[INFO] cloning repository https://github.com/COMBINE-lab/piscem
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/COMBINE-lab/piscem" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FCOMBINE-lab%2Fpiscem", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FCOMBINE-lab%2Fpiscem'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 6ef1c4c06ba0432c0b7baa6dd3d01c700a41fcec
[INFO] checking COMBINE-lab/piscem against master#8f21a5c92ea55c348c275a1bc4fedbdf181e0d64 for pr-143011
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FCOMBINE-lab%2Fpiscem" "/workspace/builds/worker-2-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-2-tc1/source'...
[INFO] [stderr] done.
[INFO] removed /workspace/builds/worker-2-tc1/source/.cargo/config.toml
[INFO] started tweaking git repo https://github.com/COMBINE-lab/piscem
[INFO] finished tweaking git repo https://github.com/COMBINE-lab/piscem
[INFO] tweaked toml for git repo https://github.com/COMBINE-lab/piscem written to /workspace/builds/worker-2-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/COMBINE-lab/piscem on toolchain 8f21a5c92ea55c348c275a1bc4fedbdf181e0d64
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+8f21a5c92ea55c348c275a1bc4fedbdf181e0d64" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/COMBINE-lab/piscem 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" "+8f21a5c92ea55c348c275a1bc4fedbdf181e0d64" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded clap v4.5.39
[INFO] [stderr]   Downloaded sha2-asm v0.6.4
[INFO] [stderr]   Downloaded needletail v0.5.1
[INFO] [stderr]   Downloaded clap_builder v4.5.39
[INFO] [stderr]   Downloaded buffer-redux v1.0.2
[INFO] [stderr]   Downloaded prepare_fasta v0.1.0
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8f21a5c92ea55c348c275a1bc4fedbdf181e0d64" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] dfb1f7a46fc38ae25847487c3f7b8cd9ec421a02d2856f6728e62b5b350954fa
[INFO] running `Command { std: "docker" "start" "-a" "dfb1f7a46fc38ae25847487c3f7b8cd9ec421a02d2856f6728e62b5b350954fa", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "dfb1f7a46fc38ae25847487c3f7b8cd9ec421a02d2856f6728e62b5b350954fa", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "dfb1f7a46fc38ae25847487c3f7b8cd9ec421a02d2856f6728e62b5b350954fa", kill_on_drop: false }`
[INFO] [stdout] dfb1f7a46fc38ae25847487c3f7b8cd9ec421a02d2856f6728e62b5b350954fa
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-2-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8f21a5c92ea55c348c275a1bc4fedbdf181e0d64" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 8f6e3d2c8da9d636179f97f445d04aa4547f1a90b4a81a7c8b5023bb2f5a33fa
[INFO] running `Command { std: "docker" "start" "-a" "8f6e3d2c8da9d636179f97f445d04aa4547f1a90b4a81a7c8b5023bb2f5a33fa", kill_on_drop: false }`
[INFO] [stderr]    Compiling cc v1.2.25
[INFO] [stderr]    Compiling proc-macro2 v1.0.95
[INFO] [stderr]    Compiling rustix v1.0.7
[INFO] [stderr]     Checking bitflags v2.9.1
[INFO] [stderr]     Checking linux-raw-sys v0.9.4
[INFO] [stderr]    Compiling serde v1.0.219
[INFO] [stderr]     Checking anstyle v1.0.10
[INFO] [stderr]     Checking anstyle-query v1.1.2
[INFO] [stderr]     Checking anstyle-parse v0.2.6
[INFO] [stderr]     Checking colorchoice v1.0.3
[INFO] [stderr]     Checking miniz_oxide v0.8.8
[INFO] [stderr]     Checking tracing-core v0.1.33
[INFO] [stderr]    Compiling anyhow v1.0.98
[INFO] [stderr]     Checking generic-array v0.14.7
[INFO] [stderr]     Checking regex-syntax v0.8.5
[INFO] [stderr]     Checking clap_lex v0.7.4
[INFO] [stderr]     Checking buffer-redux v1.0.2
[INFO] [stderr]     Checking overload v0.1.1
