[INFO] fetching crate rust-htslib 0.44.1... [INFO] checking rust-htslib-0.44.1 against master#af4a5a13a15fa0c60e06321077ef452f769b42fd for pr-122960-3 [INFO] extracting crate rust-htslib 0.44.1 into /workspace/builds/worker-2-tc1/source [INFO] validating manifest of crates.io crate rust-htslib 0.44.1 on toolchain af4a5a13a15fa0c60e06321077ef452f769b42fd [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking crates.io crate rust-htslib 0.44.1 [INFO] finished tweaking crates.io crate rust-htslib 0.44.1 [INFO] tweaked toml for crates.io crate rust-htslib 0.44.1 written to /workspace/builds/worker-2-tc1/source/Cargo.toml [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "generate-lockfile" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Locking 94 packages [INFO] [stderr] Adding ansi_term v0.11.0 (latest: v0.12.1) [INFO] [stderr] Adding bindgen v0.53.3 (latest: v0.69.4) [INFO] [stderr] Adding bitflags v1.3.2 (latest: v2.5.0) [INFO] [stderr] Adding cexpr v0.4.0 (latest: v0.6.0) [INFO] [stderr] Adding cfg-if v0.1.10 (latest: v1.0.0) [INFO] [stderr] Adding clang-sys v0.29.3 (latest: v1.7.0) [INFO] [stderr] Adding ctor v0.1.26 (latest: v0.2.7) [INFO] [stderr] Adding derive-new v0.5.9 (latest: v0.6.0) [INFO] [stderr] Adding heck v0.4.1 (latest: v0.5.0) [INFO] [stderr] Adding libdeflate-sys v0.7.5 (latest: v1.19.3) [INFO] [stderr] Adding libloading v0.5.2 (latest: v0.8.3) [INFO] [stderr] Adding linux-raw-sys v0.4.13 (latest: v0.6.4) [INFO] [stderr] Adding nom v5.1.3 (latest: v7.1.3) [INFO] [stderr] Adding peeking_take_while v0.1.2 (latest: v1.0.0) [INFO] [stderr] Adding pretty_assertions v0.6.1 (latest: v1.4.0) [INFO] [stderr] Adding quick-error v1.2.3 (latest: v2.0.1) [INFO] [stderr] Adding rustc_version v0.1.7 (latest: v0.4.0) [INFO] [stderr] Adding semver v0.1.20 (latest: v1.0.22) [INFO] [stderr] Adding shlex v0.1.1 (latest: v1.3.0) [INFO] [stderr] Adding strum_macros v0.25.3 (latest: v0.26.2) [INFO] [stderr] Adding syn v1.0.109 (latest: v2.0.57) [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded linear-map v1.2.0 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded libdeflate-sys v0.7.5 [INFO] [stderr] Downloaded ieee754 v0.2.6 [INFO] [stderr] Downloaded pretty_assertions v0.6.1 [INFO] [stderr] Downloaded hts-sys v2.1.1 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 5072a2c5ab6143170d3d984f2433dfd413f83f94df6509fde25bf2316c9eff5a [INFO] running `Command { std: "docker" "start" "-a" "5072a2c5ab6143170d3d984f2433dfd413f83f94df6509fde25bf2316c9eff5a", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "5072a2c5ab6143170d3d984f2433dfd413f83f94df6509fde25bf2316c9eff5a", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "5072a2c5ab6143170d3d984f2433dfd413f83f94df6509fde25bf2316c9eff5a", kill_on_drop: false }` [INFO] [stdout] 5072a2c5ab6143170d3d984f2433dfd413f83f94df6509fde25bf2316c9eff5a [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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" "-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+af4a5a13a15fa0c60e06321077ef452f769b42fd" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 9991fcac554713df7b35507c51a0069e334473273f79bec134c3a0111d4d8270 [INFO] running `Command { std: "docker" "start" "-a" "9991fcac554713df7b35507c51a0069e334473273f79bec134c3a0111d4d8270", kill_on_drop: false }` [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling libc v0.2.153 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Compiling syn v2.0.57 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking difference v2.0.0 [INFO] [stderr] Checking bincode v1.3.3 [INFO] [stderr] Checking serde_json v1.0.115 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Checking pretty_assertions v0.6.1 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling jobserver v0.1.28 [INFO] [stderr] Compiling cc v1.0.90 [INFO] [stderr] Compiling openssl-src v300.2.3+3.2.1 [INFO] [stderr] Compiling cmake v0.1.50 [INFO] [stderr] Compiling