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[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/gmc-norr/bayesphase" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fgmc-norr%2Fbayesphase", kill_on_drop: false }`
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[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 17e294c6a7b8c2bf2d0d94936b3cb7bf055f75f0
[INFO] checking gmc-norr/bayesphase/17e294c6a7b8c2bf2d0d94936b3cb7bf055f75f0 against master#2aabf3ce0569dd7c8c2d2a27944850056dcf2566 for pr-156508
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fgmc-norr%2Fbayesphase" "/workspace/builds/worker-2-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-2-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/gmc-norr/bayesphase
[INFO] finished tweaking git repo https://github.com/gmc-norr/bayesphase
[INFO] tweaked toml for git repo https://github.com/gmc-norr/bayesphase written to /workspace/builds/worker-2-tc1/source/Cargo.toml
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[INFO] crate git repo https://github.com/gmc-norr/bayesphase 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" "+2aabf3ce0569dd7c8c2d2a27944850056dcf2566" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "inspect" "9f78af932e987fcd3f1135350299b5bd9d344114526eb2c9e34caf311af20eec", kill_on_drop: false }`
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[INFO] [stdout] warning: unused variable: `obs_ref`
[INFO] [stdout]    --> src/evidence/dna.rs:252:13
[INFO] [stdout]     |
[INFO] [stdout] 252 |         let obs_ref = make_obs(Allele::Ref, 30, 60);
[INFO] [stdout]     |             ^^^^^^^ help: if this is intentional, prefix it with an underscore: `_obs_ref`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `term`
[INFO] [stdout]    --> src/evidence/dna.rs:305:13
[INFO] [stdout]     |
[INFO] [stdout] 305 |         let term = score_dna_fragments(&fragments, 100, 200, &mut flags);
[INFO] [stdout]     |             ^^^^ help: if this is intentional, prefix it with an underscore: `_term`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `reference` is never read
[INFO] [stdout]   --> src/combiner.rs:32:9
[INFO] [stdout]    |
[INFO] [stdout] 24 | pub struct CombinerConfig {
[INFO] [stdout]    |            -------------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 32 |     pub reference: Option<String>,
[INFO] [stdout]    |         ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `CombinerConfig` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `is_empty` and `haplotype_for` are never used
[INFO] [stdout]   --> src/phaseblocks.rs:31:12
[INFO] [stdout]    |
[INFO] [stdout] 20 | impl PhaseBlock {
[INFO] [stdout]    | --------------- methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 31 |     pub fn is_empty(&self) -> bool {
[INFO] [stdout]    |            ^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 36 |     pub fn haplotype_for(&self, pos: u64) -> Option<u8> {
[INFO] [stdout]    |            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `is_reverse` and `nm` are never read
[INFO] [stdout]   --> src/types.rs:60:9
[INFO] [stdout]    |
[INFO] [stdout] 53 | pub struct AlleleObs {
[INFO] [stdout]    |            --------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 60 |     pub is_reverse: bool,
[INFO] [stdout]    |         ^^^^^^^^^^
[INFO] [stdout] 61 |     /// NM tag: total edit distance of the read.
[INFO] [stdout] 62 |     pub nm: Option<u32>,
[INFO] [stdout]    |         ^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `AlleleObs` 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: fields `qname` and `source` are never read
[INFO] [stdout]    --> src/types.rs:100:9
[INFO] [stdout]     |
[INFO] [stdout]  99 | pub struct Fragment {
[INFO] [stdout]     |            -------- fields in this struct
[INFO] [stdout] 100 |     pub qname: String,
[INFO] [stdout]     |         ^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 104 |     pub source: FragmentSource,
[INFO] [stdout]     |         ^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `Fragment` 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: variants `Pedigree` and `CopyNumber` are never constructed
[INFO] [stdout]    --> src/types.rs:137:5
[INFO] [stdout]     |
[INFO] [stdout] 133 | pub enum EvidenceSource {
[INFO] [stdout]     |          -------------- variants in this enum
[INFO] [stdout] ...
[INFO] [stdout] 137 |     Pedigree,
[INFO] [stdout]     |     ^^^^^^^^
[INFO] [stdout] 138 |     CopyNumber,
[INFO] [stdout]     |     ^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `EvidenceSource` 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: field `reference` is never read
[INFO] [stdout]   --> src/combiner.rs:32:9
[INFO] [stdout]    |
[INFO] [stdout] 24 | pub struct CombinerConfig {
[INFO] [stdout]    |            -------------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 32 |     pub reference: Option<String>,
[INFO] [stdout]    |         ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `CombinerConfig` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `flat_prior` is never used
[INFO] [stdout]    --> src/evidence/population.rs:117:8
[INFO] [stdout]     |
[INFO] [stdout] 117 | pub fn flat_prior() -> EvidenceTerm {
[INFO] [stdout]     |        ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `prior_from_confidence` is never used
[INFO] [stdout]    --> src/evidence/population.rs:128:8
[INFO] [stdout]     |
[INFO] [stdout] 128 | pub fn prior_from_confidence(confidence: f64, is_same_haplotype: bool) -> EvidenceTerm {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `is_empty` and `haplotype_for` are never used
[INFO] [stdout]   --> src/phaseblocks.rs:31:12
[INFO] [stdout]    |
[INFO] [stdout] 20 | impl PhaseBlock {
[INFO] [stdout]    | --------------- methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 31 |     pub fn is_empty(&self) -> bool {
[INFO] [stdout]    |            ^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 36 |     pub fn haplotype_for(&self, pos: u64) -> Option<u8> {
[INFO] [stdout]    |            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `is_reverse` and `nm` are never read
[INFO] [stdout]   --> src/types.rs:60:9
[INFO] [stdout]    |
[INFO] [stdout] 53 | pub struct AlleleObs {
[INFO] [stdout]    |            --------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 60 |     pub is_reverse: bool,
[INFO] [stdout]    |         ^^^^^^^^^^
[INFO] [stdout] 61 |     /// NM tag: total edit distance of the read.
[INFO] [stdout] 62 |     pub nm: Option<u32>,
[INFO] [stdout]    |         ^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `AlleleObs` 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: fields `qname` and `source` are never read
[INFO] [stdout]    --> src/types.rs:100:9
[INFO] [stdout]     |
[INFO] [stdout]  99 | pub struct Fragment {
[INFO] [stdout]     |            -------- fields in this struct
[INFO] [stdout] 100 |     pub qname: String,
[INFO] [stdout]     |         ^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 104 |     pub source: FragmentSource,
[INFO] [stdout]     |         ^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `Fragment` 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: variants `Pedigree` and `CopyNumber` are never constructed
[INFO] [stdout]    --> src/types.rs:137:5
[INFO] [stdout]     |
[INFO] [stdout] 133 | pub enum EvidenceSource {
[INFO] [stdout]     |          -------------- variants in this enum
[INFO] [stdout] ...
[INFO] [stdout] 137 |     Pedigree,
[INFO] [stdout]     |     ^^^^^^^^
[INFO] [stdout] 138 |     CopyNumber,
[INFO] [stdout]     |     ^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `EvidenceSource` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 28s
[INFO] running `Command { std: "docker" "inspect" "9d28e6501af234576bb5bb2ea38a701ce861123549405a6d648d81095fdf0ac1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "9d28e6501af234576bb5bb2ea38a701ce861123549405a6d648d81095fdf0ac1", kill_on_drop: false }`
[INFO] [stdout] 9d28e6501af234576bb5bb2ea38a701ce861123549405a6d648d81095fdf0ac1
