[INFO] cloning repository https://github.com/mal2017/csc [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/mal2017/csc" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmal2017%2Fcsc", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmal2017%2Fcsc'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] d03c33ee5c6bc2e7583bd50315cc6203d9f34510 [INFO] checking mal2017/csc against try#5de9e0e6cf775e94e0de2003f35e183f3f77bfe8 for pr-143808 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmal2017%2Fcsc" "/workspace/builds/worker-0-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc2/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/mal2017/csc [INFO] finished tweaking git repo https://github.com/mal2017/csc [INFO] tweaked toml for git repo https://github.com/mal2017/csc written to /workspace/builds/worker-0-tc2/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/mal2017/csc on toolchain 5de9e0e6cf775e94e0de2003f35e183f3f77bfe8 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+5de9e0e6cf775e94e0de2003f35e183f3f77bfe8" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/mal2017/csc 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" "+5de9e0e6cf775e94e0de2003f35e183f3f77bfe8" "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] Updating git repository `https://github.com/mal2017/ngslib.git` [INFO] [stderr] Blocking waiting for file lock on package cache [ERROR] error running command: no output for 300 seconds [INFO] checking mal2017/csc against try#5de9e0e6cf775e94e0de2003f35e183f3f77bfe8 for pr-143808 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fmal2017%2Fcsc" "/workspace/builds/worker-0-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc2/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/mal2017/csc [INFO] finished tweaking git repo https://github.com/mal2017/csc [INFO] tweaked toml for git repo https://github.com/mal2017/csc written to /workspace/builds/worker-0-tc2/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/mal2017/csc on toolchain 5de9e0e6cf775e94e0de2003f35e183f3f77bfe8 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+5de9e0e6cf775e94e0de2003f35e183f3f77bfe8" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/mal2017/csc 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" "+5de9e0e6cf775e94e0de2003f35e183f3f77bfe8" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded bio-types v0.4.0 [INFO] [stderr] Downloaded bytecount v0.3.2 [INFO] [stderr] Downloaded clang-sys v0.22.0 [INFO] [stderr] Downloaded multimap v0.4.0 [INFO] [stderr] Downloaded bv v0.10.0 [INFO] [stderr] Downloaded bio v0.25.0 [INFO] [stderr] Downloaded statrs v0.9.0 [INFO] [stderr] Downloaded syn v0.15.31 [INFO] [stderr] Downloaded itertools v0.6.5 [INFO] [stderr] Downloaded lzma-sys v0.1.14 [INFO] [stderr] Downloaded fs-utils v1.1.0 [INFO] [stderr] Downloaded bindgen v0.36.1 [INFO] [stderr] Downloaded rust-htslib v0.22.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:cf8efcab8866f2cf4285301c7418e2f4f2a9b088c91ba69c40d5b659f81557f7" "/opt/rustwide/cargo-home/bin/cargo" "+5de9e0e6cf775e94e0de2003f35e183f3f77bfe8" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] a26048373d0b07ccb8f6f340dd41114c4935dff123ff7684eb3035280efe3c6c [INFO] running `Command { std: "docker" "start" "-a" "a26048373d0b07ccb8f6f340dd41114c4935dff123ff7684eb3035280efe3c6c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "a26048373d0b07ccb8f6f340dd41114c4935dff123ff7684eb3035280efe3c6c", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "a26048373d0b07ccb8f6f340dd41114c4935dff123ff7684eb3035280efe3c6c", kill_on_drop: false }` [INFO] [stdout] a26048373d0b07ccb8f6f340dd41114c4935dff123ff7684eb3035280efe3c6c [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:cf8efcab8866f2cf4285301c7418e2f4f2a9b088c91ba69c40d5b659f81557f7" "/opt/rustwide/cargo-home/bin/cargo" "+5de9e0e6cf775e94e0de2003f35e183f3f77bfe8" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] ba3711863eed1f97a475447f1213417b4c261b6d3751c6e781d235bb4a7bc143 [INFO] running `Command { std: "docker" "start" "-a" "ba3711863eed1f97a475447f1213417b4c261b6d3751c6e781d235bb4a7bc143", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.51 [INFO] [stderr] Compiling unicode-xid v0.1.0 [INFO] [stderr] Compiling proc-macro2 v0.4.27 [INFO] [stderr] Compiling syn v0.15.31 [INFO] [stderr] Compiling memchr v2.2.0 [INFO] [stderr] Compiling cc v1.0.35 [INFO] [stderr] Compiling serde v1.0.90 [INFO] [stderr] Compiling regex v1.1.5 [INFO] [stderr] Checking lazy_static v1.3.0 [INFO] [stderr] Compiling ucd-util v0.1.3 [INFO] [stderr] Compiling num-traits v0.2.6 [INFO] [stderr] Compiling glob v0.2.11 [INFO] [stderr] Compiling pkg-config v0.3.14 [INFO] [stderr] Compiling thread_local v0.3.6 [INFO] [stderr] Compiling utf8-ranges v1.0.2 [INFO] [stderr] Compiling quick-error v1.2.2 [INFO] [stderr] Checking either v1.5.2 [INFO] [stderr] Compiling regex-syntax v0.6.6 [INFO] [stderr] Compiling cfg-if v0.1.7 [INFO] [stderr] Compiling regex v0.2.11 [INFO] [stderr] Compiling clang-sys v0.22.0 [INFO] [stderr] Compiling libloading v0.5.0 [INFO] [stderr] Compiling quote v0.6.12 [INFO] [stderr] Compiling memchr v1.0.2 [INFO] [stderr] Compiling atty v0.2.11 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling unicode-width v0.1.5 [INFO] [stderr] Compiling nom v3.2.1 [INFO] [stderr] Compiling textwrap v0.10.0 [INFO] [stderr] Compiling aho-corasick v0.7.3 [INFO] [stderr] Compiling aho-corasick v0.6.10 [INFO] [stderr] Compiling log v0.4.6 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling humantime v1.2.0 [INFO] [stderr] Compiling regex-syntax v0.5.6 [INFO] [stderr] Compiling proc-macro2 v0.3.5 [INFO] [stderr] Compiling arrayvec v0.4.10 [INFO] [stderr] Compiling strsim v0.7.0 [INFO] [stderr] Compiling bitflags v1.0.4 [INFO] [stderr] Compiling yaml-rust v0.3.5 [INFO] [stderr] Compiling bindgen v0.36.1 [INFO] [stderr] Compiling termcolor v1.0.4 [INFO] [stderr] Compiling ansi_term v0.11.0 [INFO] [stderr] Compiling cexpr v0.2.3 [INFO] [stderr] Compiling quote v0.5.2 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling which v1.0.5 [INFO] [stderr] Compiling libz-sys v1.0.25 [INFO] [stderr] Compiling bzip2-sys v0.1.7 [INFO] [stderr] Compiling lzma-sys v0.1.14 [INFO] [stderr] Compiling serde_derive v1.0.90 [INFO] [stderr] Compiling peeking_take_while v0.1.2 [INFO] [stderr] Compiling matrixmultiply v0.1.15 [INFO] [stderr] Compiling ryu v0.2.7 [INFO] [stderr] Checking smallvec v0.6.9 [INFO] [stderr] Checking matches v0.1.8 [INFO] [stderr] Compiling byteorder v1.3.1 [INFO] [stderr] Compiling env_logger v0.5.13 [INFO] [stderr] Checking nodrop v0.1.13 [INFO] [stderr] Compiling feature-probe v0.1.1 [INFO] [stderr] Compiling num-complex v0.2.1 [INFO] [stderr] Compiling bv v0.10.0 [INFO] [stderr] Checking unicode-normalization v0.1.8 [INFO] [stderr] Checking unicode-bidi v0.3.4 [INFO] [stderr] Checking crossbeam-utils v0.2.2 [INFO] [stderr] Checking rand v0.4.6 [INFO] [stderr] Compiling fs-utils v1.1.0 [INFO] [stderr] Checking memoffset v0.2.1 [INFO] [stderr] Compiling rayon-core v1.4.1 [INFO] [stderr] Compiling num-integer v0.1.39 [INFO] [stderr] Checking scopeguard v0.3.3 [INFO] [stderr] Checking rawpointer v0.1.0 [INFO] [stderr] Compiling ndarray v0.12.1 [INFO] [stderr] Checking crossbeam-epoch v0.3.1 [INFO] [stderr] Checking idna v0.1.5 [INFO] [stderr] Checking rand v0.3.23 [INFO] [stderr] Checking csv-core v0.1.5 [INFO] [stderr] Checking itertools v0.7.11 [INFO] [stderr] Checking itoa v0.4.3 [INFO] [stderr] Checking bit-vec v0.5.1 [INFO] [stderr] Compiling bio v0.25.0 [INFO] [stderr] Checking percent-encoding v1.0.1 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking bit-set v0.5.1 [INFO] [stderr] Checking fxhash v0.2.1 [INFO] [stderr] Checking crossbeam-deque v0.2.0 [INFO] [stderr] Checking url v1.7.2 [INFO] [stderr] Checking statrs v0.9.0 [INFO] [stderr] Checking ordered-float v1.0.2 [INFO] [stderr] Checking approx v0.3.2 [INFO] [stderr] Checking itertools-num v0.1.3 [INFO] [stderr] Checking num_cpus v1.10.0 [INFO] [stderr] Checking itertools v0.6.5 [INFO] [stderr] Checking fnv v1.0.6 [INFO] [stderr] Checking bitflags v0.9.1 [INFO] [stderr] Compiling rayon v1.0.3 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Checking lazy_static v0.2.11 [INFO] [stderr] Checking bytecount v0.3.2 [INFO] [stderr] Checking itertools v0.8.0 [INFO] [stderr] Checking vec_map v0.8.1 [INFO] [stderr] Checking bio-types v0.4.0 [INFO] [stderr] Checking multimap v0.4.0 [INFO] [stderr] Checking csv v1.0.7 [INFO] [stderr] Checking clap v2.32.0 [INFO] [stderr] Compiling rust-htslib v0.22.0 [INFO] [stdout] error: expected one of `!`, `(`, `+`, `::`, or `<`, found `/` [INFO] [stdout] --> /opt/rustwide/target/debug/build/rust-htslib-e7169ef74e6bfc5e/out/bindings.rs:85:31536 [INFO] [stdout] | [INFO] [stdout] 85 | ...ruct htsFormat { pub category : htsFormatCategory , pub format : htsExactFormat , pub version : htsFormat_struct_(unnamed_at__/htslib/... [INFO] [stdout] | --------- while parsing this struct ^ expected one of `!`, `(`, `+`, `::`, or `<` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: expected one of `!`, `(`, `)`, `+`, `,`, `::`, or `<`, found `/` [INFO] [stdout] --> /opt/rustwide/target/debug/build/rust-htslib-e7169ef74e6bfc5e/out/bindings.rs:85:31809 [INFO] [stdout] | [INFO] [stdout] 85 | ...one ) ] pub struct htsFormat_struct_(unnamed_at__/htslib/htslib/hts_h_154_5) { pub major : :: std :: os :: raw :: c_short , pub minor ... [INFO] [stdout] | ^ expected one of 7 possible tokens [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam_pileup1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/pileup.rs:17:29 [INFO] [stdout] | [INFO] [stdout] 17 | slice::Iter<'a, htslib::bam_pileup1_t>, [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam_pileup1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/pileup.rs:18:20 [INFO] [stdout] | [INFO] [stdout] 18 | fn(&'a htslib::bam_pileup1_t) -> Alignment<'a>, [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam_pileup1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/pileup.rs:24:27 [INFO] [stdout] | [INFO] [stdout] 24 | inner: *const htslib::bam_pileup1_t, [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam_pileup1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/pileup.rs:47:34 [INFO] [stdout] | [INFO] [stdout] 47 | fn inner(&self) -> &[htslib::bam_pileup1_t] { [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam_pileup1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/pileup.rs:50:44 [INFO] [stdout] | [INFO] [stdout] 50 | self.inner as *mut htslib::bam_pileup1_t, [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam_pileup1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/pileup.rs:59:24 [INFO] [stdout] | [INFO] [stdout] 59 | inner: &'a htslib::bam_pileup1_t, [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam_pileup1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/pileup.rs:69:35 [INFO] [stdout] | [INFO] [stdout] 69 | pub fn new(inner: &'a htslib::bam_pileup1_t) -> Self { [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam_plp_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/pileup.rs:130:18 [INFO] [stdout] | [INFO] [stdout] 130 | itr: htslib::bam_plp_t, [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam_plp_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/pileup.rs:134:48 [INFO] [stdout] | [INFO] [stdout] 134 | pub fn new(reader: &'a mut R, itr: htslib::bam_plp_t) -> Self { [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_plp_set_maxcnt` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/pileup.rs:143:21 [INFO] [stdout] | [INFO] [stdout] 143 | htslib::bam_plp_set_maxcnt(self.itr, depth as i32); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_plp_auto` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/pileup.rs:153:38 [INFO] [stdout] | [INFO] [stdout] 153 | let inner = unsafe { htslib::bam_plp_auto(self.itr, &mut tid, &mut pos, &mut depth) }; [INFO] [stdout] | ^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_plp_reset` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/pileup.rs:171:21 [INFO] [stdout] | [INFO] [stdout] 171 | htslib::bam_plp_reset(self.itr); [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_plp_destroy` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/pileup.rs:172:21 [INFO] [stdout] | [INFO] [stdout] 172 | htslib::bam_plp_destroy(self.itr); [INFO] [stdout] | ^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:57:29 [INFO] [stdout] | [INFO] [stdout] 57 | pub inner: *mut htslib::bam1_t, [INFO] [stdout] | ^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_copy1` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:68:26 [INFO] [stdout] | [INFO] [stdout] 68 | unsafe { htslib::bam_copy1(copy.inner, self.inner) }; [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_init1` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:102:38 [INFO] [stdout] | [INFO] [stdout] 102 | let inner = unsafe { htslib::bam_init1() }; [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:112:43 [INFO] [stdout] | [INFO] [stdout] 112 | pub fn from_inner(inner: *mut htslib::bam1_t) -> Self { [INFO] [stdout] | ^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `sam_parse1` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:135:21 [INFO] [stdout] | [INFO] [stdout] 135 | htslib::sam_parse1(&mut sam_string, header_view.inner_ptr_mut(), record.inner) [INFO] [stdout] | ^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:150:49 [INFO] [stdout] | [INFO] [stdout] 150 | pub