[INFO] [stderr]     Checking cpufeatures v0.2.17
[INFO] [stderr]     Checking log v0.4.27
[INFO] [stderr]     Checking bytecount v0.6.8
[INFO] [stderr]     Checking sharded-slab v0.1.7
[INFO] [stderr]     Checking nu-ansi-term v0.46.0
[INFO] [stderr]     Checking smallvec v1.15.0
[INFO] [stderr]     Checking num_cpus v1.17.0
[INFO] [stderr]     Checking anstream v0.6.18
[INFO] [stderr]     Checking tracing-log v0.2.0
[INFO] [stderr]     Checking block-buffer v0.10.4
[INFO] [stderr]     Checking crypto-common v0.1.6
[INFO] [stderr]     Checking flate2 v1.1.1
[INFO] [stderr]     Checking digest v0.10.7
[INFO] [stderr]    Compiling quote v1.0.40
[INFO] [stderr]    Compiling syn v2.0.101
[INFO] [stderr]    Compiling cmake v0.1.54
[INFO] [stderr]     Checking terminal_size v0.4.2
[INFO] [stderr]     Checking clap_builder v4.5.39
[INFO] [stderr]     Checking regex-automata v0.4.9
[INFO] [stderr]    Compiling lzma-sys v0.1.20
[INFO] [stderr]    Compiling bzip2-sys v0.1.13+1.0.8
[INFO] [stderr]    Compiling sha2-asm v0.6.4
[INFO] [stderr]    Compiling piscem v0.13.0 (/opt/rustwide/workdir)
[INFO] [stderr]     Checking xz2 v0.1.7
[INFO] [stderr]     Checking sha2 v0.10.9
[INFO] [stderr] error: failed to run custom build command for `piscem v0.13.0 (/opt/rustwide/workdir)`
[INFO] [stderr] note: To improve backtraces for build dependencies, set the CARGO_PROFILE_DEV_BUILD_OVERRIDE_DEBUG=true environment variable to enable debug information generation.
[INFO] [stderr] 
[INFO] [stderr] Caused by:
[INFO] [stderr]   process didn't exit successfully: `/opt/rustwide/target/debug/build/piscem-1d12e0692dff1595/build-script-build` (exit status: 101)
[INFO] [stderr]   --- stdout
[INFO] [stderr]   cargo:rerun-if-changed=cuttlefish/CMakeLists.txt
[INFO] [stderr]   cargo:rerun-if-changed=piscem-cpp/CMakeLists.txt
[INFO] [stderr]   CMAKE_TOOLCHAIN_FILE_x86_64-unknown-linux-gnu = None
[INFO] [stderr]   CMAKE_TOOLCHAIN_FILE_x86_64_unknown_linux_gnu = None
[INFO] [stderr]   HOST_CMAKE_TOOLCHAIN_FILE = None
[INFO] [stderr]   CMAKE_TOOLCHAIN_FILE = None
[INFO] [stderr]   CMAKE_GENERATOR_x86_64-unknown-linux-gnu = None
[INFO] [stderr]   CMAKE_GENERATOR_x86_64_unknown_linux_gnu = None
[INFO] [stderr]   HOST_CMAKE_GENERATOR = None
[INFO] [stderr]   CMAKE_GENERATOR = None
[INFO] [stderr]   CMAKE_PREFIX_PATH_x86_64-unknown-linux-gnu = None
[INFO] [stderr]   CMAKE_PREFIX_PATH_x86_64_unknown_linux_gnu = None
[INFO] [stderr]   HOST_CMAKE_PREFIX_PATH = None
[INFO] [stderr]   CMAKE_PREFIX_PATH = None
[INFO] [stderr]   CMAKE_x86_64-unknown-linux-gnu = None
[INFO] [stderr]   CMAKE_x86_64_unknown_linux_gnu = None
[INFO] [stderr]   HOST_CMAKE = None
[INFO] [stderr]   CMAKE = None
[INFO] [stderr]   running: cd "/opt/rustwide/target/debug/build/piscem-355aba5c0ba38bc9/out/build" && CMAKE_PREFIX_PATH="" LC_ALL="C" "cmake" "/opt/rustwide/workdir/piscem-cpp" "-DCMAKE_INSTALL_PREFIX=/opt/rustwide/target/debug/build/piscem-355aba5c0ba38bc9/out" "-DCMAKE_C_FLAGS= -ffunction-sections -fdata-sections -fPIC -m64" "-DCMAKE_C_COMPILER=/usr/bin/cc" "-DCMAKE_CXX_FLAGS= -ffunction-sections -fdata-sections -fPIC -m64" "-DCMAKE_CXX_COMPILER=/usr/bin/c++" "-DCMAKE_ASM_FLAGS= -ffunction-sections -fdata-sections -fPIC -m64" "-DCMAKE_ASM_COMPILER=/usr/bin/cc" "-DCMAKE_BUILD_TYPE=Debug"
[INFO] [stderr] 
[INFO] [stderr]   --- stderr
[INFO] [stderr]   CMake Warning:
[INFO] [stderr]     Ignoring extra path from command line:
[INFO] [stderr] 
[INFO] [stderr]      "/opt/rustwide/workdir/piscem-cpp"
[INFO] [stderr] 
[INFO] [stderr] 
[INFO] [stderr]   CMake Error: The source directory "/opt/rustwide/workdir/piscem-cpp" does not appear to contain CMakeLists.txt.