thiserror-impl v1.0.58 [INFO] [stderr] Compiling strum_macros v0.25.3 [INFO] [stderr] Compiling openssl-sys v0.9.102 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling curl-sys v0.4.72+curl-8.6.0 [INFO] [stderr] Compiling hts-sys v2.1.1 [INFO] [stderr] Compiling libz-sys v1.1.16 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Checking thiserror v1.0.58 [INFO] [stderr] Checking bio-types v1.0.1 [INFO] [stderr] Checking rust-htslib v0.44.1 (/opt/rustwide/workdir) [INFO] [stdout] error: couldn't read `src/bgzf/../../test/bgzip/plain.vcf`: No such file or directory (os error 2) [INFO] [stdout] --> src/bgzf/mod.rs:309:27 [INFO] [stdout] | [INFO] [stdout] 309 | const CONTENT: &str = include_str!("../../test/bgzip/plain.vcf"); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: this error originates in the macro `include_str` (in Nightly builds, run with -Z macro-backtrace for more info) [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `bam` is imported redundantly [INFO] [stdout] --> src/bam/buffer.rs:179:9 [INFO] [stdout] | [INFO] [stdout] 178 | use super::*; [INFO] [stdout] | -------- the item `bam` is already imported here [INFO] [stdout] 179 | use crate::bam; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `Alignment` is imported redundantly [INFO] [stdout] --> src/bam/record.rs:2719:32 [INFO] [stdout] | [INFO] [stdout] 2716 | use super::*; [INFO] [stdout] | -------- the item `Alignment` is already imported here [INFO] [stdout] ... [INFO] [stdout] 2719 | use bio_types::alignment::{Alignment, AlignmentMode}; [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `AlignmentMode` is imported redundantly [INFO] [stdout] --> src/bam/record.rs:2719:43 [INFO] [stdout] | [INFO] [stdout] 2716 | use super::*; [INFO] [stdout] | -------- the item `AlignmentMode` is already imported here [INFO] [stdout] ... [INFO] [stdout] 2719 | use bio_types::alignment::{Alignment, AlignmentMode}; [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `Path` is imported redundantly [INFO] [stdout] --> src/bam/mod.rs:1506:9 [INFO] [stdout] | [INFO] [stdout] 1503 | use super::*; [INFO] [stdout] | -------- the item `Path` is already imported here [INFO] [stdout] ... [INFO] [stdout] 1506 | use std::path::Path; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `str` is imported redundantly [INFO] [stdout] --> src/bam/mod.rs:1507:9 [INFO] [stdout] | [INFO] [stdout] 1503 | use super::*; [INFO] [stdout] | -------- the item `str` is already imported here [INFO] [stdout] ... [INFO] [stdout] 1507 | use std::str; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `bcf` is imported redundantly [INFO] [stdout] --> src/bcf/buffer.rs:191:9 [INFO] [stdout] | [INFO] [stdout] 190 | use super::*; [INFO] [stdout] | -------- the item `bcf` is already imported here [INFO] [stdout] 191 | use crate::bcf; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `Reader` is imported redundantly [INFO] [stdout] --> src/bcf/mod.rs:842:9 [INFO] [stdout] | [INFO] [stdout] 838 | use super::*; [INFO] [stdout] | -------- the item `Reader` is already imported here [INFO] [stdout] ... [INFO] [stdout] 842 | use crate::bcf::Reader; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `Path` is imported redundantly [INFO] [stdout] --> src/bcf/mod.rs:846:9 [INFO] [stdout] | [INFO] [stdout] 838 | use super::*; [INFO] [stdout] | -------- the item `Path` is already imported here [INFO] [stdout] ... [INFO] [stdout] 846 | use std::path::Path; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the item `str` is imported redundantly [INFO] [stdout] --> src/bcf/mod.rs:847:9 [INFO] [stdout] | [INFO] [stdout] 838 | use super::*; [INFO] [stdout] | -------- the item `str` is already imported here [INFO] [stdout] ... [INFO] [stdout] 847 | use std::str; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `buffer` is never read [INFO] [stdout] --> src/bcf/record.rs:134:5 [INFO] [stdout] | [INFO] [stdout] 132 | pub struct BufferBacked<'a, T: 