[INFO] fetching crate extended-htslib 0.2.0... [INFO] testing extended-htslib-0.2.0 against try#8de4c7234dd9b97c9d76b58671343fdbbc9a433e+target=x86_64-unknown-linux-musl for musl_upgrade_1_2_5_with_libc_patch_0 [INFO] extracting crate extended-htslib 0.2.0 into /workspace/builds/worker-3-tc1/source [INFO] started tweaking crates.io crate extended-htslib 0.2.0 [INFO] finished tweaking crates.io crate extended-htslib 0.2.0 [INFO] tweaked toml for crates.io crate extended-htslib 0.2.0 written to /workspace/builds/worker-3-tc1/source/Cargo.toml [INFO] validating manifest of crates.io crate extended-htslib 0.2.0 on toolchain 8de4c7234dd9b97c9d76b58671343fdbbc9a433e [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate crates.io crate extended-htslib 0.2.0 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" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Updating crates.io index [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 v1.23.0 [INFO] [stderr] Downloaded bzip2-sys v0.1.12+1.0.8 [INFO] [stderr] Downloaded curl-sys v0.4.80+curl-8.12.1 [INFO] [stderr] Downloaded hts-sys v2.2.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] aeb8849f539bfa37477007ce299508e255ae66e80fce8cb0c72745c05e3be2fd [INFO] running `Command { std: "docker" "start" "-a" "aeb8849f539bfa37477007ce299508e255ae66e80fce8cb0c72745c05e3be2fd", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "aeb8849f539bfa37477007ce299508e255ae66e80fce8cb0c72745c05e3be2fd", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "aeb8849f539bfa37477007ce299508e255ae66e80fce8cb0c72745c05e3be2fd", kill_on_drop: false }` [INFO] [stdout] aeb8849f539bfa37477007ce299508e255ae66e80fce8cb0c72745c05e3be2fd [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "build" "--frozen" "--message-format=json" "--target" "x86_64-unknown-linux-musl", kill_on_drop: false }` [INFO] [stdout] a483c51e22966c305cf448244dd2fe63cffc193a8fa8dc04623684f4ad590dc5 [INFO] running `Command { std: "docker" "start" "-a" "a483c51e22966c305cf448244dd2fe63cffc193a8fa8dc04623684f4ad590dc5", kill_on_drop: false }` [INFO] [stderr] Compiling proc-macro2 v1.0.93 [INFO] [stderr] Compiling unicode-ident v1.0.17 [INFO] [stderr] Compiling libc v0.2.169 [INFO] [stderr] Compiling pkg-config v0.3.31 [INFO] [stderr] Compiling vcpkg v0.2.15 [INFO] [stderr] Compiling writeable v0.5.5 [INFO] [stderr] Compiling litemap v0.7.4 [INFO] [stderr] Compiling glob v0.3.2 [INFO] [stderr] Compiling regex-syntax v0.8.5 [INFO] [stderr] Compiling cfg-if v1.0.0 [INFO] [stderr] Compiling icu_locid_transform_data v1.5.0 [INFO] [stderr] Compiling memchr v2.7.4 [INFO] [stderr] Compiling bindgen v0.69.5 [INFO] [stderr] Compiling icu_properties_data v1.5.0 [INFO] [stderr] Compiling either v1.13.0 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling libloading v0.8.6 [INFO] [stderr] Compiling rustc-hash v1.1.0 [INFO] [stderr] Compiling icu_normalizer_data v1.5.0 [INFO] [stderr] Compiling lazy_static v1.5.0 [INFO] [stderr] Compiling bitflags v2.8.0 [INFO] [stderr] Compiling rustversion v1.0.19 [INFO] [stderr] Compiling write16 v1.0.0 [INFO] [stderr] Compiling smallvec v1.14.0 [INFO] [stderr] Compiling itertools v0.12.1 [INFO] [stderr] Compiling lazycell v1.3.0 [INFO] [stderr] Compiling utf16_iter v1.0.5 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling heck v0.5.0 [INFO] [stderr] Compiling thiserror v2.0.11 [INFO] [stderr] Compiling percent-encoding v2.3.1 [INFO] [stderr] Compiling quote v1.0.38 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling syn v2.0.98 [INFO] [stderr] Compiling clang-sys v1.8.1 [INFO] [stderr] Compiling nom v7.1.3 [INFO] [stderr] Compiling form_urlencoded v1.2.1 [INFO] [stderr] Compiling byteorder v1.5.0 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling aho-corasick v1.1.3 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling jobserver v0.1.32 [INFO] [stderr] Compiling cc v1.2.15 [INFO] [stderr] Compiling regex-automata v0.4.9 [INFO] [stderr] Compiling openssl-src v300.4.2+3.4.1 [INFO] [stderr] Compiling cmake v0.1.54 [INFO] [stderr] Compiling openssl-sys v0.9.106 [INFO] [stderr] Compiling libz-sys v1.1.21 [INFO] [stderr] Compiling bzip2-sys v0.1.12+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling curl-sys v0.4.80+curl-8.12.1 [INFO] [stderr] Compiling regex v1.11.1 [INFO] [stderr] Compiling cexpr v0.6.0 [INFO] [stderr] Compiling synstructure v0.13.1 [INFO] [stderr] Compiling zerofrom-derive v0.1.5 [INFO] [stderr] Compiling yoke-derive v0.7.5 [INFO] [stderr] Compiling zerovec-derive v0.10.3 [INFO] [stderr] Compiling displaydoc v0.2.5 [INFO] [stderr] Compiling icu_provider_macros v1.5.0 [INFO] [stderr] 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[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[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:614:39 [INFO] [stdout] | [INFO] [stdout] 614 | let (data, type_size) = match *aux { [INFO] [stdout] | ^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/record.rs:605:5 [INFO] [stdout] | [INFO] [stdout] 605 | unsafe fn read_aux_field<'a>(aux: *const u8) -> Result<(Aux<'a>, usize)> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = note: `#[warn(unsafe_op_in_unsafe_fn)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:617:28 [INFO] [stdout] | [INFO] [stdout] 617 | (Aux::Char(*aux.offset(TYPE_ID_LEN)), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:617:29 [INFO] [stdout] | [INFO] [stdout] 617 | (Aux::Char(*aux.offset(TYPE_ID_LEN)), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:621:26 [INFO] [stdout] | [INFO] [stdout] 621 | (Aux::I8(*aux.offset(TYPE_ID_LEN).cast::()), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:621:27 [INFO] [stdout] | [INFO] [stdout] 621 | (Aux::I8(*aux.offset(TYPE_ID_LEN).cast::()), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:625:26 [INFO] [stdout] | [INFO] [stdout] 625 | (Aux::U8(*aux.offset(TYPE_ID_LEN)), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:625:27 [INFO] [stdout] | [INFO] [stdout] 625 | (Aux::U8(*aux.offset(TYPE_ID_LEN)), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:631:25 [INFO] [stdout] | [INFO] [stdout] 631 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:631:47 [INFO] [stdout] | [INFO] [stdout] 631 