[INFO] fetching crate rust-htslib 0.47.0... [INFO] checking rust-htslib-0.47.0 against master#f609b7e0586f81fefb3523e3e17adf779ac416be for pr-129466-2 [INFO] extracting crate rust-htslib 0.47.0 into /workspace/builds/worker-1-tc1/source [INFO] validating manifest of crates.io crate rust-htslib 0.47.0 on toolchain f609b7e0586f81fefb3523e3e17adf779ac416be [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+f609b7e0586f81fefb3523e3e17adf779ac416be" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking crates.io crate rust-htslib 0.47.0 [INFO] finished tweaking crates.io crate rust-htslib 0.47.0 [INFO] tweaked toml for crates.io crate rust-htslib 0.47.0 written to /workspace/builds/worker-1-tc1/source/Cargo.toml [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+f609b7e0586f81fefb3523e3e17adf779ac416be" "generate-lockfile" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Locking 96 packages to latest compatible versions [INFO] [stderr] Adding ansi_term v0.11.0 (available: v0.12.1) [INFO] [stderr] Adding bindgen v0.69.4 (available: v0.70.1) [INFO] [stderr] Adding ctor v0.1.26 (available: v0.2.8) [INFO] [stderr] Adding derive-new v0.5.9 (available: v0.7.0) [INFO] [stderr] Adding derive-new v0.6.0 (available: v0.7.0) [INFO] [stderr] Adding idna v0.5.0 (available: v1.0.2) [INFO] [stderr] Adding itertools v0.12.1 (available: v0.13.0) [INFO] [stderr] Adding libdeflate-sys v0.7.5 (available: v1.21.0) [INFO] [stderr] Adding linux-raw-sys v0.4.14 (available: v0.6.5) [INFO] [stderr] Adding pretty_assertions v0.6.1 (available: v1.4.1) [INFO] [stderr] Adding quick-error v1.2.3 (available: v2.0.1) [INFO] [stderr] Adding rustc-hash v1.1.0 (available: v2.0.0) [INFO] [stderr] Adding rustc_version v0.1.7 (available: v0.4.1) [INFO] [stderr] Adding semver v0.1.20 (available: v1.0.23) [INFO] [stderr] Adding syn v1.0.109 (available: v2.0.77) [INFO] [stderr] Adding windows-sys v0.52.0 (available: v0.59.0) [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+f609b7e0586f81fefb3523e3e17adf779ac416be" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded bio-types v1.0.4 [INFO] [stderr] Downloaded libdeflate-sys v0.7.5 [INFO] [stderr] Downloaded hts-sys v2.1.4 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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:ceb6ea022f8a89cebbe621bb4987e73a935bd40dfbb726f832cfff4742a5b95a" "/opt/rustwide/cargo-home/bin/cargo" "+f609b7e0586f81fefb3523e3e17adf779ac416be" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 1b714b1c6c6b16f419708d2f1b1b4e1d6c733d272f12765aacd452d9b8ee2fd8 [INFO] running `Command { std: "docker" "start" "-a" "1b714b1c6c6b16f419708d2f1b1b4e1d6c733d272f12765aacd452d9b8ee2fd8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "1b714b1c6c6b16f419708d2f1b1b4e1d6c733d272f12765aacd452d9b8ee2fd8", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "1b714b1c6c6b16f419708d2f1b1b4e1d6c733d272f12765aacd452d9b8ee2fd8", kill_on_drop: false }` [INFO] [stdout] 1b714b1c6c6b16f419708d2f1b1b4e1d6c733d272f12765aacd452d9b8ee2fd8 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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:ceb6ea022f8a89cebbe621bb4987e73a935bd40dfbb726f832cfff4742a5b95a" "/opt/rustwide/cargo-home/bin/cargo" "+f609b7e0586f81fefb3523e3e17adf779ac416be" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 4bd3e616f5277604cad23a03abed70fe0e248d995b5577c1f12c517669e47947 [INFO] running `Command { std: "docker" "start" "-a" "4bd3e616f5277604cad23a03abed70fe0e248d995b5577c1f12c517669e47947", kill_on_drop: false }` [INFO] [stderr] Compiling memchr v2.7.4 [INFO] [stderr] Compiling regex-syntax v0.8.4 [INFO] [stderr] Compiling bindgen v0.69.4 [INFO] [stderr] Compiling either v1.13.0 [INFO] [stderr] Compiling lazycell v1.3.0 [INFO] [stderr] Compiling libc v0.2.159 [INFO] [stderr] Compiling clang-sys v1.8.1 [INFO] [stderr] Compiling libloading v0.8.5 [INFO] [stderr] Compiling rustversion v1.0.17 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling rustc-hash v1.1.0 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling lazy_static v1.5.0 [INFO] [stderr] Compiling serde v1.0.210 [INFO] [stderr] Compiling heck v0.5.0 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Compiling itertools v0.12.1 [INFO] [stderr] Checking byteorder v1.5.0 [INFO] [stderr] Checking difference v2.0.0 [INFO] [stderr] Checking once_cell v1.19.0 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Checking ansi_term v0.11.0 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking tempfile v3.12.0 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking pretty_assertions v0.6.1 [INFO] [stderr] Checking aho-corasick v1.1.3 [INFO] [stderr] Compiling nom v7.1.3 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling jobserver v0.1.32 [INFO] [stderr] Checking regex-automata v0.4.7 [INFO] [stderr] Compiling cc v1.1.21 [INFO] [stderr] Compiling openssl-src v300.3.2+3.3.2 [INFO] [stderr] Compiling cmake v0.1.51 [INFO] [stderr] Compiling cexpr v0.6.0 [INFO] [stderr] Compiling openssl-sys v0.9.103 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling bzip2-sys v0.1.11+1.0.8 [INFO] [stderr] Compiling curl-sys v0.4.76+curl-8.10.1 [INFO] [stderr] Compiling libz-sys v1.1.20 [INFO] [stderr] Checking bincode v1.3.3 [INFO] [stderr] Checking serde_json v1.0.128 [INFO] [stderr] Checking regex v1.10.6 [INFO] [stderr] Checking bio-types v1.0.4 [INFO] [stderr] Compiling hts-sys v2.1.4 [INFO] [stderr] Checking rust-htslib v0.47.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unnecessary parentheses around function argument [INFO] [stdout] --> src/bam/mod.rs:1395:45 [INFO] [stdout] | [INFO] [stdout] 1395 | let rec = htslib::sam_hdr_parse((l_text + 1), text as *const c_char); [INFO] [stdout] | ^ ^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_parens)]` on by default [INFO] [stdout] help: remove these parentheses [INFO] [stdout] | [INFO] [stdout] 1395 - let rec = htslib::sam_hdr_parse((l_text + 1), text as *const c_char); [INFO] [stdout] 1395 + let rec = htslib::sam_hdr_parse(l_text + 1, text as *const c_char); [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [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:300:27 [INFO] [stdout] | [INFO] [stdout] 300 | 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: unnecessary parentheses around function argument [INFO] [stdout] --> src/bam/mod.rs:1395:45 [INFO] [stdout] | [INFO] [stdout] 1395 | let rec = htslib::sam_hdr_parse((l_text + 1), text as *const c_char); [INFO] [stdout] | ^ ^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_parens)]` on by default [INFO] [stdout] help: remove these parentheses [INFO] [stdout] | [INFO] [stdout] 1395 - let rec = htslib::sam_hdr_parse((l_text + 1), text as *const c_char); [INFO] [stdout] 1395 + let rec = htslib::sam_hdr_parse(l_text + 1, text as *const c_char); [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:140:42 [INFO] [stdout] | [INFO] [stdout] 140 | 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: 4 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/bam/mod.rs:3030:17 [INFO] [stdout] | [INFO] [stdout] 3030 | let mut record = Record::new(); [INFO] [stdout] | ----^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 1 previous error; 2 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `rust-htslib` (lib test) due to 2 previous errors; 2 warnings emitted [INFO] running `Command { std: "docker" "inspect" "4bd3e616f5277604cad23a03abed70fe0e248d995b5577c1f12c517669e47947", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "4bd3e616f5277604cad23a03abed70fe0e248d995b5577c1f12c517669e47947", kill_on_drop: false }` [INFO] [stdout] 4bd3e616f5277604cad23a03abed70fe0e248d995b5577c1f12c517669e47947