[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] 478744301af83c223b43a034bb6eb19f1da21250
[INFO] checking COMBINE-lab/piscem against master#46424fb5054f211ec836c5c03159f92e46bb35ac for pr-139042
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FCOMBINE-lab%2Fpiscem" "/workspace/builds/worker-1-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-1-tc1/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/COMBINE-lab/piscem on toolchain 46424fb5054f211ec836c5c03159f92e46bb35ac
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+46424fb5054f211ec836c5c03159f92e46bb35ac" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[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-1-tc1/source/Cargo.toml
[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" "+46424fb5054f211ec836c5c03159f92e46bb35ac" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded cmake v0.1.53
[INFO] [stderr]   Downloaded prepare_fasta v0.1.0
[INFO] [stderr]   Downloaded clap v4.5.27
[INFO] [stderr]   Downloaded clap_derive v4.5.24
[INFO] [stderr]   Downloaded needletail v0.5.1
[INFO] [stderr]   Downloaded buffer-redux v1.0.2
[INFO] [stderr]   Downloaded cc v1.2.11
[INFO] [stderr]   Downloaded sha2-asm v0.6.4
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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@sha256:4b26683ee3c49f365255c425c23003cbf4366de097804722c29c5bbbee3624d2" "/opt/rustwide/cargo-home/bin/cargo" "+46424fb5054f211ec836c5c03159f92e46bb35ac" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 874a5933c3bc6db895ee2b50563a1fefbf31af6ff3fb936b614b26384fcbc65a
[INFO] running `Command { std: "docker" "start" "-a" "874a5933c3bc6db895ee2b50563a1fefbf31af6ff3fb936b614b26384fcbc65a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "874a5933c3bc6db895ee2b50563a1fefbf31af6ff3fb936b614b26384fcbc65a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "874a5933c3bc6db895ee2b50563a1fefbf31af6ff3fb936b614b26384fcbc65a", kill_on_drop: false }`
[INFO] [stdout] 874a5933c3bc6db895ee2b50563a1fefbf31af6ff3fb936b614b26384fcbc65a
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-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@sha256:4b26683ee3c49f365255c425c23003cbf4366de097804722c29c5bbbee3624d2" "/opt/rustwide/cargo-home/bin/cargo" "+46424fb5054f211ec836c5c03159f92e46bb35ac" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 3e8208508d50b7a0135da7f8f3d82844bf788586ccffe105eb2270bc6c50b167
[INFO] running `Command { std: "docker" "start" "-a" "3e8208508d50b7a0135da7f8f3d82844bf788586ccffe105eb2270bc6c50b167", kill_on_drop: false }`
[INFO] [stderr]    Compiling shlex v1.3.0
[INFO] [stderr]    Compiling pkg-config v0.3.31
[INFO] [stderr]    Compiling proc-macro2 v1.0.93
[INFO] [stderr]    Compiling libc v0.2.169
[INFO] [stderr]    Compiling unicode-ident v1.0.16
[INFO] [stderr]    Compiling version_check v0.9.5
[INFO] [stderr]    Compiling typenum v1.17.0
[INFO] [stderr]     Checking cfg-if v1.0.0
[INFO] [stderr]    Compiling rustix v0.38.44
[INFO] [stderr]     Checking linux-raw-sys v0.4.15
[INFO] [stderr]     Checking bitflags v2.8.0
[INFO] [stderr]     Checking utf8parse v0.2.2
[INFO] [stderr]     Checking once_cell v1.20.2
[INFO] [stderr]     Checking adler2 v2.0.0
[INFO] [stderr]     Checking memchr v2.7.4
[INFO] [stderr]     Checking is_terminal_polyfill v1.70.1
[INFO] [stderr]     Checking anstyle v1.0.10
[INFO] [stderr]     Checking anstyle-query v1.1.2
[INFO] [stderr]    Compiling serde v1.0.217
[INFO] [stderr]    Compiling cc v1.2.11
[INFO] [stderr]     Checking anstyle-parse v0.2.6
[INFO] [stderr]     Checking colorchoice v1.0.3
[INFO] [stderr]     Checking miniz_oxide v0.8.3
[INFO] [stderr]     Checking crc32fast v1.4.2
[INFO] [stderr]     Checking clap_lex v0.7.4
[INFO] [stderr]     Checking anstream v0.6.18
[INFO] [stderr]    Compiling serde_json v1.0.138
[INFO] [stderr]    Compiling heck v0.5.0
[INFO] [stderr]     Checking regex-syntax v0.6.29
[INFO] [stderr]     Checking tracing-core v0.1.33
[INFO] [stderr]     Checking strsim v0.11.1
