[INFO] fetching crate genomic_interval_pipeline 0.1.3...
[INFO] checking genomic_interval_pipeline-0.1.3 against beta-2021-10-15 for beta-1.56-3
[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 beta-2021-10-15
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2021-10-15" "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" "+beta-2021-10-15" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded bio-types v0.7.0
[INFO] [stderr]   Downloaded hdf5-derive v0.7.0
[INFO] [stderr]   Downloaded rust-htslib v0.35.2
[INFO] [stderr]   Downloaded syn v1.0.50
[INFO] [stderr]   Downloaded hdf5 v0.7.0
[INFO] [stderr]   Downloaded memrange v0.1.3
[INFO] [stderr]   Downloaded theban_interval_tree v0.7.1
[INFO] [stderr]   Downloaded hdf5-types v0.7.0
[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:a89201d6b5b9fd45c15d5952ece0a0129e7e80cb26ec023fd59cf09bc26f1604" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2021-10-15" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 8971c2f0192f22ecc7366be7d5a77fec096ef618c1f1d830faead956c65426a4
[INFO] [stderr] WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
[INFO] running `Command { std: "docker" "start" "-a" "8971c2f0192f22ecc7366be7d5a77fec096ef618c1f1d830faead956c65426a4", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "8971c2f0192f22ecc7366be7d5a77fec096ef618c1f1d830faead956c65426a4", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "8971c2f0192f22ecc7366be7d5a77fec096ef618c1f1d830faead956c65426a4", kill_on_drop: false }`
[INFO] [stdout] 8971c2f0192f22ecc7366be7d5a77fec096ef618c1f1d830faead956c65426a4
[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=warn" "-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:a89201d6b5b9fd45c15d5952ece0a0129e7e80cb26ec023fd59cf09bc26f1604" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2021-10-15" "check" "--frozen" "--all" "--all-targets" "--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] 30bdb0699667d93fe60cc1200a4e9bca68a5170039ced145e7d94ecc733a98fb
[INFO] running `Command { std: "docker" "start" "-a" "30bdb0699667d93fe60cc1200a4e9bca68a5170039ced145e7d94ecc733a98fb", kill_on_drop: false }`
[INFO] [stderr]    Compiling syn v1.0.50
[INFO] [stderr]    Compiling regex-syntax v0.6.21
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]    Compiling serde v1.0.117
[INFO] [stderr]    Compiling serde_derive v1.0.117
[INFO] [stderr]     Checking smallvec v1.5.0
[INFO] [stderr]    Compiling unicode-segmentation v1.7.0
[INFO] [stderr]    Compiling ndarray v0.13.1
[INFO] [stderr]    Compiling hdf5 v0.7.0
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]    Compiling libloading v0.6.5
[INFO] [stderr]     Checking tinyvec v1.1.0
[INFO] [stderr]    Compiling num-complex v0.2.4
[INFO] [stderr]    Compiling miniz_oxide v0.4.3
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]     Checking matrixmultiply v0.2.3
[INFO] [stderr]     Checking form_urlencoded v1.0.0
[INFO] [stderr]     Checking memrange v0.1.3
[INFO] [stderr]    Compiling libc v0.2.80
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]     Checking atty v0.2.14
[INFO] [stderr]     Checking parking_lot_core v0.7.2
[INFO] [stderr]     Checking hdf5-types v0.7.0
[INFO] [stderr]     Checking rand v0.3.23
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]     Checking clap v2.33.3
[INFO] [stderr]    Compiling derefable v0.1.0
[INFO] [stderr]     Checking pbr v1.0.3
[INFO] [stderr]    Compiling heck v0.3.1
[INFO] [stderr]     Checking theban_interval_tree v0.7.1
[INFO] [stderr]     Checking parking_lot v0.10.2
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]    Compiling jobserver v0.1.21
[INFO] [stderr]     Checking unicode-normalization v0.1.16
[INFO] [stderr]    Compiling cc v1.0.65
[INFO] [stderr]     Checking flate2 v1.0.19
[INFO] [stderr]    Compiling openssl-src v111.12.0+1.1.1h
[INFO] [stderr]     Checking idna v0.2.0
[INFO] [stderr]    Compiling regex v1.4.2
[INFO] [stderr]    Compiling libz-sys v1.1.2
[INFO] [stderr]    Compiling openssl-sys v0.9.58
[INFO] [stderr]    Compiling lzma-sys v0.1.17
[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 hts-sys v1.11.1-fix1
[INFO] [stderr]     Checking url v2.2.0
[INFO] [stderr]     Checking env_logger v0.7.1
[INFO] [stderr]    Compiling hdf5-sys v0.7.0
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[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-925201cc97290a1a/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:     0x55ffc518b31c - std::backtrace_rs::backtrace::libunwind::trace::h51faa62df48810e4
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/../../backtrace/src/backtrace/libunwind.rs:90:5
[INFO] [stderr]      1:     0x55ffc518b31c - std::backtrace_rs::backtrace::trace_unsynchronized::h91de4d8e16d607e4
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5
[INFO] [stderr]      2:     0x55ffc518b31c - std::sys_common::backtrace::_print_fmt::h71b0935f97e4322c
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/sys_common/backtrace.rs:67:5
[INFO] [stderr]      3:     0x55ffc518b31c - <std::sys_common::backtrace::_print::DisplayBacktrace as core::fmt::Display>::fmt::h9a78218788c14e18
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/sys_common/backtrace.rs:46:22
