[INFO] fetching crate genomic_interval_pipeline 0.1.3... [INFO] checking genomic_interval_pipeline-0.1.3 against master#a836d9b6413d9d593be6c09463ff8c4c70e56599 for pr-84037 [INFO] extracting crate genomic_interval_pipeline 0.1.3 into /workspace/builds/worker-4/source [INFO] validating manifest of crates.io crate genomic_interval_pipeline 0.1.3 on toolchain a836d9b6413d9d593be6c09463ff8c4c70e56599 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+a836d9b6413d9d593be6c09463ff8c4c70e56599" "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-4/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" "+a836d9b6413d9d593be6c09463ff8c4c70e56599" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4/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" "+a836d9b6413d9d593be6c09463ff8c4c70e56599" "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] de241da02e93aa94ccbc916ce4531d3723c663dd4960983f062a11a294e5bc48 [INFO] running `Command { std: "docker" "start" "-a" "de241da02e93aa94ccbc916ce4531d3723c663dd4960983f062a11a294e5bc48", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "de241da02e93aa94ccbc916ce4531d3723c663dd4960983f062a11a294e5bc48", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "de241da02e93aa94ccbc916ce4531d3723c663dd4960983f062a11a294e5bc48", kill_on_drop: false }` [INFO] [stdout] de241da02e93aa94ccbc916ce4531d3723c663dd4960983f062a11a294e5bc48 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4/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" "+a836d9b6413d9d593be6c09463ff8c4c70e56599" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] dbe7b1d4aa0a2d9f4f7b48a5889163ec3dc47f76f3b6bffd8a8d6d315beb2101 [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" "dbe7b1d4aa0a2d9f4f7b48a5889163ec3dc47f76f3b6bffd8a8d6d315beb2101", kill_on_drop: false }` [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 syn v1.0.50 [INFO] [stderr] Checking lazy_static v1.4.0 [INFO] [stderr] Compiling version_check v0.9.2 [INFO] [stderr] Compiling bitflags v1.2.1 [INFO] [stderr] Checking tinyvec_macros v0.1.0 [INFO] [stderr] Checking matches v0.1.8 [INFO] [stderr] Compiling serde_derive v1.0.117 [INFO] [stderr] Compiling log v0.4.11 [INFO] [stderr] Checking unicode-width v0.1.8 [INFO] [stderr] Checking scopeguard v1.1.0 [INFO] [stderr] Compiling ndarray v0.13.1 [INFO] [stderr] Checking percent-encoding v2.1.0 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Compiling hdf5 v0.7.0 [INFO] [stderr] Checking strsim v0.8.0 [INFO] [stderr] Checking cfg-if v1.0.0 [INFO] [stderr] Checking rustc-serialize v0.3.24 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking ansi_term v0.11.0 [INFO] [stderr] Checking ascii v1.0.0 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Compiling thread_local v1.0.1 [INFO] [stderr] Compiling libloading v0.6.5 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Checking unicode-bidi v0.3.4 [INFO] [stderr] Checking tinyvec v1.1.0 [INFO] [stderr] Checking lock_api v0.3.4 [INFO] [stderr] Checking textwrap v0.11.0 [INFO] [stderr] Checking matrixmultiply v0.2.3 [INFO] [stderr] Checking form_urlencoded v1.0.0 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking crc32fast v1.2.1 [INFO] [stderr] Checking parking_lot_core v0.7.2 [INFO] [stderr] Checking time v0.1.44 [INFO] [stderr] Checking hdf5-types v0.7.0 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling cc v1.0.65 [INFO] [stderr] Checking rand v0.3.23 [INFO] [stderr] Compiling regex v1.4.2 [INFO] [stderr] Compiling num-traits v0.2.14 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Compiling crossbeam-utils v0.7.2 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling miniz_oxide v0.4.3 [INFO] [stderr] Checking clap v2.33.3 [INFO] [stderr] Compiling derefable v0.1.0 [INFO] [stderr] Checking parking_lot v0.10.2 [INFO] [stderr] Compiling quote v1.0.7 [INFO] [stderr] Compiling openssl-src v111.12.0+1.1.1h [INFO] [stderr] Checking unicode-normalization v0.1.16 [INFO] [stderr] Checking crossbeam-channel v0.4.4 [INFO] [stderr] Checking flate2 v1.0.19 [INFO] [stderr] Checking env_logger v0.7.1 [INFO] [stderr] Checking memrange v0.1.3 [INFO] [stderr] Checking theban_interval_tree v0.7.1 [INFO] [stderr] Compiling libz-sys v1.1.2 [INFO] [stderr] Compiling openssl-sys v0.9.58 [INFO] [stderr] Compiling bzip2-sys v0.1.9+1.0.8 [INFO] [stderr] Compiling curl-sys v0.4.38+curl-7.73.0 [INFO] [stderr] Compiling lzma-sys v0.1.17 [INFO] [stderr] Compiling hts-sys v1.11.1-fix1 [INFO] [stderr] Checking pbr v1.0.3 [INFO] [stderr] Checking idna v0.2.0 [INFO] [stderr] Checking url v2.2.0 [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-1198107aee20fd2e/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: 0x559bd07fc2a0 - std::backtrace_rs::backtrace::libunwind::trace::h247d9dc800afe0ad [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/../../backtrace/src/backtrace/libunwind.rs:90:5 [INFO] [stderr] 1: 0x559bd07fc2a0 - std::backtrace_rs::backtrace::trace_unsynchronized::h9a4153306adf486c [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5 [INFO] [stderr] 2: 0x559bd07fc2a0 - std::sys_common::backtrace::_print_fmt::h1ac8daa5000ee24c [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/sys_common/backtrace.rs:67:5 [INFO] [stderr] 3: 0x559bd07fc2a0 - ::fmt::h22a8e55d2cc5363a [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/sys_common/backtrace.rs:46:22 [INFO] [stderr] 4: 0x559bd081acef - core::fmt::write::h7aa6cd0067dca82a [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/core/src/fmt/mod.rs:1094:17 [INFO] [stderr] 5: 0x559bd07f95d5 - std::io::Write::write_fmt::h441a47830651073b [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/io/mod.rs:1580:15 [INFO] [stderr] 6: 0x559bd07fe21b - std::sys_common::backtrace::_print::hd1e0ee1c195f9f05 [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/sys_common/backtrace.rs:49:5 [INFO] [stderr] 7: 0x559bd07fe21b - std::sys_common::backtrace::print::h7d1098def5c25d20 [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/sys_common/backtrace.rs:36:9 [INFO] [stderr] 8: 0x559bd07fe21b - std::panicking::default_hook::{{closure}}::h484b8b15967e42c8 [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/panicking.rs:208:50 [INFO] [stderr] 9: 0x559bd07fdcfd - std::panicking::default_hook::h82c79ca49716b79d [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/panicking.rs:225:9 [INFO] [stderr] 10: 0x559bd07fe7cd - std::panicking::rust_panic_with_hook::h6df253a3c973d6b6 [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/panicking.rs:591:17 [INFO] [stderr] 11: 0x559bd061cff3 - std::panicking::begin_panic::{{closure}}::h51a2e86939e85bae [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/panicking.rs:520:9 [INFO] [stderr] 12: 0x559bd06263b9 - std::sys_common::backtrace::__rust_end_short_backtrace::hf455566f946d7954 [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/sys_common/backtrace.rs:141:18 [INFO] [stderr] 13: 0x559bd061cf29 - std::panicking::begin_panic::h0bfed93b6ef3c066 [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/panicking.rs:519:12 [INFO] [stderr] 14: 0x559bd05f7c89 - build_script_build::LibrarySearcher::try_locate_hdf5_library::h213af3d767f83938 [INFO] [stderr] at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.0/build.rs:549:13 [INFO] [stderr] 15: 0x559bd05f949c - build_script_build::main::h9dcafbf945a5d15c [INFO] [stderr] at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.0/build.rs:647:9 [INFO] [stderr] 16: 0x559bd05fe7fb - core::ops::function::FnOnce::call_once::h2edf82da07b58417 [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/core/src/ops/function.rs:227:5 [INFO] [stderr] 17: 0x559bd0604d9e - std::sys_common::backtrace::__rust_begin_short_backtrace::hf53fe99585903ff1 [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/sys_common/backtrace.rs:125:18 [INFO] [stderr] 18: 0x559bd0602e11 - std::rt::lang_start::{{closure}}::hcdbe6e15e2757ca5 [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/rt.rs:66:18 [INFO] [stderr] 19: 0x559bd07febca - core::ops::function::impls:: for &F>::call_once::h98fbc5823393ca6f [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/core/src/ops/function.rs:259:13 [INFO] [stderr] 20: 0x559bd07febca - std::panicking::try::do_call::h210d0709dd1d5fd6 [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/panicking.rs:379:40 [INFO] [stderr] 21: 0x559bd07febca - std::panicking::try::hc60c2c01c5cf7473 [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/panicking.rs:343:19 [INFO] [stderr] 22: 0x559bd07febca - std::panic::catch_unwind::h7480a56877b30ca9 [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/panic.rs:431:14 [INFO] [stderr] 23: 0x559bd07febca - std::rt::lang_start_internal::he77194431b0ee4a2 [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/rt.rs:51:25 [INFO] [stderr] 24: 0x559bd0602df0 - std::rt::lang_start::hd67fd2a9aefb9c3f [INFO] [stderr] at /rustc/a836d9b6413d9d593be6c09463ff8c4c70e56599/library/std/src/rt.rs:65:5 [INFO] [stderr] 25: 0x559bd05fa99c - main [INFO] [stderr] 26: 0x7fa8e085e0b3 - __libc_start_main [INFO] [stderr] 27: 0x559bd05f2c8e - _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" "dbe7b1d4aa0a2d9f4f7b48a5889163ec3dc47f76f3b6bffd8a8d6d315beb2101", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "dbe7b1d4aa0a2d9f4f7b48a5889163ec3dc47f76f3b6bffd8a8d6d315beb2101", kill_on_drop: false }` [INFO] [stdout] dbe7b1d4aa0a2d9f4f7b48a5889163ec3dc47f76f3b6bffd8a8d6d315beb2101