[INFO] cloning repository https://github.com/wtzhang23/bamgen [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/wtzhang23/bamgen" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fwtzhang23%2Fbamgen", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fwtzhang23%2Fbamgen'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] 3d59832e20c0d9c88e0ea1a9b5a2cc5edb044927 [INFO] testing wtzhang23/bamgen against try#c066bf6804adc55193b71afdff6a56922f4a8689+target=x86_64-unknown-linux-musl for musl_upgrade_1_2_5_in_2025-retry-1 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fwtzhang23%2Fbamgen" "/workspace/builds/worker-5-tc2/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-5-tc2/source'... [INFO] [stderr] done. [INFO] started tweaking git repo https://github.com/wtzhang23/bamgen [INFO] finished tweaking git repo https://github.com/wtzhang23/bamgen [INFO] tweaked toml for git repo https://github.com/wtzhang23/bamgen written to /workspace/builds/worker-5-tc2/source/Cargo.toml [INFO] validating manifest of git repo https://github.com/wtzhang23/bamgen on toolchain c066bf6804adc55193b71afdff6a56922f4a8689 [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+c066bf6804adc55193b71afdff6a56922f4a8689" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate git repo https://github.com/wtzhang23/bamgen 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" "+c066bf6804adc55193b71afdff6a56922f4a8689" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+c066bf6804adc55193b71afdff6a56922f4a8689" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] c107931f7283252d0f21129c9391aa0acd155162891502019be622a51bce3761 [INFO] running `Command { std: "docker" "start" "-a" "c107931f7283252d0f21129c9391aa0acd155162891502019be622a51bce3761", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "c107931f7283252d0f21129c9391aa0acd155162891502019be622a51bce3761", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "c107931f7283252d0f21129c9391aa0acd155162891502019be622a51bce3761", kill_on_drop: false }` [INFO] [stdout] c107931f7283252d0f21129c9391aa0acd155162891502019be622a51bce3761 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+c066bf6804adc55193b71afdff6a56922f4a8689" "build" "--frozen" "--message-format=json" "--target" "x86_64-unknown-linux-musl", kill_on_drop: false }` [INFO] [stdout] 32d5049e8a56425d55d5b7662721f4b6870fb7ea1e21d9b05a2a1bd1fc5262ba [INFO] running `Command { std: "docker" "start" "-a" "32d5049e8a56425d55d5b7662721f4b6870fb7ea1e21d9b05a2a1bd1fc5262ba", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.79 [INFO] [stderr] Compiling pkg-config v0.3.18 [INFO] [stderr] Compiling proc-macro2 v1.0.24 [INFO] [stderr] Compiling unicode-xid v0.2.1 [INFO] [stderr] Compiling syn v1.0.42 [INFO] [stderr] Compiling autocfg v1.0.1 [INFO] [stderr] Compiling version_check v0.9.2 [INFO] [stderr] Compiling memchr v2.3.3 [INFO] [stderr] Compiling serde_derive v1.0.116 [INFO] [stderr] Compiling getrandom v0.1.15 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling serde v1.0.116 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling lazy_static v1.4.0 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Compiling bitflags v1.2.1 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling matches v0.1.8 [INFO] [stderr] Compiling cfg-if v0.1.10 [INFO] [stderr] Compiling tinyvec v0.3.4 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling unicode-bidi v0.3.4 [INFO] [stderr] Compiling thread_local v1.0.1 [INFO] [stderr] Compiling unicode-segmentation v1.6.0 [INFO] [stderr] Compiling regex-syntax