fn inner_mut(&mut self) -> &mut htslib::bam1_t { [INFO] [stdout] | ^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:155:37 [INFO] [stdout] | [INFO] [stdout] 155 | pub fn inner(&self) -> &htslib::bam1_t { [INFO] [stdout] | ^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_aux_get` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:468:21 [INFO] [stdout] | [INFO] [stdout] 468 | htslib::bam_aux_get( [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_aux2i` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:480:47 [INFO] [stdout] | [INFO] [stdout] 480 | Some(Aux::Integer(htslib::bam_aux2i(aux) as i64)) [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_aux2f` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:482:56 [INFO] [stdout] | [INFO] [stdout] 482 | b'f' | b'd' => Some(Aux::Float(htslib::bam_aux2f(aux))), [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_aux2A` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:483:48 [INFO] [stdout] | [INFO] [stdout] 483 | b'A' => Some(Aux::Char(htslib::bam_aux2A(aux) as u8)), [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_aux_append` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:500:44 [INFO] [stdout] | [INFO] [stdout] 500 | Aux::Integer(v) => htslib::bam_aux_append( [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_aux_append` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:507:42 [INFO] [stdout] | [INFO] [stdout] 507 | Aux::Float(v) => htslib::bam_aux_append( [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_aux_append` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:514:41 [INFO] [stdout] | [INFO] [stdout] 514 | Aux::Char(v) => htslib::bam_aux_append( [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_aux_append` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:521:43 [INFO] [stdout] | [INFO] [stdout] 521 | Aux::String(v) => htslib::bam_aux_append( [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_aux_get` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:541:21 [INFO] [stdout] | [INFO] [stdout] 541 | htslib::bam_aux_get( [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_aux_del` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:550:25 [INFO] [stdout] | [INFO] [stdout] 550 | htslib::bam_aux_del(self.inner, aux); [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_destroy1` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/record.rs:598:30 [INFO] [stdout] | [INFO] [stdout] 598 | unsafe { htslib::bam_destroy1(self.inner) }; [INFO] [stdout] | ^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `BGZF` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:30:39 [INFO] [stdout] | [INFO] [stdout] 30 | pub fn set_threads(bgzf: *mut htslib::BGZF, n_threads: usize) -> Result<(), ThreadingError> { [INFO] [stdout] | ^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bgzf_mt` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:33:25 [INFO] [stdout] | [INFO] [stdout] 33 | if unsafe { htslib::bgzf_mt(bgzf, n_threads as i32, 256) } != 0 { [INFO] [stdout] | ^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `BGZF` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:61:36 [INFO] [stdout] | [INFO] [stdout] 61 | fn bgzf(&self) -> *mut htslib::BGZF; [INFO] [stdout] | ^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bgzf_seek` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:68:36 [INFO] [stdout] | [INFO] [stdout] 68 | let ret = unsafe { htslib::bgzf_seek(self.bgzf(), offset, libc::SEEK_SET) }; [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `BGZF` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:100:24 [INFO] [stdout] | [INFO] [stdout] 100 | bgzf: *mut htslib::BGZF, [INFO] [stdout] | ^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_hdr_read` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:136:39 [INFO] [stdout] | [INFO] [stdout] 136 | let header = unsafe { htslib::bam_hdr_read(bgzf) }; [INFO] [stdout] | ^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:145:30 [INFO] [stdout] | [INFO] [stdout] 145 | record: *mut htslib::bam1_t, [INFO] [stdout] | ^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_read1` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:148:26 [INFO] [stdout] | [INFO] [stdout] 148 | unsafe { htslib::bam_read1(_self.bgzf, record) } [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_read1` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:174:32 [INFO] [stdout] | [INFO] [stdout] 174 | match unsafe { htslib::bam_read1(self.bgzf, record.inner) } { [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_plp_init` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:193:21 [INFO] [stdout] | [INFO] [stdout] 193 | htslib::bam_plp_init( [INFO] [stdout] | ^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `BGZF` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:201:36 [INFO] [stdout] | [INFO] [stdout] 201 | fn bgzf(&self) -> *mut htslib::BGZF { [INFO] [stdout] | ^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bgzf_close` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:213:21 [INFO] [stdout] | [INFO] [stdout] 213 | htslib::bgzf_close(self.bgzf); [INFO] [stdout] | ^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `BGZF` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:220:24 [INFO] [stdout] | [INFO] [stdout] 220 | bgzf: *mut htslib::BGZF, [INFO] [stdout] | ^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `hts_idx_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:222:23 [INFO] [stdout] | [INFO] [stdout] 222 | idx: *mut htslib::hts_idx_t, [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `hts_itr_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:223:30 [INFO] [stdout] | [INFO] [stdout] 223 | itr: Option<*mut htslib::hts_itr_t>, [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_hdr_read` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:254:39 [INFO] [stdout] | [INFO] [stdout] 254 | let header = unsafe { htslib::bam_hdr_read(bgzf) }; [INFO] [stdout] | ^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_idx_load` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:255:36 [INFO] [stdout] | [INFO] [stdout] 255 | let idx = unsafe { htslib::hts_idx_load(path.as_ptr(), htslib::HTS_FMT_BAI as i32) }; [INFO] [stdout] | ^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_itr_destroy` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:270:30 [INFO] [stdout] | [INFO] [stdout] 270 | unsafe { htslib::hts_itr_destroy(itr) } [INFO] [stdout] | ^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `sam_itr_queryi` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:272:36 [INFO] [stdout] | [INFO] [stdout] 272 | let itr = unsafe { htslib::sam_itr_queryi(self.idx, tid as i32, beg as i32, end as