[INFO] cloning repository https://github.com/keithyin/rsabpoa [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/keithyin/rsabpoa" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkeithyin%2Frsabpoa", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkeithyin%2Frsabpoa'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 97f9901fb57de401d931d75482b308cd6fe7cc5e [INFO] testing keithyin/rsabpoa against 1.90.0 for beta-1.91-3 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkeithyin%2Frsabpoa" "/workspace/builds/worker-0-tc1/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc1/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/keithyin/rsabpoa [INFO] finished tweaking git repo https://github.com/keithyin/rsabpoa [INFO] tweaked toml for git repo https://github.com/keithyin/rsabpoa written to /workspace/builds/worker-0-tc1/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/keithyin/rsabpoa on toolchain 1.90.0 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.90.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/keithyin/rsabpoa 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" "+1.90.0" "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] Blocking waiting for file lock on package cache [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded rustc_version v0.1.7 [INFO] [stderr] Downloaded ieee754 v0.2.6 [INFO] [stderr] Downloaded linear-map v1.2.0 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded semver v0.1.20 [INFO] [stderr] Downloaded derive-new v0.6.0 [INFO] [stderr] Downloaded itertools-num v0.1.3 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded editdistancek v1.0.2 [INFO] [stderr] Downloaded crossbeam v0.8.4 [INFO] [stderr] Downloaded bio-types v1.0.4 [INFO] [stderr] Downloaded derive-new v0.7.0 [INFO] [stderr] Downloaded triple_accel v0.4.0 [INFO] [stderr] Downloaded simba v0.9.0 [INFO] [stderr] Downloaded matrixmultiply v0.3.9 [INFO] [stderr] Downloaded zerocopy-derive v0.8.22 [INFO] [stderr] Downloaded wide v0.7.32 [INFO] [stderr] Downloaded rust-htslib v0.49.0 [INFO] [stderr] Downloaded gskits v0.13.2 [INFO] [stderr] Downloaded statrs v0.18.0 [INFO] [stderr] Downloaded zerocopy v0.8.22 [INFO] [stderr] Downloaded bio v2.2.0 [INFO] [stderr] 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"/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+1.90.0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 33593af13407d8a78f0ab1613a40287dd529c2ad2804d2a142738270ee96a423 [INFO] running `Command { std: "docker" "start" "-a" "33593af13407d8a78f0ab1613a40287dd529c2ad2804d2a142738270ee96a423", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "33593af13407d8a78f0ab1613a40287dd529c2ad2804d2a142738270ee96a423", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "33593af13407d8a78f0ab1613a40287dd529c2ad2804d2a142738270ee96a423", kill_on_drop: false }` [INFO] [stdout] 33593af13407d8a78f0ab1613a40287dd529c2ad2804d2a142738270ee96a423 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-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=warn" "-e" "RUSTDOCFLAGS=--cap-lints=warn" "-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+1.90.0" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 735f0320cae955386cb999d9ea1822df2da07984accd449b95608f4dc06c823d [INFO] running `Command { std: "docker" "start" "-a" "735f0320cae955386cb999d9ea1822df2da07984accd449b95608f4dc06c823d", kill_on_drop: false }` [INFO] [stderr] Compiling libm v0.2.11 [INFO] [stderr] Compiling byteorder v1.5.0 [INFO] [stderr] Compiling glob v0.3.2 [INFO] [stderr] Compiling serde v1.0.218 [INFO] [stderr] Compiling libc v0.2.170 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling minimal-lexical v0.2.1 [INFO] [stderr] Compiling regex-syntax v0.8.5 [INFO] [stderr] Compiling matrixmultiply v0.3.9 [INFO] [stderr] Compiling libloading v0.8.6 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling quote v1.0.39 [INFO] [stderr] Compiling either v1.15.0 [INFO] [stderr] Compiling rustversion v1.0.20 [INFO] [stderr] Compiling bytemuck v1.22.0 [INFO] [stderr] Compiling bindgen v0.69.5 [INFO] [stderr] Compiling syn v2.0.99 [INFO] [stderr] Compiling nom v7.1.3 [INFO] [stderr] Compiling 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[stderr] Compiling rsabpoa v0.4.0 (/opt/rustwide/workdir) [INFO] [stderr] Compiling libz-sys v1.1.21 [INFO] [stderr] Compiling openssl-sys v0.9.106 [INFO] [stderr] Compiling lzma-sys v0.1.20 [INFO] [stderr] Compiling bzip2-sys v0.1.13+1.0.8 [INFO] [stderr] Compiling curl-sys v0.4.80+curl-8.12.1 [INFO] [stderr] Compiling crossbeam v0.8.4 [INFO] [stderr] Compiling synstructure v0.13.1 [INFO] [stderr] Compiling zerofrom-derive v0.1.6 [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 zerocopy-derive v0.7.35 [INFO] [stderr] Compiling icu_provider_macros v1.5.0 [INFO] [stderr] Compiling serde_derive v1.0.218 [INFO] [stderr] Compiling thiserror-impl v1.0.69 [INFO] [stderr] Compiling thiserror-impl v2.0.12 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Compiling derive-new v0.7.0 [INFO] [stderr] Compiling enum-map v2.7.3 [INFO] [stderr] Compiling tracing-attributes v0.1.28 [INFO] [stderr] Compiling clap_derive v4.5.28 [INFO] [stderr] Compiling zerocopy v0.7.35 [INFO] [stderr] Compiling zerofrom v0.1.6 [INFO] [stderr] Compiling yoke v0.7.5 [INFO] [stderr] Compiling thiserror v1.0.69 [INFO] [stderr] Compiling zerovec v0.10.4 [INFO] [stderr] Compiling ppv-lite86 v0.2.20 [INFO] [stderr] Compiling tracing v0.1.41 [INFO] [stderr] Compiling bio-types v1.0.4 [INFO] [stderr] Compiling rand_chacha v0.3.1 [INFO] [stderr] Compiling rand_chacha v0.9.0 [INFO] [stderr] Compiling rand v0.9.0 [INFO] [stderr] Compiling rand v0.8.5 [INFO] [stderr] Compiling clap v4.5.31 [INFO] [stderr] Compiling tinystr v0.7.6 [INFO] [stderr] Compiling icu_collections v1.5.0 [INFO] [stderr] Compiling icu_locid v1.5.0 [INFO] [stderr] Compiling rand_distr v0.4.3 [INFO] [stderr] Compiling icu_provider v1.5.0 [INFO] [stderr] Compiling icu_locid_transform v1.5.0 [INFO] [stderr] Compiling icu_properties v1.5.1 [INFO] [stderr] Compiling hts-sys v2.2.0 [INFO] [stderr] Compiling nalgebra v0.33.2 [INFO] [stderr] Compiling icu_normalizer v1.5.0 [INFO] [stderr] Compiling idna_adapter v1.2.0 [INFO] [stderr] Compiling idna v1.0.3 [INFO] [stderr] Compiling url v2.5.4 [INFO] [stderr] Compiling csv v1.3.1 [INFO] [stderr] Compiling multimap v0.10.0 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling statrs v0.18.0 [INFO] [stderr] Compiling bio v2.2.0 [INFO] [stderr] Compiling rust-htslib v0.49.0 [INFO] [stderr] Compiling gskits v0.13.2 [INFO] [stdout] warning: type `__off_t` should have an upper camel case