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:642:25 [INFO] [stdout] | [INFO] [stdout] 642 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:642:47 [INFO] [stdout] | [INFO] [stdout] 642 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:653:25 [INFO] [stdout] | [INFO] [stdout] 653 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:653:47 [INFO] [stdout] | [INFO] [stdout] 653 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:664:25 [INFO] [stdout] | [INFO] [stdout] 664 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:664:47 [INFO] [stdout] | [INFO] [stdout] 664 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:675:25 [INFO] [stdout] | [INFO] [stdout] 675 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:675:47 [INFO] [stdout] | [INFO] [stdout] 675 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:686:25 [INFO] [stdout] | [INFO] [stdout] 686 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:686:47 [INFO] [stdout] | [INFO] [stdout] 686 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ffi::CStr::from_ptr` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:694:29 [INFO] [stdout] | [INFO] [stdout] 694 | let c_str = ffi::CStr::from_ptr(aux.offset(TYPE_ID_LEN).cast::()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:694:49 [INFO] [stdout] | [INFO] [stdout] 694 | let c_str = ffi::CStr::from_ptr(aux.offset(TYPE_ID_LEN).cast::()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:706:21 [INFO] [stdout] | [INFO] [stdout] 706 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN + ARRAY_INNER_TYPE_LEN), 4) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:706:43 [INFO] [stdout] | [INFO] [stdout] 706 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN + ARRAY_INNER_TYPE_LEN), 4) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:711:54 [INFO] [stdout] | [INFO] [stdout] 711 | let (array_data, array_size) = match *aux.offset(TYPE_ID_LEN) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:711:55 [INFO] [stdout] | [INFO] [stdout] 711 | let (array_data, array_size) = match *aux.offset(TYPE_ID_LEN) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:713:69 [INFO] [stdout] | [INFO] [stdout] 713 | Aux::ArrayI8(AuxArray::<'a, i8>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _____________________________________________________________________^ [INFO] [stdout] 714 | | aux.offset(array_data_offset), [INFO] [stdout] 715 | | length, [INFO] [stdout] 716 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:714:29 [INFO] [stdout] | [INFO] [stdout] 714 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:720:69 [INFO] [stdout] | [INFO] [stdout] 720 | Aux::ArrayU8(AuxArray::<'a, u8>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _____________________________________________________________________^ [INFO] [stdout] 721 | | aux.offset(array_data_offset), [INFO] [stdout] 722 | | length, [INFO] [stdout] 723 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:721:29 [INFO] [stdout] | [INFO] [stdout] 721 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:727:71 [INFO] [stdout] | [INFO] [stdout] 727 | Aux::ArrayI16(AuxArray::<'a, i16>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _______________________________________________________________________^ [INFO] [stdout] 728 | | aux.offset(array_data_offset), [INFO] [stdout] 729 | | length * size_of::(), [INFO] [stdout] 730 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:728:29 [INFO] [stdout] | [INFO] [stdout] 728 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:734:71 [INFO] [stdout] | [INFO] [stdout] 734 | Aux::ArrayU16(AuxArray::<'a, u16>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _______________________________________________________________________^ [INFO] [stdout] 735 | | aux.offset(array_data_offset), [INFO] [stdout] 736 | | length * size_of::(), [INFO] [stdout] 737 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:735:29 [INFO] [stdout] | [INFO] [stdout] 735 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:741:71 [INFO] [stdout] | [INFO] [stdout] 741 | Aux::ArrayI32(AuxArray::<'a, i32>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _______________________________________________________________________^ [INFO] [stdout] 742 | | aux.offset(array_data_offset), [INFO] [stdout] 743 | | length * size_of::(), [INFO] [stdout] 744 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:742:29 [INFO] [stdout] | [INFO] [stdout] 742 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:748:71 [INFO] [stdout] | [INFO] [stdout] 748 | Aux::ArrayU32(AuxArray::<'a, u32>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _______________________________________________________________________^ [INFO] [stdout] 749 | | aux.offset(array_data_offset), [INFO] [stdout] 750 | | length * size_of::(), [INFO] [stdout] 751 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:749:29 [INFO] [stdout] | [INFO] [stdout] 749 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:755:69 [INFO] [stdout] | [INFO] [stdout] 755 | Aux::ArrayFloat(AuxArray::::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _____________________________________________________________________^ [INFO] [stdout] 756 | | aux.offset(array_data_offset), [INFO] [stdout] 757 | | length * size_of::(), [INFO] [stdout] 758 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:756:29 [INFO] [stdout] | [INFO] [stdout] 756 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `core::slice::::get_unchecked` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:1608:6 [INFO] [stdout] | [INFO] [stdout] 1608 | (encoded_seq.get_unchecked(i / 2) >> ((!i & 1) << 2)) & 0b1111 [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/record.rs:1607:1 [INFO] [stdout] | [INFO] [stdout] 1607 | unsafe fn encoded_base_unchecked(encoded_seq: &[u8], i: usize) -> u8 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `bam::record::encoded_base_unchecked` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:1633:9 [INFO] [stdout] | [INFO] [stdout] 1633 | encoded_base_unchecked(self.encoded, i) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/record.rs:1632:5 [INFO] [stdout] | [INFO] [stdout] 1632 | pub unsafe fn encoded_base_unchecked(&self, i: usize) -> u8 