[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 beta-2025-09-21 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-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/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-tc2/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/keithyin/rsabpoa on toolchain beta-2025-09-21 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+beta-2025-09-21" "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" "+beta-2025-09-21" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2025-09-21" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 053165da7eae75a70cac975e2c4b6ebbd81d79a2c44cfd7d984106c38fa2ae93 [INFO] running `Command { std: "docker" "start" "-a" "053165da7eae75a70cac975e2c4b6ebbd81d79a2c44cfd7d984106c38fa2ae93", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "053165da7eae75a70cac975e2c4b6ebbd81d79a2c44cfd7d984106c38fa2ae93", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "053165da7eae75a70cac975e2c4b6ebbd81d79a2c44cfd7d984106c38fa2ae93", kill_on_drop: false }` [INFO] [stdout] 053165da7eae75a70cac975e2c4b6ebbd81d79a2c44cfd7d984106c38fa2ae93 [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=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" "+beta-2025-09-21" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] cb0c69e5e457533642fe08b77bec1e3edd2c60531e6bcde4df0f190a77f186b5 [INFO] running `Command { std: "docker" "start" "-a" "cb0c69e5e457533642fe08b77bec1e3edd2c60531e6bcde4df0f190a77f186b5", 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 regex-syntax v0.8.5 [INFO] [stderr] Compiling libc v0.2.170 [INFO] [stderr] Compiling num-traits v0.2.19 [INFO] [stderr] Compiling serde v1.0.218 [INFO] 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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)]` (part of `#[warn(nonstandard_style)]`) 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)]` (part of `#[warn(unused)]`) 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)]` (part of `#[warn(nonstandard_style)]`) 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/rustcfJXcyu/symbols.o" "<17 object files omitted>" "-Wl,--as-needed" "-Wl,-Bstatic" "/opt/rustwide/target/debug/deps/{librsabpoa-62b3515560e1a8a0,libgskits-e15a20415a0559f6,libnum_cpus-0c783957891b0191,libuuid-4edfdf11c4e11646,libsha1_smol-a320b1639232fa11,libchrono-96b35888f2e0f7eb,libiana_time_zone-98f2ac8a8c5a9959,libindicatif-5fbe73d92f6a7680,libportable_atomic-a75036a50a81e993,libnumber_prefix-6b994bedec76f9db,libconsole-d4b72b650814f172,libunicode_width-0122813f2549e4e9,libonce_cell-87ad594b4fdd0b3c,libbio-2f8f1aeb28d57229,libstrum-e3cef8f7d45a2447,libcsv-f159ad698c1b3c2e,libryu-a7164637bc4900ee,libitoa-ef40fa516293a9d3,libcsv_core-e903fcf75ed0b1a8,libbytecount-e613ba40c2456714,libtriple_accel-1fdd3e4b712d69aa,libeditdistancek-e70aa588abcfe4a9,libitertools_num-d6dae028d343d7e4,libenum_map-5ae31cf25efaa5df,libstatrs-73d14b83362121e1,libnalgebra-61993e1315e39a1e,librand_distr-1738fe1ecfff4e50,libnum_rational-b522ab0ce5ed0d31,libtypenum-f2b179c8a326fef2,libsimba-1cbcd7b5ead422ef,libwide-a80319073c475127,libsafe_arch-5de98f91bd66b784,libbytemuck-d671bd9faf1080c9,librand-663f987037bbf1b1,librand_chacha-32aa41f9f6eab812,libppv_lite86-9b7d3c9dde844ac8,libzerocopy-9fe16205b34fe1ce,librand_core-449b88d50ceee8a3,libgetrandom-596e118eec8eeea9,libcfg_if-3e7fc4e38d4a72b5,libordered_float-ad997df0