name [INFO] [stdout] --> src/abpoa_sys.rs:83:10 [INFO] [stdout] | [INFO] [stdout] 83 | pub type __off_t = ::std::os::raw::c_long; [INFO] [stdout] | ^^^^^^^ help: convert the identifier to upper camel case: `OffT` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_camel_case_types)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `__off64_t` should have an upper camel case name [INFO] [stdout] --> src/abpoa_sys.rs:84:10 [INFO] [stdout] | [INFO] [stdout] 84 | pub type __off64_t = ::std::os::raw::c_long; [INFO] [stdout] | ^^^^^^^^^ help: convert the identifier to upper camel case: `Off64T` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `__m128i` should have an upper camel case name [INFO] [stdout] --> src/abpoa_sys.rs:85:10 [INFO] [stdout] | [INFO] [stdout] 85 | pub type __m128i = [::std::os::raw::c_longlong; 2usize]; [INFO] [stdout] | ^^^^^^^ help: convert the identifier to upper camel case: `M128i` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `_IO_lock_t` should have an upper camel case name [INFO] [stdout] --> src/abpoa_sys.rs:102:10 [INFO] [stdout] | [INFO] [stdout] 102 | pub type _IO_lock_t = ::std::os::raw::c_void; [INFO] [stdout] | ^^^^^^^^^^ help: convert the identifier to upper camel case: `IoLockT` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `marker::PhantomData` [INFO] [stdout] --> src/abpoa.rs:1:23 [INFO] [stdout] | [INFO] [stdout] 1 | use std::{ffi::c_int, marker::PhantomData, ops::Deref}; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused imports: `abpoa_add_graph_alignment`, `abpoa_align_sequence_to_graph`, `abpoa_cons_t`, `abpoa_free`, `abpoa_generate_consensus`, `abpoa_generate_rc_msa`, `abpoa_init`, `abpoa_msa1`, `abpoa_post_set_para`, `abpoa_reset`, and `utils::reverse_complement` [INFO] [stdout] --> src/abpoa.rs:6:9 [INFO] [stdout] | [INFO] [stdout] 6 | abpoa_add_graph_alignment, abpoa_align_sequence_to_graph, abpoa_cons_t, abpoa_free, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^ ^^^^^^^^^^ [INFO] [stdout] 7 | abpoa_generate_consensus, abpoa_generate_rc_msa, abpoa_init, abpoa_msa, abpoa_msa1, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^ ^^^^^^^^^^ [INFO] [stdout] 8 | abpoa_para_t, abpoa_post_set_para, abpoa_res_t, abpoa_reset, abpoa_t, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^ [INFO] [stdout] 9 | }, [INFO] [stdout] 10 | utils::reverse_complement, [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `abpoa::AlignMode` [INFO] [stdout] --> src/wrapper.rs:3:13 [INFO] [stdout] | [INFO] [stdout] 3 | use crate::{abpoa::AlignMode, abpoa_sys::{ [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `_IO_read_ptr` should have a snake case name [INFO] [stdout] --> src/abpoa_sys.rs:107:9 [INFO] [stdout] | [INFO] [stdout] 107 | pub _IO_read_ptr: *mut ::std::os::raw::c_char, [INFO] [stdout] | ^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): `_io_read_ptr` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_snake_case)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `_IO_read_end` should have a snake case name [INFO] [stdout] --> src/abpoa_sys.rs:108:9 [INFO] [stdout] | [INFO] [stdout] 108 | pub _IO_read_end: *mut ::std::os::raw::c_char, [INFO] [stdout] | ^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): `_io_read_end` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `_IO_read_base` should