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `bam::record::Seq::<'a>::encoded_base_unchecked` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:1641:32 [INFO] [stdout] | [INFO] [stdout] 1641 | *decode_base_unchecked(self.encoded_base_unchecked(i)) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/record.rs:1640:5 [INFO] [stdout] | [INFO] [stdout] 1640 | pub unsafe fn decoded_base_unchecked(&self, i: usize) -> u8 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::hts_set_threads` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:45:8 [INFO] [stdout] | [INFO] [stdout] 45 | if htslib::hts_set_threads(htsfile, n_threads as i32) != 0 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/mod.rs:42:1 [INFO] [stdout] | [INFO] [stdout] 42 | unsafe fn set_threads(htsfile: *mut htslib::htsFile, n_threads: usize) -> Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::hts_set_thread_pool` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:55:8 [INFO] [stdout] | [INFO] [stdout] 55 | if htslib::hts_set_thread_pool(htsfile, &mut b.inner as *mut _) != 0 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/mod.rs:52:1 [INFO] [stdout] | [INFO] [stdout] 52 | unsafe fn set_thread_pool(htsfile: *mut htslib::htsFile, tpool: &ThreadPool) -> Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::hts_set_fai_filename` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:78:8 [INFO] [stdout] | [INFO] [stdout] 78 | if htslib::hts_set_fai_filename(htsfile, c_str.as_ptr()) == 0 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/mod.rs:65:1 [INFO] [stdout] | [INFO] [stdout] 65 | / pub unsafe fn set_fai_filename>( [INFO] [stdout] 66 | | htsfile: *mut htslib::htsFile, [INFO] [stdout] 67 | | fasta_path: P, [INFO] [stdout] 68 | | ) -> Result<()> { [INFO] [stdout] | |_______________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::sam_hdr_nref` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:831:29 [INFO] [stdout] | [INFO] [stdout] 831 | usize::try_from(hts_sys::sam_hdr_nref(h)).map_err(|_| Error::NoSequencesInReference)?; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/mod.rs:819:5 [INFO] [stdout] | [INFO] [stdout] 819 | unsafe fn slow_idxstats(&mut self) -> Result> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::mem::MaybeUninit::::assume_init` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:836:39 [INFO] [stdout] | [INFO] [stdout] 836 | let mut bb: hts_sys::bam1_t = MaybeUninit::zeroed().assume_init(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::sam_read1` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:839:19 [INFO] [stdout] | [INFO] [stdout] 839 | ret = hts_sys::sam_read1(fp, h, b); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:843:23 [INFO] [stdout] | [INFO] [stdout] 843 | let tid = (*b).core.tid; [INFO] [stdout] | ^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:855:27 [INFO] [stdout] | [INFO] [stdout] 855 | let idx = if ((*b).core.flag as u32 & hts_sys::BAM_FUNMAP) > 0 { [INFO] [stdout] | ^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:860:20 [INFO] [stdout] | [INFO] [stdout] 860 | counts[(*b).core.tid as usize][idx] += 1; [INFO] [stdout] | ^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::hts_set_threads` is unsafe and requires unsafe block [INFO] [stdout] --> src/bcf/mod.rs:172:13 [INFO] [stdout] | [INFO] [stdout] 172 | let r = htslib::hts_set_threads(hts_file, n_threads as i32); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bcf/mod.rs:169:1 [INFO] [stdout] | [INFO] [stdout] 169 | pub unsafe fn set_threads(hts_file: *mut htslib::htsFile, n_threads: usize) -> Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function `new` is never used [INFO] [stdout] --> src/bam/ext.rs:549:8 [INFO] [stdout] | [INFO] [stdout] 539 | impl RangePos { [INFO] [stdout] | ------------- associated function in this implementation [INFO] [stdout] ... [INFO] [stdout] 549 | fn new(start: i64, end: i64) -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [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] [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: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/bam/buffer.rs:160:17 [INFO] [stdout] | [INFO] [stdout] 160 | pub fn iter(&self) -> vec_deque::Iter> { [INFO] [stdout] | ^^^^^ -------------------------------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(mismatched_lifetime_syntaxes)]` on by default [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stdout] | [INFO] [stdout] 160 | pub fn iter(&self) -> vec_deque::Iter<'_, Rc> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/bam/buffer.rs:165:21 [INFO] [stdout] | [INFO] [stdout] 165 | pub fn iter_mut(&mut self) -> vec_deque::IterMut> { [INFO] [stdout] | ^^^^^^^^^ ----------------------------------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stdout] | [INFO] [stdout] 165 | pub fn iter_mut(&mut self) -> vec_deque::IterMut<'_, Rc> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/bam/header.rs:109:21 [INFO] [stdout] | [INFO] [stdout] 109 | pub fn comments(&self) -> impl Iterator> { [INFO] [stdout] | ^^^^^ -------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stdout] | [INFO] [stdout] 109 | pub fn comments(&self) -> impl Iterator> { [INFO] [stdout] | +++ [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:143:42 [INFO] [stdout] | [INFO] [stdout] 143 | 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: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/bam/record.rs:784:21 [INFO] [stdout] | [INFO] [stdout] 784 | pub fn aux_iter(&self) -> AuxIter { [INFO] [stdout] | ^^^^^ ------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stdout] | [INFO] [stdout] 784 | pub fn aux_iter(&self) -> AuxIter<'_> { [INFO] [stdout] | ++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/bam/record.rs:1069:26 [INFO] [stdout] | [INFO] [stdout] 1069 | pub fn basemods_iter(&self) -> Result { [INFO] [stdout] | ^^^^^ --------------------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stdout] | [INFO] [stdout] 1069 | pub fn basemods_iter(&self) -> Result> { [INFO] [stdout] | ++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/bam/record.rs:1076:35 [INFO] [stdout] | [INFO] [stdout] 1076 | pub fn basemods_position_iter(&self) -> Result { [INFO] [stdout] | ^^^^^ ----------------------------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stdout] | [INFO] [stdout] 1076 | pub fn basemods_position_iter(&self) -> Result> { [INFO] [stdout] | ++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/bam/record.rs:1455:17 [INFO] [stdout] | [INFO] [stdout] 1455 | pub fn iter(&self) -> AuxArrayIter { [INFO] [stdout] | ^^^^^ --------------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stdout] | [INFO] [stdout] 1455 | pub fn iter(&self) -> AuxArrayIter<'_, T> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/bam/record.rs:1649:28 [INFO] [stdout] | [INFO] [stdout] 1649 | pub fn rangeextract(&self, range: T) -> std::io::Result> [INFO] [stdout] | ^^^^^ -------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stdout] | [INFO] [stdout] 1649 | pub fn rangeextract(&self, range: T) -> std::io::Result> [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0133`. [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 2m 16s [INFO] running `Command { std: "docker" "inspect" "a483c51e22966c305cf448244dd2fe63cffc193a8fa8dc04623684f4ad590dc5", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "a483c51e22966c305cf448244dd2fe63cffc193a8fa8dc04623684f4ad590dc5", kill_on_drop: false }` [INFO] [stdout] a483c51e22966c305cf448244dd2fe63cffc193a8fa8dc04623684f4ad590dc5 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "test" "--frozen" "--no-run" "--message-format=json" "--target" "x86_64-unknown-linux-musl", kill_on_drop: false }` [INFO] [stdout] b7bff08661f9e596ef9178ea27dcd452872e061184b5595a885c4e7e4293e28b [INFO] running `Command { std: "docker" "start" "-a" "b7bff08661f9e596ef9178ea27dcd452872e061184b5595a885c4e7e4293e28b", kill_on_drop: false }` [INFO] [stderr] Compiling serde v1.0.218 [INFO] [stderr] Compiling rustix v0.38.44 [INFO] [stderr] Compiling getrandom v0.3.1 [INFO] [stderr] Compiling bitflags v2.8.0 [INFO] [stderr] Compiling linux-raw-sys v0.4.15 [INFO] [stderr] Compiling serde_json v1.0.139 [INFO] [stderr] Compiling itoa v1.0.14 [INFO] [stderr] Compiling ryu v1.0.19 [INFO] [stderr] Compiling diff v0.1.13 [INFO] [stderr] Compiling once_cell v1.20.3 [INFO] [stderr] Compiling yansi v1.0.1 [INFO] [stderr] Compiling fastrand v2.3.0 [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[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:614:39 [INFO] [stdout] | [INFO] [stdout] 614 | let (data, type_size) = match *aux { [INFO] [stdout] | ^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/record.rs:605:5 [INFO] [stdout] | [INFO] [stdout] 605 | unsafe fn read_aux_field<'a>(aux: *const u8) -> Result<(Aux<'a>, usize)> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = note: `#[warn(unsafe_op_in_unsafe_fn)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:617:28 [INFO] [stdout] | [INFO] [stdout] 617 | (Aux::Char(*aux.offset(TYPE_ID_LEN)), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:617:29 [INFO] [stdout] | [INFO] [stdout] 617 | (Aux::Char(*aux.offset(TYPE_ID_LEN)), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:621:26 [INFO] [stdout] | [INFO] [stdout] 621 | (Aux::I8(*aux.offset(TYPE_ID_LEN).cast::()), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:621:27 [INFO] [stdout] | [INFO] [stdout] 621 | (Aux::I8(*aux.offset(TYPE_ID_LEN).cast::()), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:625:26 [INFO] [stdout] | [INFO] [stdout] 625 | (Aux::U8(*aux.offset(TYPE_ID_LEN)), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:625:27 [INFO] [stdout] | [INFO] [stdout] 625 | (Aux::U8(*aux.offset(TYPE_ID_LEN)), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:631:25 [INFO] [stdout] | [INFO] [stdout] 631 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:631:47 [INFO] [stdout] | [INFO] [stdout] 631 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:642:25 [INFO] [stdout] | [INFO] [stdout] 642 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:642:47 [INFO] [stdout] | [INFO] [stdout] 642 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:653:25 [INFO] [stdout] | [INFO] [stdout] 653 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:653:47 [INFO] [stdout] | [INFO] [stdout] 653 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:664:25 [INFO] [stdout] | [INFO] [stdout] 664 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:664:47 [INFO] [stdout] | [INFO] [stdout] 664 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:675:25 [INFO] [stdout] | [INFO] [stdout] 675 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:675:47 [INFO] [stdout] | [INFO] [stdout] 675 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:686:25 [INFO] [stdout] | [INFO] [stdout] 686 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:686:47 [INFO] [stdout] | [INFO] [stdout] 686 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ffi::CStr::from_ptr` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:694:29 [INFO] [stdout] | [INFO] [stdout] 694 | let c_str = ffi::CStr::from_ptr(aux.offset(TYPE_ID_LEN).cast::()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:694:49 [INFO] [stdout] | [INFO] [stdout] 694 | let c_str = ffi::CStr::from_ptr(aux.offset(TYPE_ID_LEN).cast::()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:706:21 [INFO] [stdout] | [INFO] [stdout] 706 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN + ARRAY_INNER_TYPE_LEN), 4) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:706:43 [INFO] [stdout] | [INFO] [stdout] 706 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN + ARRAY_INNER_TYPE_LEN), 4) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:711:54 [INFO] [stdout] | [INFO] [stdout] 711 | let (array_data, array_size) = match *aux.offset(TYPE_ID_LEN) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:711:55 [INFO] [stdout] | [INFO] [stdout] 711 | let (array_data, array_size) = match *aux.offset(TYPE_ID_LEN) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:713:69 [INFO] [stdout] | [INFO] [stdout] 713 | Aux::ArrayI8(AuxArray::<'a, i8>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _____________________________________________________________________^ [INFO] [stdout] 714 | | aux.offset(array_data_offset), [INFO] [stdout] 715 | | length, [INFO] [stdout] 716 