[INFO] cloning repository https://github.com/sounkou-bioinfo/phase_mnv_rs
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/sounkou-bioinfo/phase_mnv_rs" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fsounkou-bioinfo%2Fphase_mnv_rs", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fsounkou-bioinfo%2Fphase_mnv_rs'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] c55b5ce5431e4b74d151e6e0acaf820da41ae297
[INFO] fixing sounkou-bioinfo/phase_mnv_rs against try#622891a4e29178280638a6b63a8908bde2c0c854+cargoflags=-Zfix-edition=end=2015,2024 for pr-157817-2
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fsounkou-bioinfo%2Fphase_mnv_rs" "/workspace/builds/worker-6-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/sounkou-bioinfo/phase_mnv_rs
[INFO] finished tweaking git repo https://github.com/sounkou-bioinfo/phase_mnv_rs
[INFO] tweaked toml for git repo https://github.com/sounkou-bioinfo/phase_mnv_rs written to /workspace/builds/worker-6-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/sounkou-bioinfo/phase_mnv_rs on toolchain 622891a4e29178280638a6b63a8908bde2c0c854
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+622891a4e29178280638a6b63a8908bde2c0c854" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/sounkou-bioinfo/phase_mnv_rs 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" "+622891a4e29178280638a6b63a8908bde2c0c854" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/source:/opt/rustwide/workdir:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,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" "-m" "1610612736" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:3a6becf2bc8dde7f3fa57ede90e4f284e72d296796fc446bbb1e2c7cc0530151" "sleep" "infinity", kill_on_drop: false }`
[INFO] [stdout] 7051e1a4650db54a17ae558a2147718ea17193421cb20ea62983f4e14aef4720
[INFO] running `Command { std: "docker" "start" "7051e1a4650db54a17ae558a2147718ea17193421cb20ea62983f4e14aef4720", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-w" "/opt/rustwide/workdir" "--user" "0:0" "7051e1a4650db54a17ae558a2147718ea17193421cb20ea62983f4e14aef4720" "/opt/rustwide/cargo-home/bin/cargo" "+622891a4e29178280638a6b63a8908bde2c0c854" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "7051e1a4650db54a17ae558a2147718ea17193421cb20ea62983f4e14aef4720", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=" "-e" "RUSTDOCFLAGS=" "-w" "/opt/rustwide/workdir" "--user" "0:0" "7051e1a4650db54a17ae558a2147718ea17193421cb20ea62983f4e14aef4720" "/opt/rustwide/cargo-home/bin/cargo" "+622891a4e29178280638a6b63a8908bde2c0c854" "fix" "--allow-no-vcs" "--allow-dirty" "--frozen" "--all" "--all-targets" "--message-format=json" "-Zfix-edition=end=2015,2024", kill_on_drop: false }`
[INFO] [stderr] crater-edition-check: migrating to next edition
[INFO] [stderr]    Migrating Cargo.toml from 2021 edition to 2024
[INFO] [stderr]    Compiling glob v0.3.3
[INFO] [stderr]    Compiling pkg-config v0.3.33
[INFO] [stderr]    Compiling prettyplease v0.2.37
[INFO] [stderr]    Compiling rustix v0.38.44
[INFO] [stderr]    Compiling regex-syntax v0.8.10
[INFO] [stderr]    Compiling minimal-lexical v0.2.1
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]    Compiling bitflags v2.11.1
[INFO] [stderr]    Compiling libc v0.2.186
[INFO] [stderr]     Checking memchr v2.8.0
[INFO] [stderr]    Compiling either v1.15.0
[INFO] [stderr]    Compiling syn v2.0.117
[INFO] [stderr]    Compiling linux-raw-sys v0.4.15
[INFO] [stderr]    Compiling libloading v0.8.9
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]    Compiling home v0.5.12