have a snake case name [INFO] [stdout] --> src/abpoa_sys.rs:109:9 [INFO] [stdout] | [INFO] [stdout] 109 | pub _IO_read_base: *mut ::std::os::raw::c_char, [INFO] [stdout] | ^^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): `_io_read_base` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `_IO_write_base` should have a snake case name [INFO] [stdout] --> src/abpoa_sys.rs:110:9 [INFO] [stdout] | [INFO] [stdout] 110 | pub _IO_write_base: *mut ::std::os::raw::c_char, [INFO] [stdout] | ^^^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): `_io_write_base` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `_IO_write_ptr` should have a snake case name [INFO] [stdout] --> src/abpoa_sys.rs:111:9 [INFO] [stdout] | [INFO] [stdout] 111 | pub _IO_write_ptr: *mut ::std::os::raw::c_char, [INFO] [stdout] | ^^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): `_io_write_ptr` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `_IO_write_end` should have a snake case name [INFO] [stdout] --> src/abpoa_sys.rs:112:9 [INFO] [stdout] | [INFO] [stdout] 112 | pub _IO_write_end: *mut ::std::os::raw::c_char, [INFO] [stdout] | ^^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): `_io_write_end` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `_IO_buf_base` should have a snake case name [INFO] [stdout] --> src/abpoa_sys.rs:113:9 [INFO] [stdout] | [INFO] [stdout] 113 | pub _IO_buf_base: *mut ::std::os::raw::c_char, [INFO] [stdout] | ^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): `_io_buf_base` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `_IO_buf_end` should have a snake case name [INFO] [stdout] --> src/abpoa_sys.rs:114:9 [INFO] [stdout] | [INFO] [stdout] 114 | pub _IO_buf_end: *mut ::std::os::raw::c_char, [INFO] [stdout] | ^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): `_io_buf_end` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `_IO_save_base` should have a snake case name [INFO] [stdout] --> src/abpoa_sys.rs:115:9 [INFO] [stdout] | [INFO] [stdout] 115 | pub _IO_save_base: *mut ::std::os::raw::c_char, [INFO] [stdout] | ^^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): `_io_save_base` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `_IO_backup_base` should have a snake case name [INFO] [stdout] --> src/abpoa_sys.rs:116:9 [INFO] [stdout] | [INFO] [stdout] 116 | pub _IO_backup_base: *mut ::std::os::raw::c_char, [INFO] [stdout] | ^^^^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): `_io_backup_base` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: structure field `_IO_save_end` should have a snake case name [INFO] [stdout] --> src/abpoa_sys.rs:117:9 [INFO] [stdout] | [INFO] [stdout] 117 | pub _IO_save_end: *mut ::std::os::raw::c_char, [INFO] [stdout] | ^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): `_io_save_end` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: linking with `cc` failed: exit status: 1 [INFO] [stdout] | [INFO] [stdout] = note: "cc" "-m64" "/tmp/rustc9JHFS6/symbols.o" "<17 object files