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:714:29 [INFO] [stdout] | [INFO] [stdout] 714 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:720:69 [INFO] [stdout] | [INFO] [stdout] 720 | Aux::ArrayU8(AuxArray::<'a, u8>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _____________________________________________________________________^ [INFO] [stdout] 721 | | aux.offset(array_data_offset), [INFO] [stdout] 722 | | length, [INFO] [stdout] 723 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:721:29 [INFO] [stdout] | [INFO] [stdout] 721 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:727:71 [INFO] [stdout] | [INFO] [stdout] 727 | Aux::ArrayI16(AuxArray::<'a, i16>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _______________________________________________________________________^ [INFO] [stdout] 728 | | aux.offset(array_data_offset), [INFO] [stdout] 729 | | length * size_of::(), [INFO] [stdout] 730 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:728:29 [INFO] [stdout] | [INFO] [stdout] 728 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:734:71 [INFO] [stdout] | [INFO] [stdout] 734 | Aux::ArrayU16(AuxArray::<'a, u16>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _______________________________________________________________________^ [INFO] [stdout] 735 | | aux.offset(array_data_offset), [INFO] [stdout] 736 | | length * size_of::(), [INFO] [stdout] 737 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:735:29 [INFO] [stdout] | [INFO] [stdout] 735 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:741:71 [INFO] [stdout] | [INFO] [stdout] 741 | Aux::ArrayI32(AuxArray::<'a, i32>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _______________________________________________________________________^ [INFO] [stdout] 742 | | aux.offset(array_data_offset), [INFO] [stdout] 743 | | length * size_of::(), [INFO] [stdout] 744 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:742:29 [INFO] [stdout] | [INFO] [stdout] 742 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:748:71 [INFO] [stdout] | [INFO] [stdout] 748 | Aux::ArrayU32(AuxArray::<'a, u32>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _______________________________________________________________________^ [INFO] [stdout] 749 | | aux.offset(array_data_offset), [INFO] [stdout] 750 | | length * size_of::(), [INFO] [stdout] 751 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:749:29 [INFO] [stdout] | [INFO] [stdout] 749 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:755:69 [INFO] [stdout] | [INFO] [stdout] 755 | Aux::ArrayFloat(AuxArray::::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _____________________________________________________________________^ [INFO] [stdout] 756 | | aux.offset(array_data_offset), [INFO] [stdout] 757 | | length * size_of::(), [INFO] [stdout] 758 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:756:29 [INFO] [stdout] | [INFO] [stdout] 756 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `core::slice::::get_unchecked` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:1608:6 [INFO] [stdout] | [INFO] [stdout] 1608 | (encoded_seq.get_unchecked(i / 2) >> ((!i & 1) << 2)) & 0b1111 [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/record.rs:1607:1 [INFO] [stdout] | [INFO] [stdout] 1607 | unsafe fn encoded_base_unchecked(encoded_seq: &[u8], i: usize) -> u8 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `bam::record::encoded_base_unchecked` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:1633:9 [INFO] [stdout] | [INFO] [stdout] 1633 | encoded_base_unchecked(self.encoded, i) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/record.rs:1632:5 [INFO] [stdout] | [INFO] [stdout] 1632 | pub unsafe fn encoded_base_unchecked(&self, i: usize) -> u8 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `bam::record::Seq::<'a>::encoded_base_unchecked` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:1641:32 [INFO] [stdout] | [INFO] [stdout] 1641 | *decode_base_unchecked(self.encoded_base_unchecked(i)) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/record.rs:1640:5 [INFO] [stdout] | [INFO] [stdout] 1640 | pub unsafe fn decoded_base_unchecked(&self, i: usize) -> u8 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::hts_set_threads` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:45:8 [INFO] [stdout] | [INFO] [stdout] 45 | if htslib::hts_set_threads(htsfile, n_threads as i32) != 0 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/mod.rs:42:1 [INFO] [stdout] | [INFO] [stdout] 42 | unsafe fn set_threads(htsfile: *mut htslib::htsFile, n_threads: usize) -> Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::hts_set_thread_pool` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:55:8 [INFO] [stdout] | [INFO] [stdout] 55 | if htslib::hts_set_thread_pool(htsfile, &mut b.inner as *mut _) != 0 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/mod.rs:52:1 [INFO] [stdout] | [INFO] [stdout] 52 | unsafe fn set_thread_pool(htsfile: *mut htslib::htsFile, tpool: &ThreadPool) -> Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::hts_set_fai_filename` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:78:8 [INFO] [stdout] | [INFO] [stdout] 78 | if htslib::hts_set_fai_filename(htsfile, c_str.as_ptr()) == 0 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/mod.rs:65:1 [INFO] [stdout] | [INFO] [stdout] 65 | / pub unsafe fn set_fai_filename>( [INFO] [stdout] 66 | | htsfile: *mut htslib::htsFile, [INFO] [stdout] 67 | | fasta_path: P, [INFO] [stdout] 68 | | ) -> Result<()> { [INFO] [stdout] | |_______________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::sam_hdr_nref` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:831:29 [INFO] [stdout] | [INFO] [stdout] 831 | usize::try_from(hts_sys::sam_hdr_nref(h)).map_err(|_| Error::NoSequencesInReference)?; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/mod.rs:819:5 [INFO] [stdout] | [INFO] [stdout] 819 | unsafe fn slow_idxstats(&mut self) -> Result> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::mem::MaybeUninit::::assume_init` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:836:39 [INFO] [stdout] | [INFO] [stdout] 836 | let mut bb: hts_sys::bam1_t = MaybeUninit::zeroed().assume_init(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::sam_read1` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:839:19 [INFO] [stdout] | [INFO] [stdout] 839 | ret = hts_sys::sam_read1(fp, h, b); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:843:23 [INFO] [stdout] | [INFO] [stdout] 843 | let tid = (*b).core.tid; [INFO] [stdout] | ^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:855:27 [INFO] [stdout] | [INFO] [stdout] 855 | let idx = if ((*b).core.flag as u32 & hts_sys::BAM_FUNMAP) > 0 { [INFO] [stdout] | ^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:860:20 [INFO] [stdout] | [INFO] [stdout] 860 | counts[(*b).core.tid as usize][idx] += 1; [INFO] [stdout] | ^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::hts_set_threads` is unsafe and requires unsafe block [INFO] [stdout] --> src/bcf/mod.rs:172:13 [INFO] [stdout] | [INFO] [stdout] 172 | let r = htslib::hts_set_threads(hts_file, n_threads as i32); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bcf/mod.rs:169:1 [INFO] [stdout] | [INFO] [stdout] 169 | pub unsafe fn set_threads(hts_file: *mut htslib::htsFile, n_threads: usize) -> Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: associated function `new` is never used [INFO] [stdout] --> src/bam/ext.rs:549:8 [INFO] [stdout] | [INFO] [stdout] 539 | impl RangePos { [INFO] [stdout] | ------------- associated function in this implementation [INFO] [stdout] ... [INFO] [stdout] 549 | fn new(start: i64, end: i64) -> Self { [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [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] [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: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/bam/buffer.rs:160:17 [INFO] [stdout] | [INFO] [stdout] 160 | pub fn iter(&self) -> vec_deque::Iter> { [INFO] [stdout] | ^^^^^ -------------------------------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(mismatched_lifetime_syntaxes)]` on by default [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stdout] | [INFO] [stdout] 160 | pub fn iter(&self) -> vec_deque::Iter<'_, Rc> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/bam/buffer.rs:165:21 [INFO] [stdout] | [INFO] [stdout] 165 | pub fn iter_mut(&mut self) -> vec_deque::IterMut> { [INFO] [stdout] | ^^^^^^^^^ ----------------------------------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stdout] | [INFO] [stdout] 165 | pub fn iter_mut(&mut self) -> vec_deque::IterMut<'_, Rc> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/bam/header.rs:109:21 [INFO] [stdout] | [INFO] [stdout] 109 | pub fn comments(&self) -> impl Iterator> { [INFO] [stdout] | ^^^^^ -------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stdout] | [INFO] [stdout] 109 | pub fn comments(&self) -> impl Iterator> { [INFO] [stdout] | +++ [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:143:42 [INFO] [stdout] | [INFO] [stdout] 143 | 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: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/bam/record.rs:784:21 [INFO] [stdout] | [INFO] [stdout] 784 | pub fn aux_iter(&self) -> AuxIter { [INFO] [stdout] | ^^^^^ ------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stdout] | [INFO] [stdout] 784 | pub fn aux_iter(&self) -> AuxIter<'_> { [INFO] [stdout] | ++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/bam/record.rs:1069:26 [INFO] [stdout] | [INFO] [stdout] 1069 | pub fn basemods_iter(&self) -> Result { [INFO] [stdout] | ^^^^^ --------------------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stdout] | [INFO] [stdout] 1069 | pub fn basemods_iter(&self) -> Result> { [INFO] [stdout] | ++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/bam/record.rs:1076:35 [INFO] [stdout] | [INFO] [stdout] 1076 | pub fn basemods_position_iter(&self) -> Result { [INFO] [stdout] | ^^^^^ ----------------------------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stdout] | [INFO] [stdout] 1076 | pub fn basemods_position_iter(&self) -> Result> { [INFO] [stdout] | ++++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/bam/record.rs:1455:17 [INFO] [stdout] | [INFO] [stdout] 1455 | pub fn iter(&self) -> AuxArrayIter { [INFO] [stdout] | ^^^^^ --------------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stdout] | [INFO] [stdout] 1455 | pub fn iter(&self) -> AuxArrayIter<'_, T> { [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: lifetime flowing from input to output with different syntax can be confusing [INFO] [stdout] --> src/bam/record.rs:1649:28 [INFO] [stdout] | [INFO] [stdout] 1649 | pub fn rangeextract(&self, range: T) -> std::io::Result> [INFO] [stdout] | ^^^^^ -------- the lifetime gets resolved as `'_` [INFO] [stdout] | | [INFO] [stdout] | this lifetime flows to the output [INFO] [stdout] | [INFO] [stdout] help: one option is to remove the lifetime for references and use the anonymous lifetime for paths [INFO] [stdout] | [INFO] [stdout] 1649 | pub fn rangeextract(&self, range: T) -> std::io::Result> [INFO] [stdout] | +++ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0133`. [INFO] [stdout] [INFO] [stderr] Compiling pretty_assertions v1.4.1 [INFO] [stderr] Compiling tempfile v3.17.1 [INFO] [stderr] Compiling bincode v1.3.3 [INFO] [stderr] Compiling extended-htslib v0.2.0 (/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:312:27 [INFO] [stdout] | [INFO] [stdout] 312 | const CONTENT: &str = include_str!