[INFO] [stderr]      4:     0x55ffc51aa5dc - core::fmt::write::h3381b3176fe2b3d3
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/core/src/fmt/mod.rs:1150:17
[INFO] [stderr]      5:     0x55ffc5188495 - std::io::Write::write_fmt::h1d5220480c7a2437
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/io/mod.rs:1667:15
[INFO] [stderr]      6:     0x55ffc518cd80 - std::sys_common::backtrace::_print::h4b77abc4d907ed0e
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/sys_common/backtrace.rs:49:5
[INFO] [stderr]      7:     0x55ffc518cd80 - std::sys_common::backtrace::print::hb170c60b542377ad
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/sys_common/backtrace.rs:36:9
[INFO] [stderr]      8:     0x55ffc518cd80 - std::panicking::default_hook::{{closure}}::h12bbda9af8901ee3
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/panicking.rs:210:50
[INFO] [stderr]      9:     0x55ffc518c937 - std::panicking::default_hook::h8c6c66d3f3ba6768
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/panicking.rs:227:9
[INFO] [stderr]     10:     0x55ffc518d434 - std::panicking::rust_panic_with_hook::h36f2fa0bb09f4069
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/panicking.rs:624:17
[INFO] [stderr]     11:     0x55ffc4fb6812 - std::panicking::begin_panic::{{closure}}::h6915b40650444324
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/panicking.rs:544:9
[INFO] [stderr]     12:     0x55ffc4fb65b9 - std::sys_common::backtrace::__rust_end_short_backtrace::hf917a1b40b5e2920
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/sys_common/backtrace.rs:141:18
[INFO] [stderr]     13:     0x55ffc4fb6753 - std::panicking::begin_panic::h7dd1660fa514e4f7
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/panicking.rs:543:12
[INFO] [stderr]     14:     0x55ffc4f86c17 - build_script_build::LibrarySearcher::try_locate_hdf5_library::hc17d93b6a0b7d08c
[INFO] [stderr]                                  at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.0/build.rs:549:13
[INFO] [stderr]     15:     0x55ffc4f884d7 - build_script_build::main::h393cf9fe9fb23a8c
[INFO] [stderr]                                  at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.0/build.rs:647:9
[INFO] [stderr]     16:     0x55ffc4f8c24b - core::ops::function::FnOnce::call_once::h55d85224e497e97f
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/core/src/ops/function.rs:227:5
[INFO] [stderr]     17:     0x55ffc4f92a6e - std::sys_common::backtrace::__rust_begin_short_backtrace::h0dfd37c186e06463
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/sys_common/backtrace.rs:125:18
[INFO] [stderr]     18:     0x55ffc4f92b01 - std::rt::lang_start::{{closure}}::h4405198dbce77787
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/rt.rs:63:18
[INFO] [stderr]     19:     0x55ffc518d93a - core::ops::function::impls::<impl core::ops::function::FnOnce<A> for &F>::call_once::hc590b210ed55e22f
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/core/src/ops/function.rs:259:13
[INFO] [stderr]     20:     0x55ffc518d93a - std::panicking::try::do_call::h5f0600b7a33ea1af
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/panicking.rs:403:40
[INFO] [stderr]     21:     0x55ffc518d93a - std::panicking::try::he15826df0f376a33
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/panicking.rs:367:19
[INFO] [stderr]     22:     0x55ffc518d93a - std::panic::catch_unwind::hd8af3a578b6b4c86
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/panic.rs:129:14
[INFO] [stderr]     23:     0x55ffc518d93a - std::rt::lang_start_internal::{{closure}}::h301d1329324ae1f0
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/rt.rs:45:48
[INFO] [stderr]     24:     0x55ffc518d93a - std::panicking::try::do_call::h941e8fdb0bd03655
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/panicking.rs:403:40
[INFO] [stderr]     25:     0x55ffc518d93a - std::panicking::try::ha20a77bf65530f63
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/panicking.rs:367:19
[INFO] [stderr]     26:     0x55ffc518d93a - std::panic::catch_unwind::h33afc061cc69ef90
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/panic.rs:129:14
[INFO] [stderr]     27:     0x55ffc518d93a - std::rt::lang_start_internal::hc05c244593147106
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/rt.rs:45:20
[INFO] [stderr]     28:     0x55ffc4f92ad0 - std::rt::lang_start::ha1e698804719f02f
[INFO] [stderr]                                  at /rustc/58268ff091703ace98c3c2a8c5f2fb2c3aecace2/library/std/src/rt.rs:62:5
[INFO] [stderr]     29:     0x55ffc4f899ec - main
[INFO] [stderr]     30:     0x7fae81e570b3 - __libc_start_main
[INFO] [stderr]     31:     0x55ffc4f81ede - _start
[INFO] [stderr]     32:                0x0 - <unknown>
[INFO] [stderr] warning: build failed, waiting for other jobs to finish...
[INFO] [stderr] error: build failed
[INFO] running `Command { std: "docker" "inspect" "30bdb0699667d93fe60cc1200a4e9bca68a5170039ced145e7d94ecc733a98fb", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "30bdb0699667d93fe60cc1200a4e9bca68a5170039ced145e7d94ecc733a98fb", kill_on_drop: false }`
[INFO] [stdout] 30bdb0699667d93fe60cc1200a4e9bca68a5170039ced145e7d94ecc733a98fb