i32) }; [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:284:30 [INFO] [stdout] | [INFO] [stdout] 284 | record: *mut htslib::bam1_t, [INFO] [stdout] | ^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_read1` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:289:38 [INFO] [stdout] | [INFO] [stdout] 289 | None => unsafe { htslib::bam_read1(_self.bgzf, record) }, // ordinary reading [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_plp_init` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:318:21 [INFO] [stdout] | [INFO] [stdout] 318 | htslib::bam_plp_init( [INFO] [stdout] | ^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `BGZF` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:326:36 [INFO] [stdout] | [INFO] [stdout] 326 | fn bgzf(&self) -> *mut htslib::BGZF { [INFO] [stdout] | ^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_itr_destroy` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:339:25 [INFO] [stdout] | [INFO] [stdout] 339 | htslib::hts_itr_destroy(self.itr.unwrap()); [INFO] [stdout] | ^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_idx_destroy` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:341:21 [INFO] [stdout] | [INFO] [stdout] 341 | htslib::hts_idx_destroy(self.idx); [INFO] [stdout] | ^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bgzf_close` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:342:21 [INFO] [stdout] | [INFO] [stdout] 342 | htslib::bgzf_close(self.bgzf); [INFO] [stdout] | ^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `BGZF` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:350:21 [INFO] [stdout] | [INFO] [stdout] 350 | f: *mut htslib::BGZF, [INFO] [stdout] | ^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `sam_hdr_parse` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:411:31 [INFO] [stdout] | [INFO] [stdout] 411 | let rec = htslib::sam_hdr_parse((l_text + 1) as i32, text as *const i8); [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_hdr_write` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:419:21 [INFO] [stdout] | [INFO] [stdout] 419 | htslib::bam_hdr_write(f, header_record); [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_write1` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:444:29 [INFO] [stdout] | [INFO] [stdout] 444 | if unsafe { htslib::bam_write1(self.f, record.inner) } == -1 { [INFO] [stdout] | ^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bgzf_close` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:460:21 [INFO] [stdout] | [INFO] [stdout] 460 | htslib::bgzf_close(self.f); [INFO] [stdout] | ^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `BGZF` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:635:68 [INFO] [stdout] | [INFO] [stdout] 635 | fn bgzf_open(path: &ffi::CStr, mode: &[u8]) -> Result<*mut htslib::BGZF, BGZFError> { [INFO] [stdout] | ^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bgzf_open` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:637:26 [INFO] [stdout] | [INFO] [stdout] 637 | unsafe { htslib::bgzf_open(path.as_ptr(), ffi::CString::new(mode).unwrap().as_ptr()) }; [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `BGZF` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:647:24 [INFO] [stdout] | [INFO] [stdout] 647 | bgzf: *mut htslib::BGZF, [INFO] [stdout] | ^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `hts_itr_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:648:23 [INFO] [stdout] | [INFO] [stdout] 648 | itr: *mut htslib::hts_itr_t, [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:649:26 [INFO] [stdout] | [INFO] [stdout] 649 | record: *mut htslib::bam1_t, [INFO] [stdout] | ^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_itr_next` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:652:17 [INFO] [stdout] | [INFO] [stdout] 652 | htslib::hts_itr_next( [INFO] [stdout] | ^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam_hdr_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:663:25 [INFO] [stdout] | [INFO] [stdout] 663 | inner: *mut htslib::bam_hdr_t, [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `sam_hdr_parse` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:689:31 [INFO] [stdout] | [INFO] [stdout] 689 | let rec = htslib::sam_hdr_parse((l_text + 1) as i32, text as *const i8); [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam_hdr_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:699:36 [INFO] [stdout] | [INFO] [stdout] 699 | pub fn new(inner: *mut htslib::bam_hdr_t) -> Self { [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam_hdr_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:707:36 [INFO] [stdout] | [INFO] [stdout] 707 | pub fn inner(&self) -> htslib::bam_hdr_t { [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam_hdr_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:713:47 [INFO] [stdout] | [INFO] [stdout] 713 | pub fn inner_ptr(&self) -> *const htslib::bam_hdr_t { [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bam_hdr_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:719:49 [INFO] [stdout] | [INFO] [stdout] 719 | pub fn inner_ptr_mut(&self) -> *mut htslib::bam_hdr_t { [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_name2id` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:725:21 [INFO] [stdout] | [INFO] [stdout] 725 | htslib::bam_name2id( [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_hdr_dup` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:774:37 [INFO] [stdout] | [INFO] [stdout] 774 | inner: unsafe { htslib::bam_hdr_dup(self.inner) }, [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bam_hdr_destroy` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bam/mod.rs:784:25 [INFO] [stdout] | [INFO] [stdout] 784 | htslib::bam_hdr_destroy(self.inner); [INFO] [stdout] | ^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bcf_hdr_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:35:29 [INFO] [stdout] | [INFO] [stdout] 35 | pub inner: *mut htslib::bcf_hdr_t, [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_init` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:43:37 [INFO] [stdout] | [INFO] [stdout] 43 | inner: unsafe { htslib::bcf_hdr_init(ffi::CString::new(&b"w"[..]).unwrap().as_ptr()) }, [INFO] [stdout] | ^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_dup` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:57:37 [INFO] [stdout] | [INFO] [stdout] 57 | inner: unsafe { htslib::bcf_hdr_dup(header.inner) }, [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_subset` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:80:21 [INFO] [stdout] | [INFO] [stdout] 80 | htslib::bcf_hdr_subset( [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_add_sample` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:104:21 [INFO] [stdout] | [INFO] [stdout] 104 | htslib::bcf_hdr_add_sample(self.inner, ffi::CString::new(sample).unwrap().as_ptr()) [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_append` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:121:26 [INFO] [stdout] | [INFO] [stdout] 121 | unsafe { htslib::bcf_hdr_append(self.inner, ffi::CString::new(record).unwrap().as_ptr()) }; [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_remove` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:184:21 [INFO] [stdout] | [INFO] [stdout] 184 | htslib::bcf_hdr_remove(self.inner, type_ as i32, c_str.as_ptr()); [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_destroy` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:192:26 [INFO] [stdout] | [INFO] [stdout] 192 | unsafe { htslib::bcf_hdr_destroy(self.inner) }; [INFO] [stdout] | ^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bcf_hdr_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:230:29 [INFO] [stdout] | [INFO] [stdout] 230 | pub inner: *mut htslib::bcf_hdr_t, [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bcf_hdr_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:234:36 [INFO] [stdout] | [INFO] [stdout] 234 | pub fn new(inner: *mut htslib::bcf_hdr_t) -> Self { [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bcf_hdr_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:239:32 [INFO] [stdout] | [INFO] [stdout] 239 | fn inner(&self) -> htslib::bcf_hdr_t { [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_id2int` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:266:27 [INFO] [stdout] | [INFO] [stdout] 266 | match htslib::bcf_hdr_id2int( [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_id2int` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:293:30 [INFO] [stdout] | [INFO] [stdout] 293 | let id = htslib::bcf_hdr_id2int( [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_id2int` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:330:27 [INFO] [stdout] | [INFO] [stdout] 330 | match htslib::bcf_hdr_id2int( [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_id2int` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:355:27 [INFO] [stdout] | [INFO] [stdout] 355 | match htslib::bcf_hdr_id2int( [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bcf_hrec_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:380:35 [INFO] [stdout] | [INFO] [stdout] 380 | fn parse_kv(rec: &htslib::bcf_hrec_t) -> LinearMap { [INFO] [stdout] | ^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_dup` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:440:37 [INFO] [stdout] | [INFO] [stdout] 440 | inner: unsafe { htslib::bcf_hdr_dup(self.inner) }, [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_destroy` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/header.rs:448:21 [INFO] [stdout] | [INFO] [stdout] 448 | htslib::bcf_hdr_destroy(self.inner); [INFO] [stdout] | ^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bcf1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:77:29 [INFO] [stdout] | [INFO] [stdout] 77 | pub inner: *mut htslib::bcf1_t, [INFO] [stdout] | ^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_init` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:86:33 [INFO] [stdout] | [INFO] [stdout] 86 | let inner = htslib::bcf_init(); [INFO] [stdout] | ^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_unpack` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:88:21 [INFO] [stdout] | [INFO] [stdout] 88 | htslib::bcf_unpack(inner, htslib::BCF_UN_ALL as i32); [INFO] [stdout] | ^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_unpack` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:100:26 [INFO] [stdout] | [INFO] [stdout] 100 | unsafe { htslib::bcf_unpack(self.inner, htslib::BCF_UN_ALL as i32) }; [INFO] [stdout] | ^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bcf1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:119:37 [INFO] [stdout] | [INFO] [stdout] 119 | pub fn inner(&self) -> &htslib::bcf1_t { [INFO] [stdout] | ^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bcf1_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:129:49 [INFO] [stdout] | [INFO] [stdout] 129 | pub fn inner_mut(&mut self) -> &mut htslib::bcf1_t { [INFO] [stdout] | ^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_update_id` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:181:21 [INFO] [stdout] | [INFO] [stdout] 181 | htslib::bcf_update_id( [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_update_id` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:197:21 [INFO] [stdout] | [INFO] [stdout] 197 | htslib::bcf_update_id( [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_add_id` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:213:21 [INFO] [stdout] | [INFO] [stdout] 213 | htslib::bcf_add_id( [INFO] [stdout] | ^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_update_filter` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:260:21 [INFO] [stdout] | [INFO] [stdout] 260 | htslib::bcf_update_filter( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_add_filter` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:279:21 [INFO] [stdout] | [INFO] [stdout] 279 | htslib::bcf_add_filter(self.header().inner, self.inner, *flt_id as i32); [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_remove_filter` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:291:21 [INFO] [stdout] | [INFO] [stdout] 291 | htslib::bcf_remove_filter( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_unpack` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:304:26 [INFO] [stdout] | [INFO] [stdout] 304 | unsafe { htslib::bcf_unpack(self.inner, htslib::BCF_UN_ALL as i32) }; [INFO] [stdout] | ^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_update_alleles` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:324:21 [INFO] [stdout] | [INFO] [stdout] 324 | htslib::bcf_update_alleles( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_update_format` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:430:24 [INFO] [stdout] | [INFO] [stdout] 430 | if htslib::bcf_update_format( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_update_format_string` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:469:24 [INFO] [stdout] | [INFO] [stdout] 469 | if htslib::bcf_update_format_string( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_update_info` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:508:24 [INFO] [stdout] | [INFO] [stdout] 508 | if htslib::bcf_update_info( [INFO] [stdout] | ^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_update_info` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:565:24 [INFO] [stdout] | [INFO] [stdout] 565 | if