omitted>" "-Wl,--as-needed" "-Wl,-Bstatic" "/opt/rustwide/target/debug/deps/{librsabpoa-546bdf5238895926,libgskits-a32f2d32fb7d8259,libnum_cpus-809bbf5ef9260db2,libuuid-d418e2e1c7098baa,libsha1_smol-2d5fc294961d1e58,libchrono-c9ad0ad6c95c1450,libiana_time_zone-f40fb3fd1722fffa,libindicatif-607871b5659ca0be,libportable_atomic-eaf3f0a003f51fa1,libnumber_prefix-3e2f4c7b9fa4f802,libconsole-672ae052c9cac052,libunicode_width-413e00174b63117b,libonce_cell-93805221d77d444c,libbio-fbe93b7fbe94916b,libstrum-4679d802b6eead1a,libcsv-a7eaddebc73a0932,libryu-3ba25d01f660afda,libitoa-a4ff8677f852b89f,libcsv_core-6aba7dfb7d862871,libbytecount-8234beb11e75d805,libtriple_accel-090de8c9104d455a,libeditdistancek-8e2dd773c856610d,libitertools_num-3f5879a6ffe5dfc9,libenum_map-513830e8b1ba7a7d,libstatrs-247f14b35ddf78d2,libnalgebra-36f44fa91f45a3aa,librand_distr-28f4620e13d9969c,libnum_rational-cb11104859f2743a,libtypenum-987523825771ddad,libsimba-a013d36739438392,libwide-5ac9407129a5878e,libsafe_arch-8343e93929d4a038,libbytemuck-978220b94a6d208f,librand-e680a95670287430,librand_chacha-7bb30014d3856d12,libppv_lite86-d7c996c4f0f26d7f,libzerocopy-c28ec1438b9ed37b,librand_core-89720e9345148a3c,libgetrandom-ec3c5dade0288b9d,libcfg_if-3183e62f61f23a61,libordered_float-9cf69ac56d814972,libndarray-efc3cd5951885a71,libmatrixmultiply-019e0e5668445cba,libnum_complex-c7e6152ebcfcfb8a,librawpointer-f73a58cd128df828,libmultimap-df0d600731132db9,libitertools-84d813d5e7608b24,libeither-d34eb70c8ca3ae87,libanyhow-8da934a0522d811b,libnum_integer-be3ea1656379f3aa,libbv-0e9d3d46185fde2d,libvec_map-0e1528b7d267a883,libserde-b9094f772b7cdf81,libbit_set-ba3ed83e4317f91e,libbit_vec-dfc9667cba086ae9,libfxhash-4da70fad991848bc,libpetgraph-40edfd5ae4391232,libindexmap-b4a3e93467c503d7,libequivalent-bf2cc2d551c30568,libhashbrown-20e8734fc31efad8,libfixedbitset-25768b5df1347498,libapprox-289f5f8929f44bd1,libnum_traits-7d6ef474656b24f1,librust_htslib-569e114a75b88f35,libthiserror-4d3ef9a83272e4cb,libieee754-60e2000e17500601,libhts_sys-2a668d9856c31d58,liblzma_sys-7d40bd89ffdfb68e,libcurl_sys-e916468a2fee39ea,libopenssl_sys-b1ba96ea8fcd44f3,liblibz_sys-24e2e3e00bbd8905,liblibc-317f291a841a3693,libbzip2_sys-cd77ccc27017ec70,liburl-60d63c94a2ad7a2e,libidna-6caf306df578b37e,libidna_adapter-e0313aba47c72ad7,libicu_normalizer-3fb494409f30fbc8,libicu_normalizer_data-c8b7c0341c4e2b5f,libwrite16-4c92f00e422f4b7b,libutf8_iter-311f0db35672adba,libutf16_iter-9805d00089650556,libsmallvec-2b006734e0087962,libicu_properties-056eecbaac3ba41a,libicu_properties_data-b5b9b11cefe065f7,libicu_locid_transform-d2a5ed8bd8383eda,libicu_locid_transform_data-8576e3fbdf497e17,libicu_collections-7a66f7b62c4ac9fc,libicu_provider-0fbe0f05a3ad99ce,libicu_locid-545af73c03eb1b5b,liblitemap-5d6ff1c38a537ea4,libtinystr-08c4b0817680a6b0,libzerovec-0143643654cfbf61,libwriteable-763d6213d7786cb3,libyoke-22826fa6e769a1af,libzerofrom-f6e00a8d3db05972,libstable_deref_trait-1d3ea2e5b9aa129c,libform_urlencoded-28c18a8e012ebc37,libpercent_encoding-4d821e207fbc5c85,libbio_types-5d3f760a6d83962b,libthiserror-10addc296824896d,libbyteorder-3f91e0f3212dbed5,libregex-92e861d4d10c9c11,libregex_automata-c8d14152a82e1bc7,libaho_corasick-689bc23dcdad714a,libmemchr-19b8063cb8773ce3,libregex_syntax-a2301440a5fca75a,liblinear_map-d596f9554216bf54,liblazy_static-509a3481d98abb23,libnewtype_derive-4c81d7c987eb5ade,libcustom_derive-9dcd9871da8e8905,libcrossbeam-70c37b4b75751106,libcrossbeam_deque-c4a40318fe1e21a0,libcrossbeam_channel-af82ed417ef2108d,libcrossbeam_queue-4a33ce142ea1783a,libcrossbeam_epoch-331b6a766d29dc1d,libcrossbeam