v0.6.18 [INFO] [stderr] Compiling unicode-width v0.1.8 [INFO] [stderr] Compiling hashbrown v0.9.1 [INFO] [stderr] Compiling ppv-lite86 v0.2.9 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling unicode-normalization v0.1.13 [INFO] [stderr] Compiling aho-corasick v0.7.13 [INFO] [stderr] Compiling indexmap v1.6.0 [INFO] [stderr] Compiling percent-encoding v2.1.0 [INFO] [stderr] Compiling textwrap v0.12.1 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling heck v0.3.1 [INFO] [stderr] Compiling base64 v0.12.3 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling os_str_bytes v2.3.2 [INFO] [stderr] Compiling termcolor v1.1.0 [INFO] [stderr] Compiling strsim v0.10.0 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling idna v0.2.0 [INFO] [stderr] Compiling rand_core v0.5.1 [INFO] [stderr] Compiling rand_chacha v0.2.2 [INFO] [stderr] Compiling quote v1.0.7 [INFO] [stderr] Compiling jobserver v0.1.21 [INFO] [stderr] Compiling url v2.1.1 [INFO] [stderr] Compiling rand v0.7.3 [INFO] [stderr] Compiling cc v1.0.60 [INFO] [stderr] Compiling openssl-src v111.11.0+1.1.1h [INFO] [stderr] Compiling regex v1.3.9 [INFO] [stderr] Compiling openssl-sys v0.9.58 [INFO] [stderr] Compiling libz-sys v1.1.2 [INFO] [stderr] Compiling bzip2-sys v0.1.9+1.0.8 [INFO] [stderr] Compiling curl-sys v0.4.36+curl-7.71.1 [INFO] [stderr] Compiling lzma-sys v0.1.16 [INFO] [stderr] Compiling hts-sys v1.10.3 [INFO] [stderr] Compiling derive-new v0.5.8 [INFO] [stderr] Compiling thiserror-impl v1.0.20 [INFO] [stderr] Compiling clap_derive v3.0.0-beta.2 [INFO] [stderr] Compiling thiserror v1.0.20 [INFO] [stderr] Compiling clap v3.0.0-beta.2 [INFO] [stderr] Compiling bio-types v0.7.0 [INFO] [stderr] Compiling ron v0.6.2 [INFO] [stderr] Compiling rust-htslib v0.32.0 [INFO] [stderr] Compiling bamgen v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] error: linking with `cc` failed: exit status: 1 [INFO] [stdout] | [INFO] [stdout] = note: "cc" "-m64" "/lib/rustlib/x86_64-unknown-linux-musl/lib/self-contained/rcrt1.o" "/lib/rustlib/x86_64-unknown-linux-musl/lib/self-contained/crti.o" "/lib/rustlib/x86_64-unknown-linux-musl/lib/self-contained/crtbeginS.o" "/tmp/rustcM0iON1/symbols.o" "<10 object files omitted>" "-Wl,--as-needed" "-Wl,-Bstatic" "/opt/rustwide/target/x86_64-unknown-linux-musl/debug/deps/{libron-e049713b5c2ed895.rlib,libbase64-58f9c786d7f23eb6.rlib,librust_htslib-fe7536498ca63de7.rlib,libhts_sys-f521146e33b6489d.rlib,libcurl_sys-dfcb2c890516bb34.rlib,libopenssl_sys-23c8dbb0562c6c67.rlib,liblzma_sys-59584f9efc4d97bd.rlib,libbzip2_sys-8cc994d1fa9e8a3d.rlib,liblibz_sys-83a909a31049db1d.rlib,libieee754-8632c207f9ca9a20.rlib,liburl-2e344d0b87916fd7.rlib,libpercent_encoding-3f452dc5e318e927.rlib,libidna-f4440833e81ad9c1.rlib,libunicode_normalization-bf86f367eab695fd.rlib,libtinyvec-da978a460f1be52d.rlib,libunicode_bidi-3c976b4886511d83.rlib,libmatches-d7125afe50072f5c.rlib,liblinear_map-3cadc16fd97c7847.rlib,libthiserror-6d8a0ed3fd873929.rlib,libnewtype_derive-f91eed88f8acaf26.rlib,libcustom_derive-d11a0801595e3fc6.rlib,librand-0048b7cec75d02a7.rlib,librand_chacha-eae70d5d6b23644c.rlib,libppv_lite86-fe4748cb9a4a903e.rlib,librand_core-e00441914e6927d6.rlib,libgetrandom-0e7a619dfc829dd0.rlib,libcfg_if-2d17986ae484e939.rlib,libclap-463785f32c928cc3.rlib,libstrsim-7a71560e0c2955e4.rlib,libatty-c56bc288f0e31d62.rlib,liblibc-337ec8f498c4508c.rlib,libtextwrap-f7a2553bffdec3f9.rlib,libvec_map-f5624d319d58cb9d.rlib,libos_str_bytes-dc6db456d9276e14.rlib,libtermcolor-2ea4a539468aa6b0.rlib,libunicode_width-a8c49d31449f9404.rlib,libindexmap-9de7c312a45aff79.rlib,libhashbrown-aed633c8184090a0.rlib,libbitflags-561a4f1321538a32.rlib,libbio_types-33feefecb9674fd0.rlib,libserde-a5c06bf28ab255e8.rlib,libregex-430e00fca47259de.rlib,libthread_local-c6b88a4b7954c5cd.rlib,libregex_syntax-cb353ff079726287.rlib,libaho_corasick-61bf4caab8600cce.rlib,libmemchr-66f21ea766679294.rlib,liblazy_static-4b136fc9bfbd2c4b.rlib,libquick_error-022321fe562bcedb.rlib}.rlib" "/lib/rustlib/x86_64-unknown-linux-musl/lib/{libstd-*,libpanic_unwind-*,libobject-*,libmemchr-*,libaddr2line-*,libgimli-*,librustc_demangle-*,libstd_detect-*,libhashbrown-*,librustc_std_workspace_alloc-*,libminiz_oxide-*,libadler2-*,libunwind-*}.rlib" "-lunwind" "/lib/rustlib/x86_64-unknown-linux-musl/lib/{libcfg_if-*,liblibc-*}.rlib" "-lc" "/lib/rustlib/x86_64-unknown-linux-musl/lib/{librustc_std_workspace_core-*,liballoc-*,libcore-*,libcompiler_builtins-*}.rlib" "-L" "/tmp/rustcM0iON1/raw-dylibs" "-Wl,-Bdynamic" "-Wl,--eh-frame-hdr" "-Wl,-z,noexecstack" "-nostartfiles" "-L" "/opt/rustwide/target/x86_64-unknown-linux-musl/debug/build/hts-sys-472aae8771a0d1b2/out" "-L" "/opt/rustwide/target/x86_64-unknown-linux-musl/debug/build/bzip2-sys-83d4ec6728601af9/out/lib" "-L" "/opt/rustwide/target/x86_64-unknown-linux-musl/debug/build/curl-sys-5b44834ee40fa0e7/out/build" "-L" "/opt/rustwide/target/x86_64-unknown-linux-musl/debug/build/libz-sys-9c3ced64a556ad98/out/build" "-L" "/opt/rustwide/target/x86_64-unknown-linux-musl/debug/build/openssl-sys-0d05584780686bb7/out/openssl-build/install/lib" "-L" "/opt/rustwide/target/x86_64-unknown-linux-musl/debug/build/lzma-sys-d739c13434af7643/out" "-L" "/lib/rustlib/x86_64-unknown-linux-musl/lib/self-contained" "-L" "/lib/rustlib/x86_64-unknown-linux-musl/lib" "-o" "/opt/rustwide/target/x86_64-unknown-linux-musl/debug/deps/bamgen-a23e737e2b989ae4" "-Wl,--gc-sections" "-static-pie" "-Wl,-z,relro,-z,now" "-nodefaultlibs" "/lib/rustlib/x86_64-unknown-linux-musl/lib/self-contained/crtendS.o" "/lib/rustlib/x86_64-unknown-linux-musl/lib/self-contained/crtn.o" [INFO] [stdout] = note: some arguments are omitted. use `--verbose` to show all linker arguments [INFO] [stdout] = note: /usr/bin/ld: /opt/rustwide/target/x86_64-unknown-linux-musl/debug/deps/libgetrandom-0e7a619dfc829dd0.rlib(getrandom-0e7a619dfc829dd0.getrandom.675f46982a170705-cgu.0.rcgu.o): in function `getrandom::util_libc::open_readonly': [INFO] [stdout] /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/getrandom-0.1.15/src/util_libc.rs:112:(.text._ZN9getrandom9util_libc13open_readonly17h8ca838c92c083e7dE+0x79): undefined reference to `open64' [INFO] [stdout] collect2: error: ld returned 1 exit status [INFO] [stdout] [INFO] [stdout] = note: some `extern` functions couldn't be found; some native libraries may need to be installed or have their path specified [INFO] [stdout] = note: use the `-l` flag to specify native libraries to link [INFO] [stdout] = note: use the `cargo:rustc-link-lib` directive to specify the native libraries to link with Cargo (see https://doc.rust-lang.org/cargo/reference/build-scripts.html#rustc-link-lib) [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] error: could not compile `bamgen` (bin "bamgen") due to 1 previous error [INFO] running `Command { std: "docker" "inspect" "32d5049e8a56425d55d5b7662721f4b6870fb7ea1e21d9b05a2a1bd1fc5262ba", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "32d5049e8a56425d55d5b7662721f4b6870fb7ea1e21d9b05a2a1bd1fc5262ba", kill_on_drop: false }` [INFO] [stdout] 32d5049e8a56425d55d5b7662721f4b6870fb7ea1e21d9b05a2a1bd1fc5262ba