[INFO] [stderr]   Specify --help for usage, or press the help button on the CMake GUI.
[INFO] [stderr] 
[INFO] [stderr]   thread 'main' panicked at /opt/rustwide/cargo-home/registry/src/index.crates.io-1949cf8c6b5b557f/cmake-0.1.54/src/lib.rs:1119:5:
[INFO] [stderr] 
[INFO] [stderr]   command did not execute successfully, got: exit status: 1
[INFO] [stderr] 
[INFO] [stderr]   build script failed, must exit now
[INFO] [stderr]   stack backtrace:
[INFO] [stderr]      0:     0x578f63e90042 - std::backtrace_rs::backtrace::libunwind::trace::h77d4f1ab393021ff
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/../../backtrace/src/backtrace/libunwind.rs:117:9
[INFO] [stderr]      1:     0x578f63e90042 - std::backtrace_rs::backtrace::trace_unsynchronized::h6b52b199056dc310
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/../../backtrace/src/backtrace/mod.rs:66:14
[INFO] [stderr]      2:     0x578f63e90042 - std::sys::backtrace::_print_fmt::h336a00096dca5793
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/sys/backtrace.rs:66:9
[INFO] [stderr]      3:     0x578f63e90042 - <std::sys::backtrace::BacktraceLock::print::DisplayBacktrace as core::fmt::Display>::fmt::h4e23cde6d13531e6
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/sys/backtrace.rs:39:26
[INFO] [stderr]      4:     0x578f63eb2df3 - core::fmt::rt::Argument::fmt::hd73adb1dd4f13238
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/core/src/fmt/rt.rs:173:76
[INFO] [stderr]      5:     0x578f63eb2df3 - core::fmt::write::h24956daaf3520b88
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/core/src/fmt/mod.rs:1465:25
[INFO] [stderr]      6:     0x578f63e8ccc3 - std::io::default_write_fmt::h5ad85cda2d892f3f
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/io/mod.rs:639:11
[INFO] [stderr]      7:     0x578f63e8ccc3 - std::io::Write::write_fmt::h744a9c29e898aaa0
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/io/mod.rs:1954:13
[INFO] [stderr]      8:     0x578f63e8fe92 - std::sys::backtrace::BacktraceLock::print::h80bc63112117b07d
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/sys/backtrace.rs:42:9
[INFO] [stderr]      9:     0x578f63e91326 - std::panicking::default_hook::{{closure}}::hcc0250ffe151a9a2
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/panicking.rs:300:27
[INFO] [stderr]     10:     0x578f63e91129 - std::panicking::default_hook::heb98c3e6f5363c1c
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/panicking.rs:327:9
[INFO] [stderr]     11:     0x578f63e91cf2 - std::panicking::rust_panic_with_hook::ha71490f06bda8fdd
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/panicking.rs:833:13
[INFO] [stderr]     12:     0x578f63e91a8a - std::panicking::begin_panic_handler::{{closure}}::h842d98411b820c95
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/panicking.rs:706:13
[INFO] [stderr]     13:     0x578f63e90549 - std::sys::backtrace::__rust_end_short_backtrace::hc17b54f5216e7287
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/sys/backtrace.rs:168:18
[INFO] [stderr]     14:     0x578f63e9171d - __rustc[d39aaf4d8a5bdd9]::rust_begin_unwind
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/panicking.rs:697:5