_utils-227be8784775253b,libclap-c33790339b498b40,libclap_builder-3b036ae1b07d523e,libstrsim-3c066906e8d6c466,libanstream-dfc30e3ac73f2cd5,libanstyle_query-db83a68c694b9d63,libis_terminal_polyfill-a5c67c126de8c486,libcolorchoice-a3b77acdbdb1ab0d,libanstyle_parse-29d48ff3e45feb97,libutf8parse-b4c8bbdcb9de0cd7,libclap_lex-8385a67ebf54a985,libanstyle-3993e49bc768331b}.rlib" "/lib/rustlib/x86_64-unknown-linux-gnu/lib/{libstd-*,libpanic_unwind-*,libobject-*,libmemchr-*,libaddr2line-*,libgimli-*,librustc_demangle-*,libstd_detect-*,libhashbrown-*,librustc_std_workspace_alloc-*,libminiz_oxide-*,libadler2-*,libunwind-*,libcfg_if-*,liblibc-*,librustc_std_workspace_core-*,liballoc-*,libcore-*,libcompiler_builtins-*}.rlib" "-Wl,-Bdynamic" "-lm" "-lz" "-lpthread" "-lgcc_s" "-lutil" "-lrt" "-lpthread" "-lm" "-ldl" "-lc" "-L" "/tmp/rustc9JHFS6/raw-dylibs" "-B/lib/rustlib/x86_64-unknown-linux-gnu/bin/gcc-ld" "-fuse-ld=lld" "-Wl,--eh-frame-hdr" "-Wl,-z,noexecstack" "-L" "/opt/rustwide/target/debug/build/rsabpoa-c1c553a1540d7599/out/abPOA-v1.5.3/lib" "-L" "/opt/rustwide/target/debug/build/hts-sys-3b34a9a3f9e3ad40/out" "-L" "/opt/rustwide/target/debug/build/bzip2-sys-77b0cadb4f4dfde0/out/lib" "-L" "/opt/rustwide/target/debug/build/curl-sys-9596cb501dd8db47/out/build" "-L" "/opt/rustwide/target/debug/build/libz-sys-a72077ed47be9e31/out/lib" "-L" "/opt/rustwide/target/debug/build/libz-sys-a72077ed47be9e31/out/lib" "-L" "/opt/rustwide/target/debug/build/openssl-sys-69702fa4fb56ae6e/out/openssl-build/install/lib" "-L" "/opt/rustwide/target/debug/build/lzma-sys-ad1728575f300e8f/out" "-L" "/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-o" "/opt/rustwide/target/debug/deps/abpoa_consensus-a1dc5cbbcb9cb999" "-Wl,--gc-sections" "-pie" "-Wl,-z,relro,-z,now" "-nodefaultlibs" [INFO] [stdout] = note: some arguments are omitted. use `--verbose` to show all linker arguments [INFO] [stdout] = note: rust-lld: error: duplicate symbol: kvsprintf [INFO] [stdout] >>> defined at kstring.c:9 (src/kstring.c:9) [INFO] [stdout] >>> kstring.o:(kvsprintf) in archive /opt/rustwide/target/debug/deps/librsabpoa-546bdf5238895926.rlib [INFO] [stdout] >>> defined at kstring.c:143 (/opt/rustwide/target/debug/build/hts-sys-3b34a9a3f9e3ad40/out/htslib/kstring.c:143) [INFO] [stdout] >>> 05557ae68d7d9a53-kstring.o:(.text.kvsprintf+0x0) in archive /opt/rustwide/target/debug/deps/libhts_sys-2a668d9856c31d58.rlib [INFO] [stdout] [INFO] [stdout] rust-lld: error: duplicate symbol: ksprintf [INFO] [stdout] >>> defined at kstring.c:28 (src/kstring.c:28) [INFO] [stdout] >>> kstring.o:(ksprintf) in archive /opt/rustwide/target/debug/deps/librsabpoa-546bdf5238895926.rlib [INFO] [stdout] >>> defined at kstring.c:178 (/opt/rustwide/target/debug/build/hts-sys-3b34a9a3f9e3ad40/out/htslib/kstring.c:178) [INFO] [stdout] >>> 05557ae68d7d9a53-kstring.o:(.text.ksprintf+0x0) in archive /opt/rustwide/target/debug/deps/libhts_sys-2a668d9856c31d58.rlib [INFO] [stdout] [INFO] [stdout] rust-lld: error: duplicate symbol: kstrtok [INFO] [stdout] >>> defined at kstring.c:38 (src/kstring.c:38) [INFO] [stdout] >>> kstring.o:(kstrtok) in archive /opt/rustwide/target/debug/deps/librsabpoa-546bdf5238895926.rlib [INFO] [stdout] >>> defined at kstring.c:188 (/opt/rustwide/target/debug/build/hts-sys-3b34a9a3f9e3ad40/out/htslib/kstring.c:188) [INFO] [stdout] >>> 