[INFO] [stderr]    Compiling anyhow v1.0.95
[INFO] [stderr]     Checking regex-syntax v0.8.5
[INFO] [stderr]     Checking itoa v1.0.14
[INFO] [stderr]     Checking cpufeatures v0.2.17
[INFO] [stderr]    Compiling generic-array v0.14.7
[INFO] [stderr]     Checking ryu v1.0.19
[INFO] [stderr]     Checking flate2 v1.0.35
[INFO] [stderr]     Checking bytecount v0.6.8
[INFO] [stderr]     Checking buffer-redux v1.0.2
[INFO] [stderr]     Checking overload v0.1.1
[INFO] [stderr]    Compiling quote v1.0.38
[INFO] [stderr]     Checking pin-project-lite v0.2.16
[INFO] [stderr]     Checking lazy_static v1.5.0
[INFO] [stderr]     Checking log v0.4.25
[INFO] [stderr]     Checking sharded-slab v0.1.7
[INFO] [stderr]     Checking nu-ansi-term v0.46.0
[INFO] [stderr]     Checking thread_local v1.1.8
[INFO] [stderr]     Checking tracing-log v0.2.0
[INFO] [stderr]     Checking smallvec v1.13.2
[INFO] [stderr]    Compiling syn v2.0.96
[INFO] [stderr]     Checking hex v0.4.3
[INFO] [stderr]     Checking terminal_size v0.4.1
[INFO] [stderr]     Checking num_cpus v1.16.0
[INFO] [stderr]     Checking crypto-common v0.1.6
[INFO] [stderr]     Checking block-buffer v0.10.4
[INFO] [stderr]     Checking clap_builder v4.5.27
[INFO] [stderr]     Checking digest v0.10.7
[INFO] [stderr]     Checking regex-automata v0.1.10
[INFO] [stderr]     Checking regex-automata v0.4.9
[INFO] [stderr]    Compiling cmake v0.1.53
[INFO] [stderr]    Compiling lzma-sys v0.1.20
[INFO] [stderr]    Compiling bzip2-sys v0.1.11+1.0.8
[INFO] [stderr]    Compiling sha2-asm v0.6.4
[INFO] [stderr]    Compiling piscem v0.12.2 (/opt/rustwide/workdir)
[INFO] [stderr]     Checking matchers v0.1.0
[INFO] [stderr] error: failed to run custom build command for `piscem v0.12.2 (/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-ccb8ab637939e8b2/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-f8af97f7ef9eb0ad/out/build" && CMAKE_PREFIX_PATH="" LC_ALL="C" "cmake" "/opt/rustwide/workdir/piscem-cpp" "-DCMAKE_INSTALL_PREFIX=/opt/rustwide/target/debug/build/piscem-f8af97f7ef9eb0ad/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-0.1.53/src/lib.rs:1121:5:
[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:     0x5b318e132a22 - std::backtrace_rs::backtrace::libunwind::trace::hfe33f3fca02d9d49
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/../../backtrace/src/backtrace/libunwind.rs:117:9
[INFO] [stderr]      1:     0x5b318e132a22 - std::backtrace_rs::backtrace::trace_unsynchronized::hf8c1336b7abecebc
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/../../backtrace/src/backtrace/mod.rs:66:14
[INFO] [stderr]      2:     0x5b318e132a22 - std::sys::backtrace::_print_fmt::h1cc3b7371fcb02ce
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/sys/backtrace.rs:66:9
[INFO] [stderr]      3:     0x5b318e132a22 - <std::sys::backtrace::BacktraceLock::print::DisplayBacktrace as core::fmt::Display>::fmt::h3fdbad3682625d65
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/sys/backtrace.rs:39:26
[INFO] [stderr]      4:     0x5b318e156fb3 - core::fmt::rt::Argument::fmt::hac739edf89f473e5
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/core/src/fmt/rt.rs:184:76
[INFO] [stderr]      5:     0x5b318e156fb3 - core::fmt::write::h46b3661118fd93d9
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/core/src/fmt/mod.rs:1480:21
[INFO] [stderr]      6:     0x5b318e12f883 - std::io::default_write_fmt::h07a956b98e0e549f
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/io/mod.rs:639:11
[INFO] [stderr]      7:     0x5b318e12f883 - std::io::Write::write_fmt::hefeac8c5ed2b4ca0
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/io/mod.rs:1914:13
[INFO] [stderr]      8:     0x5b318e132872 - std::sys::backtrace::BacktraceLock::print::hc92ef2ccd32eaf3d
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/sys/backtrace.rs:42:9
[INFO] [stderr]      9:     0x5b318e133d12 - std::panicking::default_hook::{{closure}}::h26c6ecc533f19c32
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/panicking.rs:300:22
