[INFO] fetching crate genomic_interval_pipeline 0.1.3... [INFO] testing genomic_interval_pipeline-0.1.3 against master#a77da2d454e6caa227a85b16410b95f93495e7e0 for pr-91031 [INFO] extracting crate genomic_interval_pipeline 0.1.3 into /workspace/builds/worker-85/source [INFO] validating manifest of crates.io crate genomic_interval_pipeline 0.1.3 on toolchain a77da2d454e6caa227a85b16410b95f93495e7e0 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+a77da2d454e6caa227a85b16410b95f93495e7e0" "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-85/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" "+a77da2d454e6caa227a85b16410b95f93495e7e0" "fetch" "--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-85/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-85/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@sha256:5736fa189c1c60b01babf4b8b698fe57b6ecc41933a7ff2e0b8d7a221459412b" "/opt/rustwide/cargo-home/bin/cargo" "+a77da2d454e6caa227a85b16410b95f93495e7e0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 1f8567b2b95e693970aa0d8e893c6187fed111c12ef64b48396a4de75c6f5862 [INFO] running `Command { std: "docker" "start" "-a" "1f8567b2b95e693970aa0d8e893c6187fed111c12ef64b48396a4de75c6f5862", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "1f8567b2b95e693970aa0d8e893c6187fed111c12ef64b48396a4de75c6f5862", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "1f8567b2b95e693970aa0d8e893c6187fed111c12ef64b48396a4de75c6f5862", kill_on_drop: false }` [INFO] [stdout] 1f8567b2b95e693970aa0d8e893c6187fed111c12ef64b48396a4de75c6f5862 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-85/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-85/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@sha256:5736fa189c1c60b01babf4b8b698fe57b6ecc41933a7ff2e0b8d7a221459412b" "/opt/rustwide/cargo-home/bin/cargo" "+a77da2d454e6caa227a85b16410b95f93495e7e0" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 0a5294e927f24ca2f402103f531fb96467b19fd2cc7127c11054779c56340eb9 [INFO] running `Command { std: "docker" "start" "-a" "0a5294e927f24ca2f402103f531fb96467b19fd2cc7127c11054779c56340eb9", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Compiling libc v0.2.80 [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] Compiling memchr v2.3.4 [INFO] [stderr] Compiling regex-syntax v0.6.21 [INFO] [stderr] Compiling version_check v0.9.2 [INFO] [stderr] Compiling cfg-if v0.1.10 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Compiling serde_derive v1.0.117 [INFO] [stderr] Compiling maybe-uninit v2.0.0 [INFO] [stderr] Compiling serde v1.0.117 [INFO] [stderr] Compiling crc32fast v1.2.1 [INFO] [stderr] Compiling log v0.4.11 [INFO] [stderr] Compiling unicode-segmentation v1.7.0 [INFO] [stderr] Compiling rawpointer v0.2.1 [INFO] [stderr] Compiling ndarray v0.13.1 [INFO] [stderr] Compiling smallvec v1.5.0 [INFO] [stderr] Compiling rustc-serialize v0.3.24 [INFO] [stderr] Compiling hdf5 v0.7.0 [INFO] [stderr] Compiling adler v0.2.3 [INFO] [stderr] Compiling ascii v1.0.0 [INFO] [stderr] Compiling custom_derive v0.1.7 [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 tinyvec v1.1.0 [INFO] [stderr] Compiling fs-utils v1.1.4 [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] Compiling unicode-bidi v0.3.4 [INFO] [stderr] Compiling form_urlencoded v1.0.0 [INFO] [stderr] Compiling lock_api v0.3.4 [INFO] [stderr] Compiling derefable v0.1.0 [INFO] [stderr] Compiling matrixmultiply v0.2.3 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling heck v0.3.1 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [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 time v0.1.44 [INFO] [stderr] Compiling rand v0.4.6 [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 cc v1.0.65 [INFO] [stderr] Compiling parking_lot v0.10.2 [INFO] [stderr] Compiling crossbeam-channel v0.4.4 [INFO] [stderr] Compiling flate2 v1.0.19 [INFO] [stderr] Compiling rand v0.3.23 [INFO] [stderr] Compiling openssl-src v111.12.0+1.1.1h [INFO] [stderr] Compiling memrange v0.1.3 [INFO] [stderr] Compiling idna v0.2.0 [INFO] [stderr] Compiling theban_interval_tree v0.7.1 [INFO] [stderr] Compiling regex v1.4.2 [INFO] [stderr] Compiling pbr v1.0.3 [INFO] [stderr] Compiling url v2.2.0 [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 lzma-sys v0.1.17 [INFO] [stderr] Compiling curl-sys v0.4.38+curl-7.73.0 [INFO] [stderr] Compiling hts-sys v1.11.1-fix1 [INFO] [stderr] Compiling env_logger v0.7.1 [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-53301e2c5b6f05e9/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: 0x56141a8f6cbc - std::backtrace_rs::backtrace::libunwind::trace::h7630ba4cba718aa0 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/../../backtrace/src/backtrace/libunwind.rs:93:5 [INFO] [stderr] 1: 0x56141a8f6cbc - std::backtrace_rs::backtrace::trace_unsynchronized::he7498e79c157f5ac [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5 [INFO] [stderr] 2: 0x56141a8f6cbc - std::sys_common::backtrace::_print_fmt::hdaebadaee17bca49 