[INFO] cloning repository https://github.com/JamesAsaki/atx_count_test
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/JamesAsaki/atx_count_test" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FJamesAsaki%2Fatx_count_test", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FJamesAsaki%2Fatx_count_test'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 191ab12f86182a5fc88a81772b65f4367809ab84
[INFO] testing JamesAsaki/atx_count_test against try#b8e88e5ddf5521a9f43ee3f62a702388c713e4bb for pr-155114
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FJamesAsaki%2Fatx_count_test" "/workspace/builds/worker-4-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-4-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/JamesAsaki/atx_count_test
[INFO] finished tweaking git repo https://github.com/JamesAsaki/atx_count_test
[INFO] tweaked toml for git repo https://github.com/JamesAsaki/atx_count_test written to /workspace/builds/worker-4-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/JamesAsaki/atx_count_test on toolchain b8e88e5ddf5521a9f43ee3f62a702388c713e4bb
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+b8e88e5ddf5521a9f43ee3f62a702388c713e4bb" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/JamesAsaki/atx_count_test 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" "+b8e88e5ddf5521a9f43ee3f62a702388c713e4bb" "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] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+b8e88e5ddf5521a9f43ee3f62a702388c713e4bb" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 072699ccb48e6f26dccfad4eb75678715e8f2b92af558db632bb8fae921b7dd6
[INFO] running `Command { std: "docker" "start" "-a" "072699ccb48e6f26dccfad4eb75678715e8f2b92af558db632bb8fae921b7dd6", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "072699ccb48e6f26dccfad4eb75678715e8f2b92af558db632bb8fae921b7dd6", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "072699ccb48e6f26dccfad4eb75678715e8f2b92af558db632bb8fae921b7dd6", kill_on_drop: false }`
[INFO] [stdout] 072699ccb48e6f26dccfad4eb75678715e8f2b92af558db632bb8fae921b7dd6
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+b8e88e5ddf5521a9f43ee3f62a702388c713e4bb" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 313b9a08d2b28d50fe2a50cd94c53bd2dd26693cf2b62b01b01189b298b2125a
[INFO] running `Command { std: "docker" "start" "-a" "313b9a08d2b28d50fe2a50cd94c53bd2dd26693cf2b62b01b01189b298b2125a", kill_on_drop: false }`
[INFO] [stderr]    Compiling Codex_ATX-count v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: struct `RraGeneRow` is never constructed
[INFO] [stdout]     --> src/main.rs:1152:8
[INFO] [stdout]      |
[INFO] [stdout] 1152 | struct RraGeneRow {
[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 `nan_count`, `min`, `q99`, and `max` are never read
[INFO] [stdout]     --> src/main.rs:1174:5
[INFO] [stdout]      |
[INFO] [stdout] 1170 | struct NativeRraPermRow {
[INFO] [stdout]      |        ---------------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 1174 |     nan_count: usize,
[INFO] [stdout]      |     ^^^^^^^^^
[INFO] [stdout] 1175 |     min: f64,
[INFO] [stdout]      |     ^^^
[INFO] [stdout] ...
