[INFO] fetching crate genomic_interval_pipeline 0.1.3... [INFO] testing genomic_interval_pipeline-0.1.3 against beta-2021-01-01 for beta-1.50-1 [INFO] extracting crate genomic_interval_pipeline 0.1.3 into /workspace/builds/worker-5/source [INFO] validating manifest of crates.io crate genomic_interval_pipeline 0.1.3 on toolchain beta-2021-01-01 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+beta-2021-01-01" "read-manifest" "--manifest-path" "Cargo.toml", 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-5/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-2021-01-01" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded linear-map v1.2.0 [INFO] [stderr] Downloaded derefable v0.1.0 [INFO] [stderr] Downloaded ieee754 v0.2.6 [INFO] [stderr] Downloaded libloading v0.6.5 [INFO] [stderr] Downloaded hdf5-sys v0.7.0 [INFO] [stderr] Downloaded ascii v1.0.0 [INFO] [stderr] Downloaded rust-htslib v0.35.2 [INFO] [stderr] Downloaded hts-sys v1.11.1-fix1 [INFO] [stderr] Downloaded lzma-sys v0.1.17 [INFO] [stderr] Downloaded hdf5 v0.7.0 [INFO] [stderr] Downloaded memrange v0.1.3 [INFO] [stderr] Downloaded curl-sys v0.4.38+curl-7.73.0 [INFO] [stderr] Downloaded theban_interval_tree v0.7.1 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded hdf5-derive v0.7.0 [INFO] [stderr] Downloaded hdf5-types v0.7.0 [INFO] [stderr] Downloaded openssl-src v111.12.0+1.1.1h [INFO] [stderr] Downloaded syn v1.0.50 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/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" "rustops/crates-build-env@sha256:c8ac004eab7d63a0ad09a2dde3d3353ba464f767bee4de425dc8f74c46a1905e" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2021-01-01" "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] 66f2ce0ba68541a2dbb0fbae9fa38de1a1a0f75c5217e615e11ff5fc69a045d9 [INFO] running `Command { std: "docker" "start" "-a" "66f2ce0ba68541a2dbb0fbae9fa38de1a1a0f75c5217e615e11ff5fc69a045d9", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "66f2ce0ba68541a2dbb0fbae9fa38de1a1a0f75c5217e615e11ff5fc69a045d9", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "66f2ce0ba68541a2dbb0fbae9fa38de1a1a0f75c5217e615e11ff5fc69a045d9", kill_on_drop: false }` [INFO] [stdout] 66f2ce0ba68541a2dbb0fbae9fa38de1a1a0f75c5217e615e11ff5fc69a045d9 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5/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" "rustops/crates-build-env@sha256:c8ac004eab7d63a0ad09a2dde3d3353ba464f767bee4de425dc8f74c46a1905e" "/opt/rustwide/cargo-home/bin/cargo" "+beta-2021-01-01" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 376fcba2fa34528dd5c0e1ffba1960cbad479b2b6c3662cc1ce8ac256d298312 [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" "376fcba2fa34528dd5c0e1ffba1960cbad479b2b6c3662cc1ce8ac256d298312", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.80 [INFO] [stderr] Compiling autocfg v1.0.1 [INFO] [stderr] Compiling pkg-config v0.3.19 [INFO] [stderr] Compiling proc-macro2 v1.0.24 [INFO] [stderr] Compiling unicode-xid v0.2.1 [INFO] [stderr] Compiling lazy_static v1.4.0 [INFO] [stderr] Compiling syn v1.0.50 [INFO] [stderr] Compiling memchr v2.3.4 [INFO] [stderr] Compiling regex-syntax v0.6.21 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling cfg-if v0.1.10 [INFO] [stderr] Compiling version_check v0.9.2 [INFO] [stderr] Compiling cfg-if v1.0.0 [INFO] [stderr] Compiling proc-macro2 v0.4.30 [INFO] [stderr] Compiling unicode-xid v0.1.0 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling matches v0.1.8 [INFO] [stderr] Compiling tinyvec_macros v0.1.0 [INFO] [stderr] Compiling bitflags v1.2.1 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Compiling serde v1.0.117 [INFO] [stderr] Compiling syn v0.15.44 [INFO] [stderr] Compiling serde_derive