling cfg-if v1.0.1 [INFO] [stderr] Compiling serde v1.0.219 [INFO] [stderr] Compiling regex-syntax v0.8.5 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling rawpointer v0.2.1 [INFO] [stderr] Compiling typenum v1.18.0 [INFO] [stderr] Compiling rustversion v1.0.21 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling matrixmultiply v0.3.10 [INFO] [stderr] Compiling syn v2.0.104 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling anyhow v1.0.98 [INFO] [stderr] Compiling thiserror v2.0.12 [INFO] [stderr] Compiling hashbrown v0.15.4 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling bit-vec v0.8.0 [INFO] [stderr] Compiling byteorder v1.5.0 [INFO] [stderr] Compiling unicode-xid v0.2.6 [INFO] [stderr] Compiling fixedbitset v0.4.2 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling fxhash v0.2.1 [INFO] [stderr] Compiling aho-corasick v1.1.3 [INFO] [stderr] Compiling csv-core v0.1.12 [INFO] [stderr] Compiling bit-set v0.8.0 [INFO] [stderr] Compiling indexmap v2.10.0 [INFO] [stderr] Compiling bytecount v0.6.9 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling strum v0.23.0 [INFO] [stderr] Compiling triple_accel v0.4.0 [INFO] [stderr] Compiling editdistancek v1.0.2 [INFO] [stderr] Compiling petgraph v0.6.5 [INFO] [stderr] Compiling getrandom v0.2.16 [INFO] [stderr] Compiling rand_core v0.6.4 [INFO] [stderr] Compiling regex-automata v0.4.9 [INFO] [stderr] Compiling num-integer v0.1.46 [INFO] [stderr] Compiling num-complex v0.4.6 [INFO] [stderr] Compiling approx v0.5.1 [INFO] [stderr] Compiling ppv-lite86 v0.2.21 [INFO] [stderr] Compiling num-rational v0.4.2 [INFO] [stderr] Compiling simba v0.5.1 [INFO] [stderr] Compiling ndarray v0.15.6 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling ordered-float v5.0.0 [INFO] [stderr] Compiling rand_chacha v0.3.1 [INFO] [stderr] Compiling rand v0.8.5 [INFO] [stderr] Compiling rand_distr v0.4.3 [INFO] [stderr] Compiling regex v1.11.1 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling enum-map-derive v0.6.0 [INFO] [stderr] Compiling serde_derive v1.0.219 [INFO] [stderr] Compiling thiserror-impl v1.0.69 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling thiserror-impl v2.0.12 [INFO] [stderr] Compiling derive_more-impl v2.0.1 [INFO] [stderr] Compiling nalgebra v0.27.1 [INFO] [stderr] Compiling lazy-regex-proc_macros v3.4.1 [INFO] [stderr] Compiling enum-map v1.1.1 [INFO] [stderr] Compiling lazy-regex v3.4.1 [INFO] [stderr] Compiling thiserror v1.0.69 [INFO] [stderr] Compiling derive_more v2.0.1 [INFO] [stderr] Compiling bio-types v1.0.4 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling csv v1.3.1 [INFO] [stderr] Compiling multimap v0.8.3 [INFO] [stderr] Compiling statrs v0.15.0 [INFO] [stderr] Compiling bio v2.3.0 [INFO] [stderr] Compiling 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)]` 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: 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)]` 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, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 23 | stop_codon_transcript_pos: Option, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 2m 58s [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 3` [INFO] running `Command { std: "docker" "inspect" "8434763b3fb3c97a31734e16f1a712173a2e34d3497bb81cccbe3648eebf4ec1", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "8434763b3fb3c97a31734e16f1a712173a2e34d3497bb81cccbe3648eebf4ec1", kill_on_drop: false }` [INFO] [stdout] 8434763b3fb3c97a31734e16f1a712173a2e34d3497bb81cccbe3648eebf4ec1 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/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 -Copt-level=3" "-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+d98a5da813da67eb189387b8ccfb73cf481275d8" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] e244f98f3857aed11c502a326f3c07c5d8cfe13c6537ab97b136af106b65e02b [INFO] running `Command { std: "docker" "start" "-a" "e244f98f3857aed11c502a326f3c07c5d8cfe13c6537ab97b136af106b65e02b", kill_on_drop: false }` [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)]` 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: 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)]` 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, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 23 | stop_codon_transcript_pos: Option, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Compiling 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)]` 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: 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)]` 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, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] 23 | stop_codon_transcript_pos: Option, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 1.64s [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 3` [INFO] running `Command { std: "docker" "inspect" "e244f98f3857aed11c502a326f3c07c5d8cfe13c6537ab97b136af106b65e02b", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "e244f98f3857aed11c502a326f3c07c5d8cfe13c6537ab97b136af106b65e02b", kill_on_drop: false }` [INFO] [stdout] e244f98f3857aed11c502a326f3c07c5d8cfe13c6537ab97b136af106b65e02b [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/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 -Copt-level=3" "-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+d98a5da813da67eb189387b8ccfb73cf481275d8" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] 33a0f3be38f51ecc42acd400b46e003a5e08bca93fee2c7efef548eb76bf949d [INFO] running `Command { std: "docker" "start" "-a" "33a0f3be38f51ecc42acd400b46e003a5e08bca93fee2c7efef548eb76bf949d", kill_on_drop: false }` [INFO] [stderr] warning: unused variable: `transcript` [INFO] [stderr] --> src/hgvs_name.rs:925:30 [INFO] [stderr] | [INFO] [stderr] 925 | fn get_ref_coords(&self, transcript: Option<&Transcript>) -> Option<(String, i64, i64)> { [INFO] [stderr] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_transcript` [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(unused_variables)]` on by default [INFO] [stderr] [INFO] [stderr] warning: unused variable: `transcript` [INFO] [stderr] --> src/hgvs_name.rs:929:30 [INFO] [stderr] | [INFO] [stderr] 929 | fn get_vcf_coords(&self, transcript: Option<&Transcript>) -> Option<(String, i64, i64)> { [INFO] [stderr] | ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_transcript` [INFO] [stderr] [INFO] [stderr] warning: unused variable: `coord` [INFO] [stderr] --> src/transcript.rs:78:41 [INFO] [stderr] | [INFO] [stderr] 78 | pub fn cdna_to_genomic_coord(&self, coord: &CDNACoord) -> u64 { [INFO] [stderr] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_coord` [INFO] [stderr] [INFO] [stderr] warning: methods `get_raw_coords`, `get_ref_coords`, and `get_vcf_coords` are never used [INFO] [stderr] --> src/hgvs_name.rs:904:8 [INFO] [stderr] | [INFO] [stderr] 369 | impl HGVSName { [INFO] [stderr] | ------------- methods in this implementation [INFO] [stderr] ... [INFO] [stderr] 904 | fn get_raw_coords(&self, transcript: Option<&Transcript>) -> Option<(String, i64, i64)> { [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 925 | fn get_ref_coords(&self, transcript: Option<&Transcript>) -> Option<(String, i64, i64)> { [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] ... [INFO] [stderr] 929 | fn get_vcf_coords(&self, transcript: Option<&Transcript>) -> Option<(String, i64, i64)> { [INFO] [stderr] | ^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` on by default [INFO] [stderr] [INFO] [stderr] warning: fields `start_codon_transcript_pos` and `stop_codon_transcript_pos` are never read [INFO] [stderr] --> src/transcript.rs:22:5 [INFO] [stderr] | [INFO] [stderr] 14 | pub struct Transcript { [INFO] [stderr] | ---------- fields in this struct [INFO] [stderr] ... [INFO] [stderr] 22 | start_codon_transcript_pos: Option, [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] 23 | stop_codon_transcript_pos: Option, [INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stderr] [INFO] [stderr] warning: `pyhgvs2` (lib) generated 5 warnings [INFO] [stderr] warning: `pyhgvs2` (lib test) generated 5 warnings (5 duplicates) [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 0.11s [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 3` [INFO] [stderr] Running unittests src/lib.rs (/opt/rustwide/target/debug/deps/pyhgvs2-23fa5d133f21a53f) [INFO] [stdout] [INFO] [stdout] running 2 tests [INFO] [stdout] test variants::tests::test_revcomp ... ok [INFO] [stdout] test genome::tests::test_genome_get ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 2 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stderr] Running unittests src/main.rs (/opt/rustwide/target/debug/deps/pyhgvs2-c1d99962205f73e2) [INFO] [stdout] [INFO] [stdout] running 0 tests [INFO] [stdout] [INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stderr] Doc-tests pyhgvs2 [INFO] [stdout] [INFO] [stdout] running 1 test [INFO] [stdout] test src/variants.rs - variants::revcomp (line 23) ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 1 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] running `Command { std: "docker" "inspect" "33a0f3be38f51ecc42acd400b46e003a5e08bca93fee2c7efef548eb76bf949d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "33a0f3be38f51ecc42acd400b46e003a5e08bca93fee2c7efef548eb76bf949d", kill_on_drop: false }` [INFO] [stdout] 33a0f3be38f51ecc42acd400b46e003a5e08bca93fee2c7efef548eb76bf949d