[INFO] [stdout] 1178 |     q99: f64,
[INFO] [stdout]      |     ^^^
[INFO] [stdout] 1179 |     max: f64,
[INFO] [stdout]      |     ^^^
[INFO] [stdout]      |
[INFO] [stdout]      = note: `NativeRraPermRow` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `choose_rra_path` is never used
[INFO] [stdout]     --> src/main.rs:1197:4
[INFO] [stdout]      |
[INFO] [stdout] 1197 | fn choose_rra_path(flags: &HashMap<String, Vec<String>>) -> String {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `write_rra_input` is never used
[INFO] [stdout]     --> src/main.rs:1214:4
[INFO] [stdout]      |
[INFO] [stdout] 1214 | fn write_rra_input(
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `run_rra_command` is never used
[INFO] [stdout]     --> src/main.rs:1241:4
[INFO] [stdout]      |
[INFO] [stdout] 1241 | fn run_rra_command(input: &str, output: &str, cutoff: f64, adjust_cutoff: bool, rra_path: &str) -> AppResult<()> {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `parse_rra_output` is never used
[INFO] [stdout]     --> src/main.rs:1270:4
[INFO] [stdout]      |
[INFO] [stdout] 1270 | fn parse_rra_output(path: &str) -> AppResult<HashMap<String, RraGeneRow>> {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `compute_gene_stats_with_external_rra` is never used
[INFO] [stdout]     --> src/main.rs:1316:4
[INFO] [stdout]      |
[INFO] [stdout] 1316 | fn compute_gene_stats_with_external_rra(
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `match_guide_with_status` is never used
[INFO] [stdout]     --> src/main.rs:2157:4
[INFO] [stdout]      |
[INFO] [stdout] 2157 | fn match_guide_with_status(
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `match_no_n` is never used
[INFO] [stdout]     --> src/main.rs:2213:4
[INFO] [stdout]      |
[INFO] [stdout] 2213 | fn match_no_n(
[INFO] [stdout]      |    ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `resolve_n_candidates` is never used
[INFO] [stdout]     --> src/main.rs:2305:4
[INFO] [stdout]      |
[INFO] [stdout] 2305 | fn resolve_n_candidates(
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `exact_lookup` is never used
[INFO] [stdout]     --> src/main.rs:2543:4
[INFO] [stdout]      |
[INFO] [stdout] 2543 | fn exact_lookup(
[INFO] [stdout]      |    ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `min_window_hamming` is never used
[INFO] [stdout]     --> src/main.rs:2612:4
[INFO] [stdout]      |
[INFO] [stdout] 2612 | fn min_window_hamming(read: &str, guide: &str, max_mismatch: usize) -> Option<usize> {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `build_sample_groups` is never used
[INFO] [stdout]     --> src/main.rs:3083:4
[INFO] [stdout]      |
[INFO] [stdout] 3083 | fn build_sample_groups(
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `estimate_shrunk_dispersions` is never used
[INFO] [stdout]     --> src/main.rs:3104:4
[INFO] [stdout]      |
[INFO] [stdout] 3104 | fn estimate_shrunk_dispersions(norm: &[Vec<f64>]) -> Vec<f64> {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `nb_glm_lrt` is never used
[INFO] [stdout]     --> src/main.rs:3127:4
[INFO] [stdout]      |
[INFO] [stdout] 3127 | fn nb_glm_lrt(y: &[u64], size_factors: &[f64], groups: &[f64], alpha: f64) -> (f64, f64, f64) {
[INFO] [stdout]      |    ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `NbFit0` is never constructed
[INFO] [stdout]     --> src/main.rs:3143:8
[INFO] [stdout]      |
[INFO] [stdout] 3143 | struct NbFit0 {
[INFO] [stdout]      |        ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `NbFit1` is never constructed
[INFO] [stdout]     --> src/main.rs:3147:8
[INFO] [stdout]      |
[INFO] [stdout] 3147 | struct NbFit1 {
[INFO] [stdout]      |        ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `fit_nb_intercept_only` is never used
[INFO] [stdout]     --> src/main.rs:3153:4
[INFO] [stdout]      |