'a + fmt::Debug, B: Borrow + 'a> { [INFO] [stdout] | ------------ field in this struct [INFO] [stdout] 133 | value: T, [INFO] [stdout] 134 | buffer: B, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `BufferBacked` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `hts_format` is never read [INFO] [stdout] --> src/tbx/mod.rs:94:5 [INFO] [stdout] | [INFO] [stdout] 87 | pub struct Reader { [INFO] [stdout] | ------ field in this struct [INFO] [stdout] ... [INFO] [stdout] 94 | hts_format: htslib::htsExactFormat, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Reader` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: the type `hts_sys::bam1_t` does not permit being left uninitialized [INFO] [stdout] --> src/bam/record.rs:128:42 [INFO] [stdout] | [INFO] [stdout] 128 | let mut inner = unsafe { MaybeUninit::uninit().assume_init() }; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | this code causes undefined behavior when executed [INFO] [stdout] | help: use `MaybeUninit` instead, and only call `assume_init` after initialization is done [INFO] [stdout] | [INFO] [stdout] = note: integers must be initialized [INFO] [stdout] = note: `#[warn(invalid_value)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 3 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error; 9 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `rust-htslib` (lib test) due to 2 previous errors; 9 warnings emitted [INFO] running `Command { std: "docker" "inspect" "9991fcac554713df7b35507c51a0069e334473273f79bec134c3a0111d4d8270", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "9991fcac554713df7b35507c51a0069e334473273f79bec134c3a0111d4d8270", kill_on_drop: false }` [INFO] [stdout] 9991fcac554713df7b35507c51a0069e334473273f79bec134c3a0111d4d8270 [INFO] checking rust-htslib-0.44.1 against try#36dbcaee1a55543dfc181be52a69d99ff46ff62f for pr-122960-3 [INFO] extracting crate rust-htslib 0.44.1 into /workspace/builds/worker-2-tc2/source [INFO] validating manifest of crates.io crate rust-htslib 0.44.1 on toolchain 36dbcaee1a55543dfc181be52a69d99ff46ff62f [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking crates.io crate rust-htslib 0.44.1 [INFO] finished tweaking crates.io crate rust-htslib 0.44.1 [INFO] tweaked toml for crates.io crate rust-htslib 0.44.1 written to /workspace/builds/worker-2-tc2/source/Cargo.toml [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "generate-lockfile" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 07ddb536f8caac4c28745ac0c9cb6b04b9bfcf36834a5968c1d7f678b46bf67e [INFO] running `Command { std: "docker" "start" "-a" "07ddb536f8caac4c28745ac0c9cb6b04b9bfcf36834a5968c1d7f678b46bf67e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "07ddb536f8caac4c28745ac0c9cb6b04b9bfcf36834a5968c1d7f678b46bf67e", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "07ddb536f8caac4c28745ac0c9cb6b04b9bfcf36834a5968c1d7f678b46bf67e", kill_on_drop: false }` [INFO] [stdout] 07ddb536f8caac4c28745ac0c9cb6b04b9bfcf36834a5968c1d7f678b46bf67e [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-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@sha256:2788e3201cd34a07e3172128adcd8b3090168a8e3bcc40d7c032b9dda1df7d1c" "/opt/rustwide/cargo-home/bin/cargo" "+36dbcaee1a55543dfc181be52a69d99ff46ff62f" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] e113a43f9ca83870a3445ca6bb4ea0c941c7bb37a052856e5fa9787587dc2d92 [INFO] running `Command { std: "docker" "start" "-a" "e113a43f9ca83870a3445ca6bb4ea0c941c7bb37a052856e5fa9787587dc2d92", kill_on_drop: false }` [INFO] [stderr] Copying to /tmp/fixit [INFO] [stderr] skipping non-2021 edition `2018` [INFO] running `Command { std: "docker" "inspect" "e113a43f9ca83870a3445ca6bb4ea0c941c7bb37a052856e5fa9787587dc2d92", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "e113a43f9ca83870a3445ca6bb4ea0c941c7bb37a052856e5fa9787587dc2d92", kill_on_drop: false }` [INFO] [stdout] e113a43f9ca83870a3445ca6bb4ea0c941c7bb37a052856e5fa9787587dc2d92