[INFO] [stderr]    Compiling bindgen v0.69.5
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]    Compiling itertools v0.12.1
[INFO] [stderr]    Compiling lazycell v1.3.0
[INFO] [stderr]    Compiling log v0.4.29
[INFO] [stderr]    Compiling clang-sys v1.8.1
[INFO] [stderr]     Checking percent-encoding v2.3.2
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking form_urlencoded v1.2.2
[INFO] [stderr]     Checking aho-corasick v1.1.4
[INFO] [stderr]    Compiling nom v7.1.3
[INFO] [stderr]    Compiling regex-automata v0.4.14
[INFO] [stderr]    Compiling jobserver v0.1.34
[INFO] [stderr]    Compiling cc v1.2.61
[INFO] [stderr]    Compiling cexpr v0.6.0
[INFO] [stderr]    Compiling which v4.4.2
[INFO] [stderr]    Compiling cmake v0.1.58
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]    Compiling hts-sys v2.2.0
[INFO] [stderr]    Compiling libz-sys v1.1.28
[INFO] [stderr]    Compiling regex v1.12.3
[INFO] [stderr]    Compiling synstructure v0.13.2
[INFO] [stderr]    Compiling zerofrom-derive v0.1.7
[INFO] [stderr]    Compiling yoke-derive v0.8.2
[INFO] [stderr]    Compiling zerovec-derive v0.11.3
[INFO] [stderr]    Compiling displaydoc v0.2.5
[INFO] [stderr]    Compiling thiserror-impl v1.0.69
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]     Checking zerofrom v0.1.7
[INFO] [stderr]     Checking thiserror v1.0.69
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[INFO] [stderr]     Checking url v2.5.8
[INFO] [stderr]    Compiling phase_tools-rs v0.1.0 (/opt/rustwide/workdir)
[INFO] [stderr]    Migrating build.rs from 2021 edition to 2024
[INFO] [stderr]     Checking rust-htslib v0.46.0
[INFO] [stderr]    Migrating src/lib.rs from 2021 edition to 2024
[INFO] [stderr]        Fixed /opt/rustwide/target/debug/build/phase_tools-rs-f8af58653a8a20f5/out/fermi_lite_bindings.rs (4 fixes)
[INFO] [stderr]    Migrating src/bin/multi_region_joint_detect.rs from 2021 edition to 2024
[INFO] [stderr]    Migrating src/bin/fermi_lite_assemble.rs from 2021 edition to 2024
[INFO] [stderr]    Migrating src/bin/bam_contamination.rs from 2021 edition to 2024
[INFO] [stderr]    Migrating src/bin/bam_ancestry.rs from 2021 edition to 2024
[INFO] [stderr]    Migrating src/bin/unphase_vcf.rs from 2021 edition to 2024
[INFO] [stderr]    Migrating src/bin/phase_adjudicate.rs from 2021 edition to 2024
[INFO] [stderr]    Migrating src/bin/phase_compare.rs from 2021 edition to 2024
[INFO] [stderr]    Migrating src/main.rs from 2021 edition to 2024
[INFO] [stderr]    Migrating src/bin/bam_error_model.rs from 2021 edition to 2024
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 47.04s
[INFO] [stderr] crater-edition-check: phase_tools-rs v0.1.0 (/opt/rustwide/workdir) updating edition from 2021 to 2024
[INFO] [stderr]    Compiling phase_tools-rs v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] error: extern blocks must be unsafe
[INFO] [stdout]  --> /opt/rustwide/target/debug/build/phase_tools-rs-f8af58653a8a20f5/out/fermi_lite_bindings.rs:3:13764
[INFO] [stdout]   |
[INFO] [stdout] 3 | ... , stringify ! (ovlp))) ; } extern "C" { pub static mut fm_verbose : :: std :: os :: raw :: c_int ; } extern "C" { # [doc = " Init...
[INFO] [stdout]   |                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error: extern blocks must be unsafe
[INFO] [stdout]  --> /opt/rustwide/target/debug/build/phase_tools-rs-f8af58653a8a20f5/out/fermi_lite_bindings.rs:3:13838
[INFO] [stdout]   |
[INFO] [stdout] 3 | ... } extern "C" { # [doc = " Initialize default parameters\n\n @param opt      (out) pointer to parameters"] pub fn fml_opt_init (opt : * mut fml_opt_t) ; } ex...