[INFO] [stdout] 3153 | fn fit_nb_intercept_only(y: &[f64], offsets: &[f64], alpha: f64) -> NbFit0 {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `fit_nb_with_group` is never used
[INFO] [stdout]     --> src/main.rs:3183:4
[INFO] [stdout]      |
[INFO] [stdout] 3183 | fn fit_nb_with_group(y: &[f64], offsets: &[f64], groups: &[f64], alpha: f64) -> NbFit1 {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `nb_logpmf` is never used
[INFO] [stdout]     --> src/main.rs:3240:4
[INFO] [stdout]      |
[INFO] [stdout] 3240 | fn nb_logpmf(y: f64, mu: f64, alpha: f64) -> f64 {
[INFO] [stdout]      |    ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `rra_pvalue_from_ranks` is never used
[INFO] [stdout]     --> src/main.rs:3261:4
[INFO] [stdout]      |
[INFO] [stdout] 3261 | fn rra_pvalue_from_ranks(ranks: &[usize], total_guides: usize) -> f64 {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `chi_square_1df_sf` is never used
[INFO] [stdout]     --> src/main.rs:3282:4
[INFO] [stdout]      |
[INFO] [stdout] 3282 | fn chi_square_1df_sf(x: f64) -> f64 {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `regularized_incomplete_beta` is never used
[INFO] [stdout]     --> src/main.rs:3290:4
[INFO] [stdout]      |
[INFO] [stdout] 3290 | fn regularized_incomplete_beta(a: f64, b: f64, x: f64) -> f64 {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `betacf` is never used
[INFO] [stdout]     --> src/main.rs:3306:4
[INFO] [stdout]      |
[INFO] [stdout] 3306 | fn betacf(a: f64, b: f64, x: f64) -> f64 {
[INFO] [stdout]      |    ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `log_gamma` is never used
[INFO] [stdout]     --> src/main.rs:3352:4
[INFO] [stdout]      |
[INFO] [stdout] 3352 | fn log_gamma(z: f64) -> f64 {
[INFO] [stdout]      |    ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `mean` is never used
[INFO] [stdout]     --> src/main.rs:3492:4
[INFO] [stdout]      |
[INFO] [stdout] 3492 | fn mean(vals: &[f64]) -> f64 {
[INFO] [stdout]      |    ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `variance` is never used
[INFO] [stdout]     --> src/main.rs:3500:4
[INFO] [stdout]      |
[INFO] [stdout] 3500 | fn variance(vals: &[f64]) -> f64 {
[INFO] [stdout]      |    ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `benjamini_hochberg` is never used
[INFO] [stdout]     --> src/main.rs:3522:4
[INFO] [stdout]      |
[INFO] [stdout] 3522 | fn benjamini_hochberg(pvals: &[f64]) -> Vec<f64> {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1.60s
[INFO] running `Command { std: "docker" "inspect" "313b9a08d2b28d50fe2a50cd94c53bd2dd26693cf2b62b01b01189b298b2125a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "313b9a08d2b28d50fe2a50cd94c53bd2dd26693cf2b62b01b01189b298b2125a", kill_on_drop: false }`
[INFO] [stdout] 313b9a08d2b28d50fe2a50cd94c53bd2dd26693cf2b62b01b01189b298b2125a
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+b8e88e5ddf5521a9f43ee3f62a702388c713e4bb" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] e119216f05a981690b8a698cfe5e75374bc18e245a5766f3dceffc4f17cd6140
[INFO] running `Command { std: "docker" "start" "-a" "e119216f05a981690b8a698cfe5e75374bc18e245a5766f3dceffc4f17cd6140", kill_on_drop: false }`
[INFO] [stderr]    Compiling Codex_ATX-count v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: struct `RraGeneRow` is never constructed
[INFO] [stdout]     --> src/main.rs:1152:8
[INFO] [stdout]      |
[INFO] [stdout] 1152 | struct RraGeneRow {
[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 `nan_count`, `min`, `q99`, and `max` are never read
[INFO] [stdout]     --> src/main.rs:1174:5
[INFO] [stdout]      |
[INFO] [stdout] 1170 | struct NativeRraPermRow {
[INFO] [stdout]      |        ---------------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 1174 |     nan_count: usize,
[INFO] [stdout]      |     ^^^^^^^^^
[INFO] [stdout] 1175 |     min: f64,
[INFO] [stdout]      |     ^^^
[INFO] [stdout] ...