("../../test/bgzip/plain.vcf"); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [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: unused import: `super::*` [INFO] [stdout] --> src/bcf/header.rs:554:9 [INFO] [stdout] | [INFO] [stdout] 554 | use super::*; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:614:39 [INFO] [stdout] | [INFO] [stdout] 614 | let (data, type_size) = match *aux { [INFO] [stdout] | ^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/record.rs:605:5 [INFO] [stdout] | [INFO] [stdout] 605 | unsafe fn read_aux_field<'a>(aux: *const u8) -> Result<(Aux<'a>, usize)> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] = note: `#[warn(unsafe_op_in_unsafe_fn)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:617:28 [INFO] [stdout] | [INFO] [stdout] 617 | (Aux::Char(*aux.offset(TYPE_ID_LEN)), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:617:29 [INFO] [stdout] | [INFO] [stdout] 617 | (Aux::Char(*aux.offset(TYPE_ID_LEN)), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:621:26 [INFO] [stdout] | [INFO] [stdout] 621 | (Aux::I8(*aux.offset(TYPE_ID_LEN).cast::()), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:621:27 [INFO] [stdout] | [INFO] [stdout] 621 | (Aux::I8(*aux.offset(TYPE_ID_LEN).cast::()), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:625:26 [INFO] [stdout] | [INFO] [stdout] 625 | (Aux::U8(*aux.offset(TYPE_ID_LEN)), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:625:27 [INFO] [stdout] | [INFO] [stdout] 625 | (Aux::U8(*aux.offset(TYPE_ID_LEN)), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:631:25 [INFO] [stdout] | [INFO] [stdout] 631 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:631:47 [INFO] [stdout] | [INFO] [stdout] 631 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:642:25 [INFO] [stdout] | [INFO] [stdout] 642 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:642:47 [INFO] [stdout] | [INFO] [stdout] 642 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:653:25 [INFO] [stdout] | [INFO] [stdout] 653 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:653:47 [INFO] [stdout] | [INFO] [stdout] 653 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:664:25 [INFO] [stdout] | [INFO] [stdout] 664 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:664:47 [INFO] [stdout] | [INFO] [stdout] 664 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:675:25 [INFO] [stdout] | [INFO] [stdout] 675 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:675:47 [INFO] [stdout] | [INFO] [stdout] 675 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:686:25 [INFO] [stdout] | [INFO] [stdout] 686 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:686:47 [INFO] [stdout] | [INFO] [stdout] 686 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN), type_size) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ffi::CStr::from_ptr` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:694:29 [INFO] [stdout] | [INFO] [stdout] 694 | let c_str = ffi::CStr::from_ptr(aux.offset(TYPE_ID_LEN).cast::()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:694:49 [INFO] [stdout] | [INFO] [stdout] 694 | let c_str = ffi::CStr::from_ptr(aux.offset(TYPE_ID_LEN).cast::()); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:706:21 [INFO] [stdout] | [INFO] [stdout] 706 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN + ARRAY_INNER_TYPE_LEN), 4) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:706:43 [INFO] [stdout] | [INFO] [stdout] 706 | slice::from_raw_parts(aux.offset(TYPE_ID_LEN + ARRAY_INNER_TYPE_LEN), 4) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:711:54 [INFO] [stdout] | [INFO] [stdout] 711 | let (array_data, array_size) = match *aux.offset(TYPE_ID_LEN) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:711:55 [INFO] [stdout] | [INFO] [stdout] 711 | let (array_data, array_size) = match *aux.offset(TYPE_ID_LEN) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:713:69 [INFO] [stdout] | [INFO] [stdout] 713 | Aux::ArrayI8(AuxArray::<'a, i8>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _____________________________________________________________________^ [INFO] [stdout] 714 | | aux.offset(array_data_offset), [INFO] [stdout] 715 | | length, [INFO] [stdout] 716 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:714:29 [INFO] [stdout] | [INFO] [stdout] 714 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:720:69 [INFO] [stdout] | [INFO] [stdout] 720 | Aux::ArrayU8(AuxArray::<'a, u8>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _____________________________________________________________________^ [INFO] [stdout] 721 | | aux.offset(array_data_offset), [INFO] [stdout] 722 | | length, [INFO] [stdout] 723 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:721:29 [INFO] [stdout] | [INFO] [stdout] 721 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:727:71 [INFO] [stdout] | [INFO] [stdout] 727 | Aux::ArrayI16(AuxArray::<'a, i16>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _______________________________________________________________________^ [INFO] [stdout] 728 | | aux.offset(array_data_offset), [INFO] [stdout] 729 | | length * size_of::(), [INFO] [stdout] 730 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:728:29 [INFO] [stdout] | [INFO] [stdout] 728 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:734:71 [INFO] [stdout] | [INFO] [stdout] 734 | Aux::ArrayU16(AuxArray::<'a, u16>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _______________________________________________________________________^ [INFO] [stdout] 735 | | aux.offset(array_data_offset), [INFO] [stdout] 736 | | length * size_of::(), [INFO] [stdout] 737 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:735:29 [INFO] [stdout] | [INFO] [stdout] 735 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:741:71 [INFO] [stdout] | [INFO] [stdout] 741 | Aux::ArrayI32(AuxArray::<'a, i32>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _______________________________________________________________________^ [INFO] [stdout] 742 | | aux.offset(array_data_offset), [INFO] [stdout] 743 | | length * size_of::(), [INFO] [stdout] 744 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:742:29 [INFO] [stdout] | [INFO] [stdout] 742 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:748:71 [INFO] [stdout] | [INFO] [stdout] 748 | Aux::ArrayU32(AuxArray::<'a, u32>::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _______________________________________________________________________^ [INFO] [stdout] 749 | | aux.offset(array_data_offset), [INFO] [stdout] 750 | | length * size_of::(), [INFO] [stdout] 751 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:749:29 [INFO] [stdout] | [INFO] [stdout] 749 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::slice::from_raw_parts` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:755:69 [INFO] [stdout] | [INFO] [stdout] 755 | Aux::ArrayFloat(AuxArray::::from_bytes(slice::from_raw_parts( [INFO] [stdout] | _____________________________________________________________________^ [INFO] [stdout] 756 | | aux.offset(array_data_offset), [INFO] [stdout] 757 | | length * size_of::(), [INFO] [stdout] 758 | | ))), [INFO] [stdout] | |_________________________^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::ptr::const_ptr::::offset` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:756:29 [INFO] [stdout] | [INFO] [stdout] 756 | ... aux.offset(array_data_offset), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `core::slice::::get_unchecked` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:1608:6 [INFO] [stdout] | [INFO] [stdout] 1608 | (encoded_seq.get_unchecked(i / 2) >> ((!i & 1) << 2)) & 0b1111 [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/record.rs:1607:1 [INFO] [stdout] | [INFO] [stdout] 1607 | unsafe fn encoded_base_unchecked(encoded_seq: &[u8], i: usize) -> u8 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `bam::record::encoded_base_unchecked` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:1633:9 [INFO] [stdout] | [INFO] [stdout] 1633 | encoded_base_unchecked(self.encoded, i) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/record.rs:1632:5 [INFO] [stdout] | [INFO] [stdout] 1632 | pub unsafe fn encoded_base_unchecked(&self, i: usize) -> u8 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `bam::record::Seq::<'a>::encoded_base_unchecked` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/record.rs:1641:32 [INFO] [stdout] | [INFO] [stdout] 1641 | *decode_base_unchecked(self.encoded_base_unchecked(i)) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/record.rs:1640:5 [INFO] [stdout] | [INFO] [stdout] 1640 | pub unsafe fn decoded_base_unchecked(&self, i: usize) -> u8 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::hts_set_threads` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:45:8 [INFO] [stdout] | [INFO] [stdout] 45 | if htslib::hts_set_threads(htsfile, n_threads as i32) != 0 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/mod.rs:42:1 [INFO] [stdout] | [INFO] [stdout] 42 | unsafe fn set_threads(htsfile: *mut htslib::htsFile, n_threads: usize) -> Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::hts_set_thread_pool` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:55:8 [INFO] [stdout] | [INFO] [stdout] 55 | if htslib::hts_set_thread_pool(htsfile, &mut b.inner as *mut _) != 0 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/mod.rs:52:1 [INFO] [stdout] | [INFO] [stdout] 52 | unsafe fn set_thread_pool(htsfile: *mut htslib::htsFile, tpool: &ThreadPool) -> Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::hts_set_fai_filename` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:78:8 [INFO] [stdout] | [INFO] [stdout] 78 | if htslib::hts_set_fai_filename(htsfile, c_str.as_ptr()) == 0 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/mod.rs:65:1 [INFO] [stdout] | [INFO] [stdout] 65 | / pub unsafe fn set_fai_filename>( [INFO] [stdout] 66 | | htsfile: *mut htslib::htsFile, [INFO] [stdout] 67 | | fasta_path: P, [INFO] [stdout] 68 | | ) -> Result<()> { [INFO] [stdout] | |_______________^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::sam_hdr_nref` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:831:29 [INFO] [stdout] | [INFO] [stdout] 831 | usize::try_from(hts_sys::sam_hdr_nref(h)).map_err(|_| Error::NoSequencesInReference)?; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bam/mod.rs:819:5 [INFO] [stdout] | [INFO] [stdout] 819 | unsafe fn slow_idxstats(&mut self) -> Result> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `std::mem::MaybeUninit::::assume_init` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:836:39 [INFO] [stdout] | [INFO] [stdout] 836 | let mut bb: hts_sys::bam1_t = MaybeUninit::zeroed().assume_init(); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: call to unsafe function `hts_sys::sam_read1` is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:839:19 [INFO] [stdout] | [INFO] [stdout] 839 | ret = hts_sys::sam_read1(fp, h, b); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:843:23 [INFO] [stdout] | [INFO] [stdout] 843 | let tid = (*b).core.tid; [INFO] [stdout] | ^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:855:27 [INFO] [stdout] | [INFO] [stdout] 855 | let idx = if ((*b).core.flag as u32 & hts_sys::BAM_FUNMAP) > 0 { [INFO] [stdout] | ^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning[E0133]: dereference of raw pointer is unsafe and requires unsafe block [INFO] [stdout] --> src/bam/mod.rs:860:20 [INFO] [stdout] | [INFO] [stdout] 860 | counts[(*b).core.tid as usize][idx] += 1; [INFO] [stdout] | ^^^^ dereference of raw pointer [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: raw pointers may be null, dangling or unaligned; they can violate aliasing rules and cause data races: all of these are undefined behavior [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] warning[E0133]: call to unsafe function `hts_sys::hts_set_threads` is unsafe and requires unsafe block [INFO] [stdout] --> src/bcf/mod.rs:172:13 [INFO] [stdout] | [INFO] [stdout] 172 | let r = htslib::hts_set_threads(hts_file, n_threads as i32); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ call to unsafe function [INFO] [stdout] | [INFO] [stdout] = note: for more information, see [INFO] [stdout] = note: consult the function's documentation for information on how to avoid undefined behavior [INFO] [stdout] note: an unsafe function restricts its caller, but its body is safe by default [INFO] [stdout] --> src/bcf/mod.rs:169:1 [INFO] [stdout] | [INFO] [stdout] 169 | pub unsafe fn set_threads(hts_file: *mut htslib::htsFile, n_threads: usize) -> Result<()> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] For more information about this error, try `rustc --explain E0133`. [INFO] [stdout] [INFO] [stderr] error: could not compile `extended-htslib` (lib test) due to 1 previous error; 55 warnings emitted [INFO] running `Command { std: "docker" "inspect" "b7bff08661f9e596ef9178ea27dcd452872e061184b5595a885c4e7e4293e28b", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "b7bff08661f9e596ef9178ea27dcd452872e061184b5595a885c4e7e4293e28b", kill_on_drop: false }` [INFO] [stdout] b7bff08661f9e596ef9178ea27dcd452872e061184b5595a885c4e7e4293e28b