[INFO] [stdout]   |       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error: extern blocks must be unsafe
[INFO] [stdout]  --> /opt/rustwide/target/debug/build/phase_tools-rs-f8af58653a8a20f5/out/fermi_lite_bindings.rs:3:13990
[INFO] [stdout]   |
[INFO] [stdout] 3 | ... } extern "C" { # [doc = " Assemble a list of se...:: os :: raw :: c_int) -> * mut fml_utg_t ; } ex...
[INFO] [stdout]   |       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^...^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error: extern blocks must be unsafe
[INFO] [stdout]  --> /opt/rustwide/target/debug/build/phase_tools-rs-f8af58653a8a20f5/out/fermi_lite_bindings.rs:3:14435
[INFO] [stdout]   |
[INFO] [stdout] 3 | ... } extern "C" { # [doc = " Free unitigs\n\n @param n_utg    number of unitigs\n @param utg      array of unitigs"] pub fn fml_utg_destroy (n_utg : :: std :: os :: raw :: c_int , utg : * mut fml_utg_t) ; }
[INFO] [stdout]   |       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error: extern blocks must be unsafe
[INFO] [stdout]  --> /opt/rustwide/target/debug/build/phase_tools-rs-f8af58653a8a20f5/out/fermi_lite_bindings.rs:3:13764
[INFO] [stdout]   |
[INFO] [stdout] 3 | ... , stringify ! (ovlp))) ; } extern "C" { pub static mut fm_verbose : :: std :: os :: raw :: c_int ; } extern "C" { # [doc = " Init...
[INFO] [stdout]   |                                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error: extern blocks must be unsafe
[INFO] [stdout]  --> /opt/rustwide/target/debug/build/phase_tools-rs-f8af58653a8a20f5/out/fermi_lite_bindings.rs:3:13838
[INFO] [stdout]   |
[INFO] [stdout] 3 | ... } extern "C" { # [doc = " Initialize default parameters\n\n @param opt      (out) pointer to parameters"] pub fn fml_opt_init (opt : * mut fml_opt_t) ; } ex...
[INFO] [stdout]   |       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error: extern blocks must be unsafe
[INFO] [stdout]  --> /opt/rustwide/target/debug/build/phase_tools-rs-f8af58653a8a20f5/out/fermi_lite_bindings.rs:3:13990
[INFO] [stdout]   |
[INFO] [stdout] 3 | ... } extern "C" { # [doc = " Assemble a list of se...:: os :: raw :: c_int) -> * mut fml_utg_t ; } ex...
[INFO] [stdout]   |       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^...^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] error: extern blocks must be unsafe
[INFO] [stdout]  --> /opt/rustwide/target/debug/build/phase_tools-rs-f8af58653a8a20f5/out/fermi_lite_bindings.rs:3:14435
[INFO] [stdout]   |
[INFO] [stdout] 3 | ... } extern "C" { # [doc = " Free unitigs\n\n @param n_utg    number of unitigs\n @param utg      array of unitigs"] pub fn fml_utg_destroy (n_utg : :: std :: os :: raw :: c_int , utg : * mut fml_utg_t) ; }
[INFO] [stdout]   |       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr] error: could not compile `phase_tools-rs` (lib) due to 4 previous errors
[INFO] [stderr] warning: build failed, waiting for other jobs to finish...
[INFO] [stderr] error: could not compile `phase_tools-rs` (lib test) due to 4 previous errors
[INFO] running `Command { std: "docker" "inspect" "7051e1a4650db54a17ae558a2147718ea17193421cb20ea62983f4e14aef4720", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "7051e1a4650db54a17ae558a2147718ea17193421cb20ea62983f4e14aef4720", kill_on_drop: false }`
[INFO] [stdout] 7051e1a4650db54a17ae558a2147718ea17193421cb20ea62983f4e14aef4720