[INFO] [stdout] 1178 |     q99: f64,
[INFO] [stdout]      |     ^^^
[INFO] [stdout] 1179 |     max: f64,
[INFO] [stdout]      |     ^^^
[INFO] [stdout]      |
[INFO] [stdout]      = note: `NativeRraPermRow` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `choose_rra_path` is never used
[INFO] [stdout]     --> src/main.rs:1197:4
[INFO] [stdout]      |
[INFO] [stdout] 1197 | fn choose_rra_path(flags: &HashMap<String, Vec<String>>) -> String {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `write_rra_input` is never used
[INFO] [stdout]     --> src/main.rs:1214:4
[INFO] [stdout]      |
[INFO] [stdout] 1214 | fn write_rra_input(
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `run_rra_command` is never used
[INFO] [stdout]     --> src/main.rs:1241:4
[INFO] [stdout]      |
[INFO] [stdout] 1241 | fn run_rra_command(input: &str, output: &str, cutoff: f64, adjust_cutoff: bool, rra_path: &str) -> AppResult<()> {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `parse_rra_output` is never used
[INFO] [stdout]     --> src/main.rs:1270:4
[INFO] [stdout]      |
[INFO] [stdout] 1270 | fn parse_rra_output(path: &str) -> AppResult<HashMap<String, RraGeneRow>> {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `compute_gene_stats_with_external_rra` is never used
[INFO] [stdout]     --> src/main.rs:1316:4
[INFO] [stdout]      |
[INFO] [stdout] 1316 | fn compute_gene_stats_with_external_rra(
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `build_sample_groups` is never used
[INFO] [stdout]     --> src/main.rs:3083:4
[INFO] [stdout]      |
[INFO] [stdout] 3083 | fn build_sample_groups(
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `estimate_shrunk_dispersions` is never used
[INFO] [stdout]     --> src/main.rs:3104:4
[INFO] [stdout]      |
[INFO] [stdout] 3104 | fn estimate_shrunk_dispersions(norm: &[Vec<f64>]) -> Vec<f64> {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `nb_glm_lrt` is never used
[INFO] [stdout]     --> src/main.rs:3127:4
[INFO] [stdout]      |
[INFO] [stdout] 3127 | fn nb_glm_lrt(y: &[u64], size_factors: &[f64], groups: &[f64], alpha: f64) -> (f64, f64, f64) {
[INFO] [stdout]      |    ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `NbFit0` is never constructed
[INFO] [stdout]     --> src/main.rs:3143:8
[INFO] [stdout]      |
[INFO] [stdout] 3143 | struct NbFit0 {
[INFO] [stdout]      |        ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `NbFit1` is never constructed
[INFO] [stdout]     --> src/main.rs:3147:8
[INFO] [stdout]      |
[INFO] [stdout] 3147 | struct NbFit1 {
[INFO] [stdout]      |        ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `fit_nb_intercept_only` is never used
[INFO] [stdout]     --> src/main.rs:3153:4
[INFO] [stdout]      |
[INFO] [stdout] 3153 | fn fit_nb_intercept_only(y: &[f64], offsets: &[f64], alpha: f64) -> NbFit0 {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `fit_nb_with_group` is never used
[INFO] [stdout]     --> src/main.rs:3183:4
[INFO] [stdout]      |
[INFO] [stdout] 3183 | fn fit_nb_with_group(y: &[f64], offsets: &[f64], groups: &[f64], alpha: f64) -> NbFit1 {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `nb_logpmf` is never used
[INFO] [stdout]     --> src/main.rs:3240:4
[INFO] [stdout]      |
[INFO] [stdout] 3240 | fn nb_logpmf(y: f64, mu: f64, alpha: f64) -> f64 {
[INFO] [stdout]      |    ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `rra_pvalue_from_ranks` is never used
[INFO] [stdout]     --> src/main.rs:3261:4
[INFO] [stdout]      |
[INFO] [stdout] 3261 | fn rra_pvalue_from_ranks(ranks: &[usize], total_guides: usize) -> f64 {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `chi_square_1df_sf` is never used
[INFO] [stdout]     --> src/main.rs:3282:4
[INFO] [stdout]      |
[INFO] [stdout] 3282 | fn chi_square_1df_sf(x: f64) -> f64 {
[INFO] [stdout]      |    ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `mean` is never used