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/sys_common/backtrace.rs:67:5 [INFO] [stderr] 3: 0x56141a8f6cbc - ::fmt::h82b0e3aaf8a96140 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/sys_common/backtrace.rs:46:22 [INFO] [stderr] 4: 0x56141a91598c - core::fmt::write::h72801a82c94e6ff1 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/core/src/fmt/mod.rs:1149:17 [INFO] [stderr] 5: 0x56141a8f3485 - std::io::Write::write_fmt::hc2da38dc44811df8 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/io/mod.rs:1697:15 [INFO] [stderr] 6: 0x56141a8f8630 - std::sys_common::backtrace::_print::h1c9a1d19c48821c1 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/sys_common/backtrace.rs:49:5 [INFO] [stderr] 7: 0x56141a8f8630 - std::sys_common::backtrace::print::h7ce8802039fa9d0e [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/sys_common/backtrace.rs:36:9 [INFO] [stderr] 8: 0x56141a8f8630 - std::panicking::default_hook::{{closure}}::hb2a74a8c1499c326 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/panicking.rs:211:50 [INFO] [stderr] 9: 0x56141a8f81db - std::panicking::default_hook::hf4f180b00076f2b2 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/panicking.rs:228:9 [INFO] [stderr] 10: 0x56141a8f8ce4 - std::panicking::rust_panic_with_hook::he85ce8435493b711 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/panicking.rs:606:17 [INFO] [stderr] 11: 0x56141a8317d2 - std::panicking::begin_panic::{{closure}}::hafc230cfe784b652 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/panicking.rs:526:9 [INFO] [stderr] 12: 0x56141a825449 - std::sys_common::backtrace::__rust_end_short_backtrace::hfb45804dfe0c0fae [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/sys_common/backtrace.rs:139:18 [INFO] [stderr] 13: 0x56141a831713 - std::panicking::begin_panic::h2c5d6d9bac9c6dc1 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/panicking.rs:525:12 [INFO] [stderr] 14: 0x56141a6f29f7 - build_script_build::LibrarySearcher::try_locate_hdf5_library::h6337d3c9461a7eed [INFO] [stderr] at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.0/build.rs:549:13 [INFO] [stderr] 15: 0x56141a6f4197 - build_script_build::main::h81c990578c106a0f [INFO] [stderr] at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.0/build.rs:647:9 [INFO] [stderr] 16: 0x56141a6f817b - core::ops::function::FnOnce::call_once::h59a543cc1174e7e9 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/core/src/ops/function.rs:227:5 [INFO] [stderr] 17: 0x56141a6fe45e - std::sys_common::backtrace::__rust_begin_short_backtrace::hecf89bd6314de8e1 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/sys_common/backtrace.rs:123:18 [INFO] [stderr] 18: 0x56141a6fb681 - std::rt::lang_start::{{closure}}::hf0767b1e31813cf7 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/rt.rs:145:18 [INFO] [stderr] 19: 0x56141a8f6501 - core::ops::function::impls:: for &F>::call_once::h0e73392810ecd318 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/core/src/ops/function.rs:259:13 [INFO] [stderr] 20: 0x56141a8f6501 - std::panicking::try::do_call::h12dcb4a4f352a507 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/panicking.rs:406:40 [INFO] [stderr] 21: 0x56141a8f6501 - std::panicking::try::h0d978c76ab4a3863 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/panicking.rs:370:19 [INFO] [stderr] 22: 0x56141a8f6501 - std::panic::catch_unwind::hab40227675186980 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/panic.rs:133:14 [INFO] [stderr] 23: 0x56141a8f6501 - std::rt::lang_start_internal::{{closure}}::hc34786299e7d2cf7 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/rt.rs:128:48 [INFO] [stderr] 24: 0x56141a8f6501 - std::panicking::try::do_call::h38e7a9128f21d387 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/panicking.rs:406:40 [INFO] [stderr] 25: 0x56141a8f6501 - std::panicking::try::h32d4e72fd8922bce [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/panicking.rs:370:19 [INFO] [stderr] 26: 0x56141a8f6501 - std::panic::catch_unwind::h9a345671d889d41f [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/panic.rs:133:14 [INFO] [stderr] 27: 0x56141a8f6501 - std::rt::lang_start_internal::h9e691a4f557eb2a3 [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/rt.rs:128:20 [INFO] [stderr] 28: 0x56141a6fb650 - std::rt::lang_start::h1a3492a64025ffec [INFO] [stderr] at /rustc/a77da2d454e6caa227a85b16410b95f93495e7e0/library/std/src/rt.rs:144:17 [INFO] [stderr] 29: 0x56141a6f563c - main [INFO] [stderr] 30: 0x7f7346cdf0b3 - __libc_start_main [INFO] [stderr] 31: 0x56141a6edd9e - _start [INFO] [stderr] 32: 0x0 - [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stderr] error: build failed [INFO] running `Command { std: "docker" "inspect" "0a5294e927f24ca2f402103f531fb96467b19fd2cc7127c11054779c56340eb9", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "0a5294e927f24ca2f402103f531fb96467b19fd2cc7127c11054779c56340eb9", kill_on_drop: false }` [INFO] [stdout] 0a5294e927f24ca2f402103f531fb96467b19fd2cc7127c11054779c56340eb9