[INFO] [stderr]     15:     0x578f63eb1cc0 - core::panicking::panic_fmt::hafddcaa47f3ecc5a
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/core/src/panicking.rs:75:14
[INFO] [stderr]     16:     0x578f63dfd92b - cmake::fail::h593b3bc3c5c1ac20
[INFO] [stderr]     17:     0x578f63dfd172 - cmake::run::h2ab137053bb46a4a
[INFO] [stderr]     18:     0x578f63df9464 - cmake::Config::build::hf6cc0cbb5f32919e
[INFO] [stderr]     19:     0x578f63df2ea1 - build_script_build::main::h57a4cb4485ded3ba
[INFO] [stderr]     20:     0x578f63df01b3 - core::ops::function::FnOnce::call_once::h5b2ab14e1c69cbf1
[INFO] [stderr]     21:     0x578f63df00f6 - std::sys::backtrace::__rust_begin_short_backtrace::hc9270bc75f32354a
[INFO] [stderr]     22:     0x578f63df0029 - std::rt::lang_start::{{closure}}::hc5043942dbd02cea
[INFO] [stderr]     23:     0x578f63e889d0 - core::ops::function::impls::<impl core::ops::function::FnOnce<A> for &F>::call_once::ha6f9c4d44e1a5001
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/core/src/ops/function.rs:284:21
[INFO] [stderr]     24:     0x578f63e889d0 - std::panicking::catch_unwind::do_call::hf103a4d58b5b21e2
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/panicking.rs:589:40
[INFO] [stderr]     25:     0x578f63e889d0 - std::panicking::catch_unwind::hd0c31cdd71304f17
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/panicking.rs:552:19
[INFO] [stderr]     26:     0x578f63e889d0 - std::panic::catch_unwind::h434b753bad4487d0
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/panic.rs:359:14
[INFO] [stderr]     27:     0x578f63e889d0 - std::rt::lang_start_internal::{{closure}}::h26129cc9f6eb7a93
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/rt.rs:175:24
[INFO] [stderr]     28:     0x578f63e889d0 - std::panicking::catch_unwind::do_call::had764bf67fcbab3f
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/panicking.rs:589:40
[INFO] [stderr]     29:     0x578f63e889d0 - std::panicking::catch_unwind::h4085a8f2f773b27d
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/panicking.rs:552:19
[INFO] [stderr]     30:     0x578f63e889d0 - std::panic::catch_unwind::h3198cebd91ce9b7d
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/panic.rs:359:14
[INFO] [stderr]     31:     0x578f63e889d0 - std::rt::lang_start_internal::hf25b94b42aad689d
[INFO] [stderr]                                  at /rustc/8f21a5c92ea55c348c275a1bc4fedbdf181e0d64/library/std/src/rt.rs:171:5
[INFO] [stderr]     32:     0x578f63df0011 - std::rt::lang_start::ha5a556a50bb9179e
[INFO] [stderr]     33:     0x578f63df4d45 - main
[INFO] [stderr]     34:     0x74085d59a1ca - <unknown>
[INFO] [stderr]     35:     0x74085d59a28b - __libc_start_main
[INFO] [stderr]     36:     0x578f63defe35 - _start
[INFO] [stderr]     37:                0x0 - <unknown>
[INFO] [stderr] warning: build failed, waiting for other jobs to finish...
[INFO] running `Command { std: "docker" "inspect" "8f6e3d2c8da9d636179f97f445d04aa4547f1a90b4a81a7c8b5023bb2f5a33fa", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "8f6e3d2c8da9d636179f97f445d04aa4547f1a90b4a81a7c8b5023bb2f5a33fa", kill_on_drop: false }`
[INFO] [stdout] 8f6e3d2c8da9d636179f97f445d04aa4547f1a90b4a81a7c8b5023bb2f5a33fa