05557ae68d7d9a53-kstring.o:(.text.kstrtok+0x0) in archive /opt/rustwide/target/debug/deps/libhts_sys-2a668d9856c31d58.rlib [INFO] [stdout] [INFO] [stdout] rust-lld: error: duplicate symbol: ksplit_core [INFO] [stdout] >>> defined at kstring.c:66 (src/kstring.c:66) [INFO] [stdout] >>> kstring.o:(ksplit_core) in archive /opt/rustwide/target/debug/deps/librsabpoa-546bdf5238895926.rlib [INFO] [stdout] >>> defined at kstring.c:225 (/opt/rustwide/target/debug/build/hts-sys-3b34a9a3f9e3ad40/out/htslib/kstring.c:225) [INFO] [stdout] >>> 05557ae68d7d9a53-kstring.o:(.text.ksplit_core+0x0) in archive /opt/rustwide/target/debug/deps/libhts_sys-2a668d9856c31d58.rlib [INFO] [stdout] [INFO] [stdout] rust-lld: error: duplicate symbol: kgetline [INFO] [stdout] >>> defined at kstring.c:110 (src/kstring.c:110) [INFO] [stdout] >>> kstring.o:(kgetline) in archive /opt/rustwide/target/debug/deps/librsabpoa-546bdf5238895926.rlib [INFO] [stdout] >>> defined at kstring.c:271 (/opt/rustwide/target/debug/build/hts-sys-3b34a9a3f9e3ad40/out/htslib/kstring.c:271) [INFO] [stdout] >>> 05557ae68d7d9a53-kstring.o:(.text.kgetline+0x0) in archive /opt/rustwide/target/debug/deps/libhts_sys-2a668d9856c31d58.rlib [INFO] [stdout] [INFO] [stdout] rust-lld: error: duplicate symbol: kmemmem [INFO] [stdout] >>> defined at kstring.c:177 (src/kstring.c:177) [INFO] [stdout] >>> kstring.o:(kmemmem) in archive /opt/rustwide/target/debug/deps/librsabpoa-546bdf5238895926.rlib [INFO] [stdout] >>> defined at kstring.c:378 (/opt/rustwide/target/debug/build/hts-sys-3b34a9a3f9e3ad40/out/htslib/kstring.c:378) [INFO] [stdout] >>> 05557ae68d7d9a53-kstring.o:(.text.kmemmem+0x0) in archive /opt/rustwide/target/debug/deps/libhts_sys-2a668d9856c31d58.rlib [INFO] [stdout] [INFO] [stdout] rust-lld: error: duplicate symbol: kstrstr [INFO] [stdout] >>> defined at kstring.c:198 (src/kstring.c:198) [INFO] [stdout] >>> kstring.o:(kstrstr) in archive /opt/rustwide/target/debug/deps/librsabpoa-546bdf5238895926.rlib [INFO] [stdout] >>> defined at kstring.c:400 (/opt/rustwide/target/debug/build/hts-sys-3b34a9a3f9e3ad40/out/htslib/kstring.c:400) [INFO] [stdout] >>> 05557ae68d7d9a53-kstring.o:(.text.kstrstr+0x0) in archive /opt/rustwide/target/debug/deps/libhts_sys-2a668d9856c31d58.rlib [INFO] [stdout] [INFO] [stdout] rust-lld: error: duplicate symbol: kstrnstr [INFO] [stdout] >>> defined at kstring.c:203 (src/kstring.c:203) [INFO] [stdout] >>> kstring.o:(kstrnstr) in archive /opt/rustwide/target/debug/deps/librsabpoa-546bdf5238895926.rlib [INFO] [stdout] >>> defined at kstring.c:405 (/opt/rustwide/target/debug/build/hts-sys-3b34a9a3f9e3ad40/out/htslib/kstring.c:405) [INFO] [stdout] >>> 05557ae68d7d9a53-kstring.o:(.text.kstrnstr+0x0) in archive /opt/rustwide/target/debug/deps/libhts_sys-2a668d9856c31d58.rlib [INFO] [stdout] collect2: error: ld returned 1 exit status [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `rsabpoa` (bin "abpoa_consensus") due to 1 previous error [INFO] running `Command { std: "docker" "inspect" "735f0320cae955386cb999d9ea1822df2da07984accd449b95608f4dc06c823d", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "735f0320cae955386cb999d9ea1822df2da07984accd449b95608f4dc06c823d", kill_on_drop: false }` [INFO] [stdout] 735f0320cae955386cb999d9ea1822df2da07984accd449b95608f4dc06c823d