[INFO] [stderr]     10:     0x5b318e133b15 - std::panicking::default_hook::he6d1a5a8f8627255
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/panicking.rs:327:9
[INFO] [stderr]     11:     0x5b318e1346f2 - std::panicking::rust_panic_with_hook::hc6a05938888c0a6d
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/panicking.rs:833:13
[INFO] [stderr]     12:     0x5b318e13447a - std::panicking::begin_panic_handler::{{closure}}::hce41832356916883
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/panicking.rs:706:13
[INFO] [stderr]     13:     0x5b318e132f29 - std::sys::backtrace::__rust_end_short_backtrace::h809ad2921436b614
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/sys/backtrace.rs:168:18
[INFO] [stderr]     14:     0x5b318e13410d - __rustc[13f85059a3e01eb3]::rust_begin_unwind
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/panicking.rs:697:5
[INFO] [stderr]     15:     0x5b318e155e10 - core::panicking::panic_fmt::h7e568a56ffdf448b
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/core/src/panicking.rs:75:14
[INFO] [stderr]     16:     0x5b318e0b06fb - cmake::fail::ha3c42fd0cf154190
[INFO] [stderr]     17:     0x5b318e0aff62 - cmake::run::hdbd370e41a421588
[INFO] [stderr]     18:     0x5b318e0ac2fc - cmake::Config::build::heb984d31168157e9
[INFO] [stderr]     19:     0x5b318e09d5fc - build_script_build::main::h1dcdafab1ca1d6bf
[INFO] [stderr]     20:     0x5b318e09ab33 - core::ops::function::FnOnce::call_once::h7aafc493271e59bf
[INFO] [stderr]     21:     0x5b318e09aab6 - std::sys::backtrace::__rust_begin_short_backtrace::h5ba81034a4940847
[INFO] [stderr]     22:     0x5b318e09a9f9 - std::rt::lang_start::{{closure}}::h2f9da13dd5c59486
[INFO] [stderr]     23:     0x5b318e12b2b0 - core::ops::function::impls::<impl core::ops::function::FnOnce<A> for &F>::call_once::h07820d99f666c4f4
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/core/src/ops/function.rs:284:13
[INFO] [stderr]     24:     0x5b318e12b2b0 - std::panicking::try::do_call::hcb349621034e7d22
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/panicking.rs:589:40
[INFO] [stderr]     25:     0x5b318e12b2b0 - std::panicking::try::h14d805015e715701
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/panicking.rs:552:19
[INFO] [stderr]     26:     0x5b318e12b2b0 - std::panic::catch_unwind::he07ff3323b1b1ad4
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/panic.rs:359:14
[INFO] [stderr]     27:     0x5b318e12b2b0 - std::rt::lang_start_internal::{{closure}}::he746c4aa7e6c87ae
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/rt.rs:168:24
[INFO] [stderr]     28:     0x5b318e12b2b0 - std::panicking::try::do_call::h5c36b323e35fe62d
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/panicking.rs:589:40
[INFO] [stderr]     29:     0x5b318e12b2b0 - std::panicking::try::hb9a2d1353ef314fe
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/panicking.rs:552:19
[INFO] [stderr]     30:     0x5b318e12b2b0 - std::panic::catch_unwind::he0661a914ab09041
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/panic.rs:359:14
[INFO] [stderr]     31:     0x5b318e12b2b0 - std::rt::lang_start_internal::h690c392d3d3c052a
[INFO] [stderr]                                  at /rustc/46424fb5054f211ec836c5c03159f92e46bb35ac/library/std/src/rt.rs:164:5
[INFO] [stderr]     32:     0x5b318e09a9e1 - std::rt::lang_start::h0ad573dc8de25522
[INFO] [stderr]     33:     0x5b318e09f465 - main
[INFO] [stderr]     34:     0x7ff7a7d051ca - <unknown>
[INFO] [stderr]     35:     0x7ff7a7d0528b - __libc_start_main
[INFO] [stderr]     36:     0x5b318e09a815 - _start
[INFO] [stderr]     37:                0x0 - <unknown>
[INFO] [stderr] warning: build failed, waiting for other jobs to finish...
[INFO] running `Command { std: "docker" "inspect" "3e8208508d50b7a0135da7f8f3d82844bf788586ccffe105eb2270bc6c50b167", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "3e8208508d50b7a0135da7f8f3d82844bf788586ccffe105eb2270bc6c50b167", kill_on_drop: false }`
[INFO] [stdout] 3e8208508d50b7a0135da7f8f3d82844bf788586ccffe105eb2270bc6c50b167