htslib::bcf_update_info( [INFO] [stdout] | ^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_trim_alleles` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:583:32 [INFO] [stdout] | [INFO] [stdout] 583 | match unsafe { htslib::bcf_trim_alleles(self.header().inner, self.inner) } { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `kbs_init` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:590:39 [INFO] [stdout] | [INFO] [stdout] 590 | let rm_set = unsafe { htslib::kbs_init(remove.len()) }; [INFO] [stdout] | ^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `kbs_insert` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:595:29 [INFO] [stdout] | [INFO] [stdout] 595 | htslib::kbs_insert(rm_set, i as i32); [INFO] [stdout] | ^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_remove_allele_set` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:600:36 [INFO] [stdout] | [INFO] [stdout] 600 | let ret = unsafe { htslib::bcf_remove_allele_set(self.header().inner, self.inner, rm_set) }; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `kbs_destroy` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:603:21 [INFO] [stdout] | [INFO] [stdout] 603 | htslib::kbs_destroy(rm_set); [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_destroy` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:705:26 [INFO] [stdout] | [INFO] [stdout] 705 | unsafe { htslib::bcf_destroy(self.inner) }; [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_get_info_values` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:723:21 [INFO] [stdout] | [INFO] [stdout] 723 | htslib::bcf_get_info_values( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bcf_fmt_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:801:25 [INFO] [stdout] | [INFO] [stdout] 801 | inner: *mut htslib::bcf_fmt_t, [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_get_fmt` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:808:21 [INFO] [stdout] | [INFO] [stdout] 808 | htslib::bcf_get_fmt( [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bcf_fmt_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:821:37 [INFO] [stdout] | [INFO] [stdout] 821 | pub fn inner(&self) -> &htslib::bcf_fmt_t { [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bcf_fmt_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:825:49 [INFO] [stdout] | [INFO] [stdout] 825 | pub fn inner_mut(&mut self) -> &mut htslib::bcf_fmt_t { [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_get_format_values` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/record.rs:837:21 [INFO] [stdout] | [INFO] [stdout] 837 | htslib::bcf_get_format_values( [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `htsFile` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:65:25 [INFO] [stdout] | [INFO] [stdout] 65 | inner: *mut htslib::htsFile, [INFO] [stdout] | ^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `htsFile` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:72:43 [INFO] [stdout] | [INFO] [stdout] 72 | pub fn set_threads(hts_file: *mut htslib::htsFile, n_threads: usize) -> Result<(), ThreadingError> { [INFO] [stdout] | ^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_set_threads` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:75:30 [INFO] [stdout] | [INFO] [stdout] 75 | let r = unsafe { htslib::hts_set_threads(hts_file, n_threads as i32) }; [INFO] [stdout] | ^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_read` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:104:39 [INFO] [stdout] | [INFO] [stdout] 104 | let header = unsafe { htslib::bcf_hdr_read(htsfile) }; [INFO] [stdout] | ^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_read` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:114:32 [INFO] [stdout] | [INFO] [stdout] 114 | match unsafe { htslib::bcf_read(self.inner, self.header.inner, record.inner) } { [INFO] [stdout] | ^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_unpack` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:118:29 [INFO] [stdout] | [INFO] [stdout] 118 | htslib::bcf_unpack(record.inner_mut(), htslib::BCF_UN_ALL as i32); [INFO] [stdout] | ^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_close` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:149:21 [INFO] [stdout] | [INFO] [stdout] 149 | htslib::hts_close(self.inner); [INFO] [stdout] | ^^^^^^^^^ help: a function with a similar name exists: `hts_log` [INFO] [stdout] | [INFO] [stdout] ::: /opt/rustwide/target/debug/build/rust-htslib-e7169ef74e6bfc5e/out/bindings.rs:85:27989 [INFO] [stdout] | [INFO] [stdout] 85 | ... { pub fn hts_log ( severity : htsLogLevel , context : * const :: std :: os :: raw :: c_char , format : * const :: std :: os :: raw :: c_char , ... ) ; } ... [INFO] [stdout] | ---------------------------------------------------------------------------------------------------------------------------------------------------- similarly named function `hts_log` defined here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bcf_srs_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:158:25 [INFO] [stdout] | [INFO] [stdout] 158 | inner: *mut htslib::bcf_srs_t, [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_sr_init` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:195:43 [INFO] [stdout] | [INFO] [stdout] 195 | let ser_reader = unsafe { htslib::bcf_sr_init() }; [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_sr_set_opt` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:197:21 [INFO] [stdout] | [INFO] [stdout] 197 | htslib::bcf_sr_set_opt(ser_reader, 0); [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_sr_add_reader` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:200:29 [INFO] [stdout] | [INFO] [stdout] 200 | if unsafe { htslib::bcf_sr_add_reader(ser_reader, path.as_ptr()) } >= 0 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_dup` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:202:25 [INFO] [stdout] | [INFO] [stdout] 202 | htslib::bcf_hdr_dup((*(*ser_reader).readers.offset(0)).header) [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_sr_seek` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:226:29 [INFO] [stdout] | [INFO] [stdout] 226 | if unsafe { htslib::bcf_sr_seek(self.inner, contig, start as i32) } != 0 { [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_sr_next_line` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:237:32 [INFO] [stdout] | [INFO] [stdout] 237 | match unsafe { htslib::bcf_sr_next_line(self.inner) } { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_copy` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:252:29 [INFO] [stdout] | [INFO] [stdout] 252 | htslib::bcf_copy( [INFO] [stdout] | ^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_sr_set_threads` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:284:34 [INFO] [stdout] | [INFO] [stdout] 