f608dfd8,libndarray-f3dbb19aeacb5098,libmatrixmultiply-ddac031fb8d682d7,libnum_complex-de0f148ddde8d101,librawpointer-10d892ea69c462d6,libmultimap-5340741f2b21cef7,libitertools-0dfe3b49e26bab2a,libeither-e5ea87bd27ac73a9,libanyhow-48c4874d2e1f3573,libnum_integer-a7d0e87a7fc7a339,libbv-06f46757c7b761dc,libvec_map-2d9b6417eaea377d,libserde-650859d2bc5b5234,libbit_set-9437a56bb8d38131,libbit_vec-b1d1b68c2b4b1dac,libfxhash-1df546a36b8e6f44,libpetgraph-f7aad15ee0ba4b8d,libindexmap-8ebc8986b19a2375,libequivalent-6a754676e6af62ae,libhashbrown-acdfbba63b345327,libfixedbitset-625fd2a9d775ed11,libapprox-1c2c3b6fd50ba239,libnum_traits-ed73480dc23f78f5,librust_htslib-211a8e9f9f26328c,libthiserror-9de0a883c490a9d0,libieee754-1424436d24ee8d5d,libhts_sys-73d6040835406699,liblzma_sys-68297cb5dd998419,libcurl_sys-e13eb88bc3d272d9,libopenssl_sys-81d07ccdee78f6e9,liblibz_sys-7ee92a4292af739d,liblibc-8e8176b617406ce8,libbzip2_sys-51eadda005b6e17a,liburl-54e47f1806976a93,libidna-0a539d573b3c7a01,libidna_adapter-55fe0e1355aaef02,libicu_normalizer-66631a5fe8a538a4,libicu_normalizer_data-5f7d7c19a0e21ea1,libwrite16-e996c39ad8ba5f0b,libutf8_iter-51566bbad89f3a68,libutf16_iter-7ca3c212f3ee1c68,libsmallvec-2bd8f6be8d3c93fd,libicu_properties-48dcd6ae7f404e24,libicu_properties_data-61b2e4b1f2e1f988,libicu_locid_transform-d0cb3f1dce318c82,libicu_locid_transform_data-94513cffde0b2fcb,libicu_collections-a7e4bf7165c38a59,libicu_provider-71789949433752a3,libicu_locid-f5a461e6ce6c2fdf,liblitemap-79485f3bd9d9879d,libtinystr-7633c1005c7a53d4,libzerovec-eb6a85844789661e,libwriteable-1e5dea0053e4c229,libyoke-d36d0cd3e8194a8d,libzerofrom-aa0b685e1d5aa49b,libstable_deref_trait-14e4a70bda35dfe8,libform_urlencoded-ccbcef42f8ae53ab,libpercent_encoding-e42b7a0b4a5edca5,libbio_types-dd08c7054236fb89,libthiserror-a18f5e67f83b983a,libbyteorder-8f59b6d1bfdaa844,libregex-024cfaa467e434b3,libregex_automata-76225e55779c4bfe,libaho_corasick-94236398dd0ecfc1,libmemchr-eec2dd93b0d498c5,libregex_syntax-cf9ef9729ec61e4c,liblinear_map-b99ada3a08e58c15,liblazy_static-3674be3f4245d19b,libnewtype_derive-f9e88944c691be4b,libcustom_derive-c3c046709babbb4b,libcrossbeam-3f202050ed3bfe4c,libcrossbeam_deque-3ac6784ac69db859,libcrossbeam_channel-3321244dddfdc6a0,libcrossbeam_queue-61685dce9e51d53a,libcrossbeam_epoch-bd51de1fb2e91121,libcrossbeam_utils-02f58a81c9899c97,libclap-afbb57546615a61a,libclap_builder-cfde7ea5cb2a027a,libstrsim-4d1ed08a123238dc,libanstream-46109e2ca4391c70,libanstyle_query-6b2b2868060db38b,libis_terminal_polyfill-e39671344234c74d,libcolorchoice-c3c00c022d852059,libanstyle_parse-2a1cfd0795883160,libutf8parse-92d0158219063202,libclap_lex-b423203a2eab4856,libanstyle-e80e21c5036b9344}.rlib" "/lib/rustlib/x86_64-unknown-linux-gnu/lib/{libstd-*,libpanic_unwind-*,libobject-*,libmemchr-*,libaddr2line-*,libgimli-*,libcfg_if-*,librustc_demangle-*,libstd_detect-*,libhashbrown-*,librustc_std_workspace_alloc-*,libminiz_oxide-*,libadler2-*,libunwind-*,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/rustcfJXcyu/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-325202c264696683/out/abPOA-v1.5.3/lib" "-L" "/opt/rustwide/target/debug/build/hts-sys-924f921363ac24bd/out" "-L" "/opt/rustwide/target/debug/build/bzip2-sys-e8fb0906b4559cd3/out/lib" "-L" "/opt/rustwide/target/debug/build/curl-sys-ff730a75965fd096/out/build" "-L" "/opt/rustwide/target/debug/build/libz-sys-02109fc032136c20/out/lib" "-L" "/opt/rustwide/target/debug/build/openssl-sys-b93555db907bbaef/out/openssl-build/install/lib" "-L" "/opt/rustwide/target/debug/build/lzma-sys-4bad8ad8bf5ffb7c/out" "-L" "/lib/rustlib/x86_64-unknown-linux-gnu/lib" "-o" "/opt/rustwide/target/debug/deps/abpoa_consensus-ea88a0dcf6e6fe12" "-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-62b3515560e1a8a0.rlib [INFO] [stdout] >>> defined at kstring.c:143 (/opt/rustwide/target/debug/build/hts-sys-924f921363ac24bd/out/htslib/kstring.c:143) [INFO] [stdout] >>> 723f8a53fdb3cbfe-kstring.o:(.text.kvsprintf+0x0) in archive /opt/rustwide/target/debug/deps/libhts_sys-73d6040835406699.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-62b3515560e1a8a0.rlib [INFO] [stdout] >>> defined at kstring.c:178 (/opt/rustwide/target/debug/build/hts-sys-924f921363ac24bd/out/htslib/kstring.c:178) [INFO] [stdout] >>> 723f8a53fdb3cbfe-kstring.o:(.text.ksprintf+0x0) in archive /opt/rustwide/target/debug/deps/libhts_sys-73d6040835406699.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-62b3515560e1a8a0.rlib [INFO] [stdout] >>> defined at kstring.c:188 (/opt/rustwide/target/debug/build/hts-sys-924f921363ac24bd/out/htslib/kstring.c:188) [INFO] [stdout] >>> 723f8a53fdb3cbfe-kstring.o:(.text.kstrtok+0x0) in archive /opt/rustwide/target/debug/deps/libhts_sys-73d6040835406699.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-62b3515560e1a8a0.rlib [INFO] [stdout] >>> defined at kstring.c:225 (/opt/rustwide/target/debug/build/hts-sys-924f921363ac24bd/out/htslib/kstring.c:225) [INFO] [stdout] >>> 723f8a53fdb3cbfe-kstring.o:(.text.ksplit_core+0x0) in archive /opt/rustwide/target/debug/deps/libhts_sys-73d6040835406699.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-62b3515560e1a8a0.rlib [INFO] [stdout] >>> defined at kstring.c:271 (/opt/rustwide/target/debug/build/hts-sys-924f921363ac24bd/out/htslib/kstring.c:271) [INFO] [stdout] >>> 723f8a53fdb3cbfe-kstring.o:(.text.kgetline+0x0) in archive /opt/rustwide/target/debug/deps/libhts_sys-73d6040835406699.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-62b3515560e1a8a0.rlib [INFO] [stdout] >>> defined at kstring.c:378 (/opt/rustwide/target/debug/build/hts-sys-924f921363ac24bd/out/htslib/kstring.c:378) [INFO] [stdout] >>> 723f8a53fdb3cbfe-kstring.o:(.text.kmemmem+0x0) in archive /opt/rustwide/target/debug/deps/libhts_sys-73d6040835406699.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-62b3515560e1a8a0.rlib [INFO] [stdout] >>> defined at kstring.c:400 (/opt/rustwide/target/debug/build/hts-sys-924f921363ac24bd/out/htslib/kstring.c:400) [INFO] [stdout] >>> 723f8a53fdb3cbfe-kstring.o:(.text.kstrstr+0x0) in archive /opt/rustwide/target/debug/deps/libhts_sys-73d6040835406699.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-62b3515560e1a8a0.rlib [INFO] [stdout] >>> defined at kstring.c:405 (/opt/rustwide/target/debug/build/hts-sys-924f921363ac24bd/out/htslib/kstring.c:405) [INFO] [stdout] >>> 723f8a53fdb3cbfe-kstring.o:(.text.kstrnstr+0x0) in archive /opt/rustwide/target/debug/deps/libhts_sys-73d6040835406699.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" "cb0c69e5e457533642fe08b77bec1e3edd2c60531e6bcde4df0f190a77f186b5", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "cb0c69e5e457533642fe08b77bec1e3edd2c60531e6bcde4df0f190a77f186b5", kill_on_drop: false }` [INFO] [stdout] cb0c69e5e457533642fe08b77bec1e3edd2c60531e6bcde4df0f190a77f186b5