v1.0.117 [INFO] [stderr] Compiling maybe-uninit v2.0.0 [INFO] [stderr] Compiling log v0.4.11 [INFO] [stderr] Compiling smallvec v1.5.0 [INFO] [stderr] Compiling scopeguard v1.1.0 [INFO] [stderr] Compiling ndarray v0.13.1 [INFO] [stderr] Compiling rawpointer v0.2.1 [INFO] [stderr] Compiling percent-encoding v2.1.0 [INFO] [stderr] Compiling unicode-segmentation v1.7.0 [INFO] [stderr] Compiling crc32fast v1.2.1 [INFO] [stderr] Compiling unicode-width v0.1.8 [INFO] [stderr] Compiling ascii v1.0.0 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling hdf5 v0.7.0 [INFO] [stderr] Compiling rustc-serialize v0.3.24 [INFO] [stderr] Compiling strsim v0.8.0 [INFO] [stderr] Compiling adler v0.2.3 [INFO] [stderr] Compiling ansi_term v0.11.0 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling termcolor v1.1.2 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling libloading v0.6.5 [INFO] [stderr] Compiling thread_local v1.0.1 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling humantime v1.3.0 [INFO] [stderr] Compiling unicode-bidi v0.3.4 [INFO] [stderr] Compiling tinyvec v1.1.0 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling num-traits v0.2.14 [INFO] [stderr] Compiling crossbeam-utils v0.7.2 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling miniz_oxide v0.4.3 [INFO] [stderr] Compiling lock_api v0.3.4 [INFO] [stderr] Compiling matrixmultiply v0.2.3 [INFO] [stderr] Compiling textwrap v0.11.0 [INFO] [stderr] Compiling form_urlencoded v1.0.0 [INFO] [stderr] Compiling heck v0.3.1 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling unicode-normalization v0.1.16 [INFO] [stderr] Compiling aho-corasick v0.7.15 [INFO] [stderr] Compiling jobserver v0.1.21 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling rand v0.4.6 [INFO] [stderr] Compiling time v0.1.44 [INFO] [stderr] Compiling parking_lot_core v0.7.2 [INFO] [stderr] Compiling hdf5-types v0.7.0 [INFO] [stderr] Compiling quote v1.0.7 [INFO] [stderr] Compiling clap v2.33.3 [INFO] [stderr] Compiling quote v0.6.13 [INFO] [stderr] Compiling cc v1.0.65 [INFO] [stderr] Compiling memrange v0.1.3 [INFO] [stderr] Compiling parking_lot v0.10.2 [INFO] [stderr] Compiling flate2 v1.0.19 [INFO] [stderr] Compiling rand v0.3.23 [INFO] [stderr] Compiling idna v0.2.0 [INFO] [stderr] Compiling regex v1.4.2 [INFO] [stderr] Compiling theban_interval_tree v0.7.1 [INFO] [stderr] Compiling crossbeam-channel v0.4.4 [INFO] [stderr] Compiling openssl-src v111.12.0+1.1.1h [INFO] [stderr] Compiling url v2.2.0 [INFO] [stderr] Compiling pbr v1.0.3 [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 derefable v0.1.0 [INFO] [stderr] Compiling hdf5-sys v0.7.0 [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-815c782e2c1fde7f/build-script-build` (exit code: 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: 0x56327c9ebd87 - std::backtrace_rs::backtrace::libunwind::trace::hcd6e187547b8deec [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/../../backtrace/src/backtrace/libunwind.rs:90:5 [INFO] [stderr] 1: 0x56327c9ebd87 - std::backtrace_rs::backtrace::trace_unsynchronized::hde10036eb783fbc7 [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5 [INFO] [stderr] 2: 0x56327c9ebd87 - std::sys_common::backtrace::_print_fmt::h63987b8f86dfc82a [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/sys_common/backtrace.rs:67:5 [INFO] [stderr] 3: 0x56327c9ebd87 - ::fmt::hc33f3ac4cc9c4196 [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/sys_common/backtrace.rs:46:22 [INFO] [stderr] 4: 0x56327ca07bec - core::fmt::write::hfdcdeb08fb2b3afa [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/core/src/fmt/mod.rs:1078:17 [INFO] [stderr] 5: 0x56327c9e8912 - std::io::Write::write_fmt::h83a843778fa2a815 [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/io/mod.rs:1519:15 [INFO] [stderr] 6: 0x56327c9ede25 - std::sys_common::backtrace::_print::hf179508b01f66878 [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/sys_common/backtrace.rs:49:5 [INFO] [stderr] 7: 0x56327c9ede25 - std::sys_common::backtrace::print::ha97d11adb39266a6 [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/sys_common/backtrace.rs:36:9 [INFO] [stderr] 8: 0x56327c9ede25 - std::panicking::default_hook::{{closure}}::h8da9985a98bd1582 [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/panicking.rs:208:50 [INFO] [stderr] 9: 0x56327c9ed97a - std::panicking::default_hook::hbc0ee792993c2ef2 [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/panicking.rs:225:9 [INFO] [stderr] 10: 0x56327c9ee5c1 - std::panicking::rust_panic_with_hook::h9fb9cda33a10f084 [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/panicking.rs:591:17 [INFO] [stderr] 11: 0x56327c943a9e - std::panicking::begin_panic::{{closure}}::hbe22389b3adb3b8c [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/panicking.rs:520:9 [INFO] [stderr] 12: 0x56327c9172b9 - std::sys_common::backtrace::__rust_end_short_backtrace::h7c93498253efc327 [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/sys_common/backtrace.rs:141:18 [INFO] [stderr] 13: 0x56327c9439cb - std::panicking::begin_panic::ha4cd5f3756cde95e [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/panicking.rs:519:12 [INFO] [stderr] 14: 0x56327c7c615b - build_script_build::LibrarySearcher::try_locate_hdf5_library::h6282229af8cb53e2 [INFO] [stderr] at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.0/build.rs:549:13 [INFO] [stderr] 15: 0x56327c7c7a33 - build_script_build::main::h9429bcfc5700a1ae [INFO] [stderr] at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.0/build.rs:647:9 [INFO] [stderr] 16: 0x56327c7d3c4b - core::ops::function::FnOnce::call_once::h6524f3c07fa6a372 [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/core/src/ops/function.rs:227:5 [INFO] [stderr] 17: 0x56327c7cadfe - std::sys_common::backtrace::__rust_begin_short_backtrace::hce07c54ae8d726cb [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/sys_common/backtrace.rs:125:18 [INFO] [stderr] 18: 0x56327c7d2f71 - std::rt::lang_start::{{closure}}::h9ec4e620ed0c69a7 [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/rt.rs:66:18 [INFO] [stderr] 19: 0x56327c9ee9e7 - core::ops::function::impls:: for &F>::call_once::hb5ab992a536e3d7c [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/core/src/ops/function.rs:259:13 [INFO] [stderr] 20: 0x56327c9ee9e7 - std::panicking::try::do_call::h1bda883686bc1816 [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/panicking.rs:379:40 [INFO] [stderr] 21: 0x56327c9ee9e7 - std::panicking::try::ha7167c079f243e71 [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/panicking.rs:343:19 [INFO] [stderr] 22: 0x56327c9ee9e7 - std::panic::catch_unwind::he11c3de53f0b5853 [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/panic.rs:396:14 [INFO] [stderr] 23: 0x56327c9ee9e7 - std::rt::lang_start_internal::h45c3666b51d25060 [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/rt.rs:51:25 [INFO] [stderr] 24: 0x56327c7d2f47 - std::rt::lang_start::hcb5141fd8f662615 [INFO] [stderr] at /rustc/25b3db3aa752d9d4633c983c9d4bf5e48f9baff1/library/std/src/rt.rs:65:5 [INFO] [stderr] 25: 0x56327c7c907a - main [INFO] [stderr] 26: 0x7f44e3e040b3 - __libc_start_main [INFO] [stderr] 27: 0x56327c7c10be - _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" "376fcba2fa34528dd5c0e1ffba1960cbad479b2b6c3662cc1ce8ac256d298312", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "376fcba2fa34528dd5c0e1ffba1960cbad479b2b6c3662cc1ce8ac256d298312", kill_on_drop: false }` [INFO] [stdout] 376fcba2fa34528dd5c0e1ffba1960cbad479b2b6c3662cc1ce8ac256d298312