[INFO] [stdout]     --> src/main.rs:3492:4
[INFO] [stdout]      |
[INFO] [stdout] 3492 | fn mean(vals: &[f64]) -> f64 {
[INFO] [stdout]      |    ^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `variance` is never used
[INFO] [stdout]     --> src/main.rs:3500:4
[INFO] [stdout]      |
[INFO] [stdout] 3500 | fn variance(vals: &[f64]) -> f64 {
[INFO] [stdout]      |    ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.98s
[INFO] running `Command { std: "docker" "inspect" "e119216f05a981690b8a698cfe5e75374bc18e245a5766f3dceffc4f17cd6140", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "e119216f05a981690b8a698cfe5e75374bc18e245a5766f3dceffc4f17cd6140", kill_on_drop: false }`
[INFO] [stdout] e119216f05a981690b8a698cfe5e75374bc18e245a5766f3dceffc4f17cd6140
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+b8e88e5ddf5521a9f43ee3f62a702388c713e4bb" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] a5007f551743f1f42273ae62d31ebfc594709e9ba675b3a44a2d14110ff90ede
[INFO] running `Command { std: "docker" "start" "-a" "a5007f551743f1f42273ae62d31ebfc594709e9ba675b3a44a2d14110ff90ede", kill_on_drop: false }`
[INFO] [stderr] warning: struct `RraGeneRow` is never constructed
[INFO] [stderr]     --> src/main.rs:1152:8
[INFO] [stderr]      |
[INFO] [stderr] 1152 | struct RraGeneRow {
[INFO] [stderr]      |        ^^^^^^^^^^
[INFO] [stderr]      |
[INFO] [stderr]      = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: fields `nan_count`, `min`, `q99`, and `max` are never read
[INFO] [stderr]     --> src/main.rs:1174:5
[INFO] [stderr]      |
[INFO] [stderr] 1170 | struct NativeRraPermRow {
[INFO] [stderr]      |        ---------------- fields in this struct
[INFO] [stderr] ...
[INFO] [stderr] 1174 |     nan_count: usize,
[INFO] [stderr]      |     ^^^^^^^^^
[INFO] [stderr] 1175 |     min: f64,
[INFO] [stderr]      |     ^^^
[INFO] [stderr] ...
[INFO] [stderr] 1178 |     q99: f64,
[INFO] [stderr]      |     ^^^
[INFO] [stderr] 1179 |     max: f64,
[INFO] [stderr]      |     ^^^
[INFO] [stderr]      |
[INFO] [stderr]      = note: `NativeRraPermRow` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stderr] 
[INFO] [stderr] warning: function `choose_rra_path` is never used
[INFO] [stderr]     --> src/main.rs:1197:4
[INFO] [stderr]      |
[INFO] [stderr] 1197 | fn choose_rra_path(flags: &HashMap<String, Vec<String>>) -> String {
[INFO] [stderr]      |    ^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `write_rra_input` is never used
[INFO] [stderr]     --> src/main.rs:1214:4
[INFO] [stderr]      |
[INFO] [stderr] 1214 | fn write_rra_input(
[INFO] [stderr]      |    ^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `run_rra_command` is never used
[INFO] [stderr]     --> src/main.rs:1241:4
[INFO] [stderr]      |
[INFO] [stderr] 1241 | fn run_rra_command(input: &str, output: &str, cutoff: f64, adjust_cutoff: bool, rra_path: &str) -> AppResult<()> {
[INFO] [stderr]      |    ^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `parse_rra_output` is never used
[INFO] [stderr]     --> src/main.rs:1270:4
[INFO] [stderr]      |
[INFO] [stderr] 1270 | fn parse_rra_output(path: &str) -> AppResult<HashMap<String, RraGeneRow>> {
[INFO] [stderr]      |    ^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `compute_gene_stats_with_external_rra` is never used
[INFO] [stderr]     --> src/main.rs:1316:4
[INFO] [stderr]      |
[INFO] [stderr] 1316 | fn compute_gene_stats_with_external_rra(
[INFO] [stderr]      |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `build_sample_groups` is never used
[INFO] [stderr]     --> src/main.rs:3083:4
[INFO] [stderr]      |
[INFO] [stderr] 3083 | fn build_sample_groups(
[INFO] [stderr]      |    ^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `estimate_shrunk_dispersions` is never used
[INFO] [stderr]     --> src/main.rs:3104:4
[INFO] [stderr]      |