284 | let r = unsafe { htslib::bcf_sr_set_threads(self.inner, n_threads as i32) }; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_sr_destroy` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:303:26 [INFO] [stdout] | [INFO] [stdout] 303 | unsafe { htslib::bcf_sr_destroy(self.inner) }; [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `bcf_srs_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:338:31 [INFO] [stdout] | [INFO] [stdout] 338 | inner: *mut ::htslib::bcf_srs_t, [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_sr_init` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:351:44 [INFO] [stdout] | [INFO] [stdout] 351 | let inner = unsafe { ::htslib::bcf_sr_init() }; [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_sr_set_opt` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:374:27 [INFO] [stdout] | [INFO] [stdout] 374 | ::htslib::bcf_sr_set_opt(self.inner, 1, bitmask); [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_sr_add_reader` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:384:44 [INFO] [stdout] | [INFO] [stdout] 384 | unsafe { ::htslib::bcf_sr_add_reader(self.inner, p_cstring.as_ptr()) }; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_dup` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:388:39 [INFO] [stdout] | [INFO] [stdout] 388 | ... ::htslib::bcf_hdr_dup((*(*self.inner).readers.offset(i)).header) [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_sr_remove_reader` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:406:31 [INFO] [stdout] | [INFO] [stdout] 406 | ::htslib::bcf_sr_remove_reader(self.inner, idx as i32); [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_sr_next_line` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:419:42 [INFO] [stdout] | [INFO] [stdout] 419 | let num = unsafe { ::htslib::bcf_sr_next_line(self.inner) as u32 }; [INFO] [stdout] | ^^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_copy` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:465:31 [INFO] [stdout] | [INFO] [stdout] 465 | ::htslib::bcf_copy( [INFO] [stdout] | ^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_sr_seek` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:502:33 [INFO] [stdout] | [INFO] [stdout] 502 | if unsafe { htslib::bcf_sr_seek(self.inner, contig, start as i32) } != 0 { [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_sr_destroy` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:513:32 [INFO] [stdout] | [INFO] [stdout] 513 | unsafe { ::htslib::bcf_sr_destroy(self.inner) }; [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `htsFile` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:522:25 [INFO] [stdout] | [INFO] [stdout] 522 | inner: *mut htslib::htsFile, [INFO] [stdout] | ^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_write` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:588:26 [INFO] [stdout] | [INFO] [stdout] 588 | unsafe { htslib::bcf_hdr_write(htsfile, header.inner) }; [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_hdr_dup` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:592:25 [INFO] [stdout] | [INFO] [stdout] 592 | htslib::bcf_hdr_dup(header.inner) [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_translate` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:617:21 [INFO] [stdout] | [INFO] [stdout] 617 | htslib::bcf_translate(self.header.inner, record.header().inner, record.inner); [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_subset` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:630:25 [INFO] [stdout] | [INFO] [stdout] 630 | htslib::bcf_subset( [INFO] [stdout] | ^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `bcf_write` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:647:29 [INFO] [stdout] | [INFO] [stdout] 647 | if unsafe { htslib::bcf_write(self.inner, self.header.inner, record.inner) } == -1 { [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_close` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:668:21 [INFO] [stdout] | [INFO] [stdout] 668 | htslib::hts_close(self.inner); [INFO] [stdout] | ^^^^^^^^^ help: a function with a similar name exists: `hts_log` [INFO] [stdout] | [INFO] [stdout] ::: /opt/rustwide/target/debug/build/rust-htslib-e7169ef74e6bfc5e/out/bindings.rs:85:27989 [INFO] [stdout] | [INFO] [stdout] 85 | ... { pub fn hts_log ( severity : htsLogLevel , context : * const :: std :: os :: raw :: c_char , format : * const :: std :: os :: raw :: c_char , ... ) ; } ... [INFO] [stdout] | ---------------------------------------------------------------------------------------------------------------------------------------------------- similarly named function `hts_log` defined here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `htsFile` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:731:62 [INFO] [stdout] | [INFO] [stdout] 731 | fn bcf_open(path: &[u8], mode: &[u8]) -> Result<*mut htslib::htsFile, BCFError> { [INFO] [stdout] | ^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_open` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/bcf/mod.rs:733:32 [INFO] [stdout] | [INFO] [stdout] 733 | let ret = unsafe { htslib::hts_open(p.as_ptr(), ffi::CString::new(mode).unwrap().as_ptr()) }; [INFO] [stdout] | ^^^^^^^^ not found in `htslib` [INFO] [stdout] | [INFO] [stdout] note: function `sam::hts_open` exists but is inaccessible [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/sam/mod.rs:25:1 [INFO] [stdout] | [INFO] [stdout] 25 | fn hts_open(path: &ffi::CStr, mode: &[u8]) -> Result<*mut htslib::htsFile, WriterError> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ not accessible [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `htsFile` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/sam/mod.rs:20:21 [INFO] [stdout] | [INFO] [stdout] 20 | f: *mut htslib::htsFile, [INFO] [stdout] | ^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `htsFile` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/sam/mod.rs:25:67 [INFO] [stdout] | [INFO] [stdout] 25 | fn hts_open(path: &ffi::CStr, mode: &[u8]) -> Result<*mut htslib::htsFile, WriterError> { [INFO] [stdout] | ^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_open` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/sam/mod.rs:26:32 [INFO] [stdout] | [INFO] [stdout] 26 | let ret = unsafe { htslib::hts_open(path.as_ptr(), ffi::CString::new(mode).unwrap().as_ptr()) }; [INFO] [stdout] | ^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `sam_hdr_write` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/sam/mod.rs:66:21 [INFO] [stdout] | [INFO] [stdout] 66 | htslib::sam_hdr_write(f, &header_view.inner()); [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `sam_write1` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/sam/mod.rs:80:29 [INFO] [stdout] | [INFO] [stdout] 80 | if unsafe { htslib::sam_write1(self.f, &self.header.inner(), record.inner) } == -1 { [INFO] [stdout] | ^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_close` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/sam/mod.rs:91:21 [INFO] [stdout] | [INFO] [stdout] 91 | htslib::hts_close(self.f); [INFO] [stdout] | ^^^^^^^^^ help: a function with a similar name exists: `hts_log` [INFO] [stdout] | [INFO] [stdout] ::: /opt/rustwide/target/debug/build/rust-htslib-e7169ef74e6bfc5e/out/bindings.rs:85:27989 [INFO] [stdout] | [INFO] [stdout] 85 | ... { pub fn hts_log ( severity : htsLogLevel , context : * const :: std :: os :: raw :: c_char , format : * const :: std :: os :: raw :: c_char , ... ) ; } ... [INFO] [stdout] | ---------------------------------------------------------------------------------------------------------------------------------------------------- similarly named function `hts_log` defined here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `htsFile` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:89:28 [INFO] [stdout] | [INFO] [stdout] 89 | hts_file: *mut htslib::htsFile, [INFO] [stdout] | ^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `tbx_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:93:23 [INFO] [stdout] | [INFO] [stdout] 93 | tbx: *mut htslib::tbx_t, [INFO] [stdout] | ^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0412]: cannot find type `hts_itr_t` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:97:30 [INFO] [stdout] | [INFO] [stdout] 97 | itr: Option<*mut htslib::hts_itr_t>, [INFO] [stdout] | ^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_open` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:138:30 [INFO] [stdout] | [INFO] [stdout] 138 | unsafe { htslib::hts_open(path.as_ptr(), ffi::CString::new("r").unwrap().as_ptr()) }; [INFO] [stdout] | ^^^^^^^^ not found in `htslib` [INFO] [stdout] | [INFO] [stdout] note: function `sam::hts_open` exists but is inaccessible [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/sam/mod.rs:25:1 [INFO] [stdout] | [INFO] [stdout] 25 | fn hts_open(path: &ffi::CStr, mode: &[u8]) -> Result<*mut htslib::htsFile, WriterError> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ not accessible [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_get_format` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:139:45 [INFO] [stdout] | [INFO] [stdout] 139 | let hts_format = unsafe { (*htslib::hts_get_format(hts_file)).format }; [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `tbx_index_load` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:140:36 [INFO] [stdout] | [INFO] [stdout] 140 | let tbx = unsafe { htslib::tbx_index_load(path.as_ptr()) }; [INFO] [stdout] | ^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_getline` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:148:27 [INFO] [stdout] | [INFO] [stdout] 148 | while htslib::hts_getline(hts_file, KS_SEP_LINE, &mut buf) >= 0 { [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `tbx_name2id` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:178:21 [INFO] [stdout] | [INFO] [stdout] 178 | htslib::tbx_name2id( [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_itr_destroy` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:198:25 [INFO] [stdout] | [INFO] [stdout] 198 | htslib::hts_itr_destroy(itr); [INFO] [stdout] | ^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_itr_query` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:202:21 [INFO] [stdout] | [INFO] [stdout] 202 | htslib::hts_itr_query( [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find value `tbx_readrec` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:207:30 [INFO] [stdout] | [INFO] [stdout] 207 | Some(htslib::tbx_readrec), [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `tbx_seqnames` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:224:37 [INFO] [stdout] | [INFO] [stdout] 224 | let seqs = unsafe { htslib::tbx_seqnames(self.tbx, &mut nseq) }; [INFO] [stdout] | ^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_set_threads` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:250:34 [INFO] [stdout] | [INFO] [stdout] 250 | let r = unsafe { htslib::hts_set_threads(self.hts_file, n_threads as i32) }; [INFO] [stdout] | ^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_itr_next` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:271:33 [INFO] [stdout] | [INFO] [stdout] 271 | htslib::hts_itr_next( [INFO] [stdout] | ^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_get_bgzfp` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:272:37 [INFO] [stdout] | [INFO] [stdout] 272 | ... htslib::hts_get_bgzfp(self.hts_file), [INFO] [stdout] | ^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_itr_destroy` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:314:25 [INFO] [stdout] | [INFO] [stdout] 314 | htslib::hts_itr_destroy(self.itr.unwrap()); [INFO] [stdout] | ^^^^^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `tbx_destroy` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:316:21 [INFO] [stdout] | [INFO] [stdout] 316 | htslib::tbx_destroy(self.tbx); [INFO] [stdout] | ^^^^^^^^^^^ not found in `htslib` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0425]: cannot find function `hts_close` in module `htslib` [INFO] [stdout] --> /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/rust-htslib-0.22.0/src/tbx/mod.rs:317:21 [INFO] [stdout] | [INFO] [stdout] 317 | htslib::hts_close(self.hts_file); [INFO] [stdout] | ^^^^^^^^^ help: a function with a similar name exists: `hts_log` [INFO] [stdout] | [INFO] [stdout] ::: /opt/rustwide/target/debug/build/rust-htslib-e7169ef74e6bfc5e/out/bindings.rs:85:27989 [INFO] [stdout] | [INFO] [stdout] 85 | ... { pub fn hts_log ( severity : htsLogLevel , context : * const :: std :: os :: raw :: c_char , format : * const :: std :: os :: raw :: c_char , ... ) ; } ... [INFO] [stdout] | ---------------------------------------------------------------------------------------------------------------------------------------------------- similarly named function `hts_log` defined here [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0412, E0425. [INFO] [stdout] [INFO] [stdout] For more information about an error, try `rustc --explain E0412`. [INFO] [stdout] [INFO] [stderr] error: could not compile `rust-htslib` (lib) due to 187 previous errors [INFO] running `Command { std: "docker" "inspect" "ba3711863eed1f97a475447f1213417b4c261b6d3751c6e781d235bb4a7bc143", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "ba3711863eed1f97a475447f1213417b4c261b6d3751c6e781d235bb4a7bc143", kill_on_drop: false }` [INFO] [stdout] ba3711863eed1f97a475447f1213417b4c261b6d3751c6e781d235bb4a7bc143