[INFO] fetching crate genomic_interval_pipeline 0.1.3... [INFO] testing genomic_interval_pipeline-0.1.3 against master#99e3aef02079e9c10583638520cd0c134dc3a01d for pr-85530 [INFO] extracting crate genomic_interval_pipeline 0.1.3 into /workspace/builds/worker-1/source [INFO] validating manifest of crates.io crate genomic_interval_pipeline 0.1.3 on toolchain 99e3aef02079e9c10583638520cd0c134dc3a01d [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+99e3aef02079e9c10583638520cd0c134dc3a01d" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking crates.io crate genomic_interval_pipeline 0.1.3 [INFO] finished tweaking crates.io crate genomic_interval_pipeline 0.1.3 [INFO] tweaked toml for crates.io crate genomic_interval_pipeline 0.1.3 written to /workspace/builds/worker-1/source/Cargo.toml [INFO] crate crates.io crate genomic_interval_pipeline 0.1.3 already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+99e3aef02079e9c10583638520cd0c134dc3a01d" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/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@sha256:20528e8c29e4536546f0102ce88568b16ea7538393a33fcca951030f7af10457" "/opt/rustwide/cargo-home/bin/cargo" "+99e3aef02079e9c10583638520cd0c134dc3a01d" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] [stdout] 9cc03138c2c2557124422385d9a1ed7ab10b6608f22ba86c0afccce325326378 [INFO] running `Command { std: "docker" "start" "-a" "9cc03138c2c2557124422385d9a1ed7ab10b6608f22ba86c0afccce325326378", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "9cc03138c2c2557124422385d9a1ed7ab10b6608f22ba86c0afccce325326378", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "9cc03138c2c2557124422385d9a1ed7ab10b6608f22ba86c0afccce325326378", kill_on_drop: false }` [INFO] [stdout] 9cc03138c2c2557124422385d9a1ed7ab10b6608f22ba86c0afccce325326378 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1/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" "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@sha256:20528e8c29e4536546f0102ce88568b16ea7538393a33fcca951030f7af10457" "/opt/rustwide/cargo-home/bin/cargo" "+99e3aef02079e9c10583638520cd0c134dc3a01d" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. [INFO] [stdout] 35fd7e4552933b1c0b5a525b5a51f2a98a21d4b8f0074576991ad7b6021c79fe [INFO] running `Command { std: "docker" "start" "-a" "35fd7e4552933b1c0b5a525b5a51f2a98a21d4b8f0074576991ad7b6021c79fe", kill_on_drop: false }` [INFO] [stderr] Compiling syn v1.0.50 [INFO] [stderr] Compiling regex-syntax v0.6.21 [INFO] [stderr] Compiling proc-macro2 v0.4.30 [INFO] [stderr] Compiling matches v0.1.8 [INFO] [stderr] Compiling tinyvec_macros v0.1.0 [INFO] [stderr] Compiling unicode-xid v0.1.0 [INFO] [stderr] Compiling syn v0.15.44 [INFO] [stderr] Compiling serde v1.0.117 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Compiling serde_derive v1.0.117 [INFO] [stderr] Compiling crc32fast v1.2.1 [INFO] [stderr] Compiling smallvec v1.5.0 [INFO] [stderr] Compiling ndarray v0.13.1 [INFO] [stderr] Compiling log v0.4.11 [INFO] [stderr] Compiling percent-encoding v2.1.0 [INFO] [stderr] Compiling unicode-segmentation v1.7.0 [INFO] [stderr] Compiling ansi_term v0.11.0 [INFO] [stderr] Compiling hdf5 v0.7.0 [INFO] [stderr] Compiling strsim v0.8.0 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling rustc-serialize v0.3.24 [INFO] [stderr] Compiling ascii v1.0.0 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling thread_local v1.0.1 [INFO] [stderr] Compiling libloading v0.6.5 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling lock_api v0.3.4 [INFO] [stderr] Compiling matrixmultiply v0.2.3 [INFO] [stderr] Compiling tinyvec v1.1.0 [INFO] [stderr] Compiling unicode-bidi v0.3.4 [INFO] [stderr] Compiling form_urlencoded v1.0.0 [INFO] [stderr] Compiling heck v0.3.1 [INFO] [stderr] Compiling jobserver v0.1.21 [INFO] [stderr] Compiling rand v0.4.6 [INFO] [stderr] Compiling parking_lot_core v0.7.2 [INFO] [stderr] Compiling time v0.1.44 [INFO] [stderr] Compiling hdf5-types v0.7.0 [INFO] [stderr] Compiling clap v2.33.3 [INFO] [stderr] Compiling flate2 v1.0.19 [INFO] [stderr] Compiling parking_lot v0.10.2 [INFO] [stderr] Compiling cc v1.0.65 [INFO] [stderr] Compiling pbr v1.0.3 [INFO] [stderr] Compiling rand v0.3.23 [INFO] [stderr] Compiling quote v0.6.13 [INFO] [stderr] Compiling unicode-normalization v0.1.16 [INFO] [stderr] Compiling regex v1.4.2 [INFO] [stderr] Compiling memrange v0.1.3 [INFO] [stderr] Compiling openssl-src v111.12.0+1.1.1h [INFO] [stderr] Compiling theban_interval_tree v0.7.1 [INFO] [stderr] Compiling idna v0.2.0 [INFO] [stderr] Compiling openssl-sys v0.9.58 [INFO] [stderr] Compiling libz-sys v1.1.2 [INFO] [stderr] Compiling curl-sys v0.4.38+curl-7.73.0 [INFO] [stderr] Compiling bzip2-sys v0.1.9+1.0.8 [INFO] [stderr] Compiling lzma-sys v0.1.17 [INFO] [stderr] Compiling hts-sys v1.11.1-fix1 [INFO] [stderr] Compiling env_logger v0.7.1 [INFO] [stderr] Compiling url v2.2.0 [INFO] [stderr] Compiling hdf5-sys v0.7.0 [INFO] [stderr] Compiling derefable v0.1.0 [INFO] [stderr] error: failed to run custom build command for `hdf5-sys v0.7.0` [INFO] [stderr] [INFO] [stderr] Caused by: [INFO] [stderr] process didn't exit successfully: `/opt/rustwide/target/debug/build/hdf5-sys-2c00444c28d6f7b4/build-script-build` (exit status: 101) [INFO] [stderr] --- stdout [INFO] [stderr] Attempting to find HDF5 via pkg-config... [INFO] [stderr] cargo:rerun-if-env-changed=HDF5_NO_PKG_CONFIG [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG [INFO] [stderr] cargo:rerun-if-env-changed=HDF5_STATIC [INFO] [stderr] cargo:rerun-if-env-changed=HDF5_DYNAMIC [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_ALL_STATIC [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_ALL_DYNAMIC [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_PATH_x86_64-unknown-linux-gnu [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_PATH_x86_64_unknown_linux_gnu [INFO] [stderr] cargo:rerun-if-env-changed=HOST_PKG_CONFIG_PATH [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_PATH [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_LIBDIR_x86_64-unknown-linux-gnu [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_LIBDIR_x86_64_unknown_linux_gnu [INFO] [stderr] cargo:rerun-if-env-changed=HOST_PKG_CONFIG_LIBDIR [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_LIBDIR [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_SYSROOT_DIR_x86_64-unknown-linux-gnu [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_SYSROOT_DIR_x86_64_unknown_linux_gnu [INFO] [stderr] cargo:rerun-if-env-changed=HOST_PKG_CONFIG_SYSROOT_DIR [INFO] [stderr] cargo:rerun-if-env-changed=PKG_CONFIG_SYSROOT_DIR [INFO] [stderr] [INFO] [stderr] --- stderr [INFO] [stderr] thread 'main' panicked at 'Unable to locate HDF5 root directory and/or headers.', /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.0/build.rs:549:13 [INFO] [stderr] stack backtrace: [INFO] [stderr] 0: 0x55efbf157440 - std::backtrace_rs::backtrace::libunwind::trace::h1037ca7e6eeef65c [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/../../backtrace/src/backtrace/libunwind.rs:90:5 [INFO] [stderr] 1: 0x55efbf157440 - std::backtrace_rs::backtrace::trace_unsynchronized::haaefac1bc3669450 [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5 [INFO] [stderr] 2: 0x55efbf157440 - std::sys_common::backtrace::_print_fmt::h863a6f5e6d995885 [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/sys_common/backtrace.rs:67:5 [INFO] [stderr] 3: 0x55efbf157440 - ::fmt::h767e17e1aa7df6a8 [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/sys_common/backtrace.rs:46:22 [INFO] [stderr] 4: 0x55efbf17598c - core::fmt::write::h7aa6cd0067dca82a [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/core/src/fmt/mod.rs:1110:17 [INFO] [stderr] 5: 0x55efbf154855 - std::io::Write::write_fmt::h4c802b6f761026c1 [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/io/mod.rs:1584:15 [INFO] [stderr] 6: 0x55efbf1594ab - std::sys_common::backtrace::_print::h2769edb26a7eb606 [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/sys_common/backtrace.rs:49:5 [INFO] [stderr] 7: 0x55efbf1594ab - std::sys_common::backtrace::print::ha71f3549862b4cb6 [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/sys_common/backtrace.rs:36:9 [INFO] [stderr] 8: 0x55efbf1594ab - std::panicking::default_hook::{{closure}}::h95488a3bade217f6 [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/panicking.rs:208:50 [INFO] [stderr] 9: 0x55efbf158f81 - std::panicking::default_hook::h290aa602c0fb11df [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/panicking.rs:225:9 [INFO] [stderr] 10: 0x55efbf159b51 - std::panicking::rust_panic_with_hook::hf32c4fa635e215f2 [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/panicking.rs:622:17 [INFO] [stderr] 11: 0x55efbef802e3 - std::panicking::begin_panic::{{closure}}::he2935c8cca4ed4fd [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/panicking.rs:542:9 [INFO] [stderr] 12: 0x55efbef66c29 - std::sys_common::backtrace::__rust_end_short_backtrace::hcf68c6f8cb3f8c01 [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/sys_common/backtrace.rs:141:18 [INFO] [stderr] 13: 0x55efbef80219 - std::panicking::begin_panic::hf9e29e8540d0278d [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/panicking.rs:541:12 [INFO] [stderr] 14: 0x55efbef51db7 - build_script_build::LibrarySearcher::try_locate_hdf5_library::h950f4ebaf753c295 [INFO] [stderr] at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.0/build.rs:549:13 [INFO] [stderr] 15: 0x55efbef535eb - build_script_build::main::h66e0e787fc613fc2 [INFO] [stderr] at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.0/build.rs:647:9 [INFO] [stderr] 16: 0x55efbef56c8b - core::ops::function::FnOnce::call_once::h44a73daba8e085a5 [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/core/src/ops/function.rs:227:5 [INFO] [stderr] 17: 0x55efbef562ee - std::sys_common::backtrace::__rust_begin_short_backtrace::h049ce33a2ff81f35 [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/sys_common/backtrace.rs:125:18 [INFO] [stderr] 18: 0x55efbef5e031 - std::rt::lang_start::{{closure}}::hd3b0c03c13bbf915 [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/rt.rs:49:18 [INFO] [stderr] 19: 0x55efbf15a049 - core::ops::function::impls:: for &F>::call_once::h04259e4a34d07c2f [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/core/src/ops/function.rs:259:13 [INFO] [stderr] 20: 0x55efbf15a049 - std::panicking::try::do_call::hb8da45704d5cfbbf [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/panicking.rs:401:40 [INFO] [stderr] 21: 0x55efbf15a049 - std::panicking::try::h4beadc19a78fec52 [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/panicking.rs:365:19 [INFO] [stderr] 22: 0x55efbf15a049 - std::panic::catch_unwind::hc58016cd36ba81a4 [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/panic.rs:433:14 [INFO] [stderr] 23: 0x55efbf15a049 - std::rt::lang_start_internal::hc51399759a90501a [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/rt.rs:34:21 [INFO] [stderr] 24: 0x55efbef5e010 - std::rt::lang_start::h85308f7d353a501c [INFO] [stderr] at /rustc/99e3aef02079e9c10583638520cd0c134dc3a01d/library/std/src/rt.rs:48:5 [INFO] [stderr] 25: 0x55efbef54adc - main [INFO] [stderr] 26: 0x7f6af99f50b3 - __libc_start_main [INFO] [stderr] 27: 0x55efbef4cf0e - _start [INFO] [stderr] 28: 0x0 - [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stderr] error: build failed [INFO] running `Command { std: "docker" "inspect" "35fd7e4552933b1c0b5a525b5a51f2a98a21d4b8f0074576991ad7b6021c79fe", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "35fd7e4552933b1c0b5a525b5a51f2a98a21d4b8f0074576991ad7b6021c79fe", kill_on_drop: false }` [INFO] [stdout] 35fd7e4552933b1c0b5a525b5a51f2a98a21d4b8f0074576991ad7b6021c79fe