[INFO] [stderr] 3104 | fn estimate_shrunk_dispersions(norm: &[Vec<f64>]) -> Vec<f64> {
[INFO] [stderr]      |    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `nb_glm_lrt` is never used
[INFO] [stderr]     --> src/main.rs:3127:4
[INFO] [stderr]      |
[INFO] [stderr] 3127 | fn nb_glm_lrt(y: &[u64], size_factors: &[f64], groups: &[f64], alpha: f64) -> (f64, f64, f64) {
[INFO] [stderr]      |    ^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: struct `NbFit0` is never constructed
[INFO] [stderr]     --> src/main.rs:3143:8
[INFO] [stderr]      |
[INFO] [stderr] 3143 | struct NbFit0 {
[INFO] [stderr]      |        ^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: struct `NbFit1` is never constructed
[INFO] [stderr]     --> src/main.rs:3147:8
[INFO] [stderr]      |
[INFO] [stderr] 3147 | struct NbFit1 {
[INFO] [stderr]      |        ^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `fit_nb_intercept_only` is never used
[INFO] [stderr]     --> src/main.rs:3153:4
[INFO] [stderr]      |
[INFO] [stderr] 3153 | fn fit_nb_intercept_only(y: &[f64], offsets: &[f64], alpha: f64) -> NbFit0 {
[INFO] [stderr]      |    ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `fit_nb_with_group` is never used
[INFO] [stderr]     --> src/main.rs:3183:4
[INFO] [stderr]      |
[INFO] [stderr] 3183 | fn fit_nb_with_group(y: &[f64], offsets: &[f64], groups: &[f64], alpha: f64) -> NbFit1 {
[INFO] [stderr]      |    ^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `nb_logpmf` is never used
[INFO] [stderr]     --> src/main.rs:3240:4
[INFO] [stderr]      |
[INFO] [stderr] 3240 | fn nb_logpmf(y: f64, mu: f64, alpha: f64) -> f64 {
[INFO] [stderr]      |    ^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `rra_pvalue_from_ranks` is never used
[INFO] [stderr]     --> src/main.rs:3261:4
[INFO] [stderr]      |
[INFO] [stderr] 3261 | fn rra_pvalue_from_ranks(ranks: &[usize], total_guides: usize) -> f64 {
[INFO] [stderr]      |    ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `chi_square_1df_sf` is never used
[INFO] [stderr]     --> src/main.rs:3282:4
[INFO] [stderr]      |
[INFO] [stderr] 3282 | fn chi_square_1df_sf(x: f64) -> f64 {
[INFO] [stderr]      |    ^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `mean` is never used
[INFO] [stderr]     --> src/main.rs:3492:4
[INFO] [stderr]      |
[INFO] [stderr] 3492 | fn mean(vals: &[f64]) -> f64 {
[INFO] [stderr]      |    ^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `variance` is never used
[INFO] [stderr]     --> src/main.rs:3500:4
[INFO] [stderr]      |
[INFO] [stderr] 3500 | fn variance(vals: &[f64]) -> f64 {
[INFO] [stderr]      |    ^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: `Codex_ATX-count` (bin "Codex_ATX-count" test) generated 19 warnings
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.02s
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/Codex_ATX_count-a26c74882d3c595d)
[INFO] [stdout] 
[INFO] [stdout] running 9 tests
[INFO] [stdout] test tests::anchored_match_requires_guide_at_trim_start ... ok
[INFO] [stdout] test tests::bh_shape ... ok
[INFO] [stdout] test tests::exact_lookup_reports_match_start ... ok
[INFO] [stdout] test tests::infer_guide_start_handles_ns ... ok
[INFO] [stdout] test tests::gamma_and_beta_sanity ... ok
[INFO] [stdout] test tests::mismatch_match_works ... ok
[INFO] [stdout] test tests::sample_parse ... ok
[INFO] [stdout] test tests::trim_works ... ok
[INFO] [stdout] test tests::infer_trim_from_fastq_sample ... ok
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 9 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "a5007f551743f1f42273ae62d31ebfc594709e9ba675b3a44a2d14110ff90ede", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "a5007f551743f1f42273ae62d31ebfc594709e9ba675b3a44a2d14110ff90ede", kill_on_drop: false }`
[INFO] [stdout] a5007f551743f1f42273ae62d31ebfc594709e9ba675b3a44a2d14110ff90ede
