[INFO] fetching crate genomic_interval_pipeline 0.1.3... [INFO] checking genomic_interval_pipeline-0.1.3 against master#5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f for pr-87248 [INFO] extracting crate genomic_interval_pipeline 0.1.3 into /workspace/builds/worker-0/source [INFO] validating manifest of crates.io crate genomic_interval_pipeline 0.1.3 on toolchain 5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f" "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-0/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" "+5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f" "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-0/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/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@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 66a4ff0904d5d1e7e058ee2f10ce41dd5792495e9bd3cdfa08b4a1ba59c17404 [INFO] running `Command { std: "docker" "start" "-a" "66a4ff0904d5d1e7e058ee2f10ce41dd5792495e9bd3cdfa08b4a1ba59c17404", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "66a4ff0904d5d1e7e058ee2f10ce41dd5792495e9bd3cdfa08b4a1ba59c17404", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "66a4ff0904d5d1e7e058ee2f10ce41dd5792495e9bd3cdfa08b4a1ba59c17404", kill_on_drop: false }` [INFO] [stdout] 66a4ff0904d5d1e7e058ee2f10ce41dd5792495e9bd3cdfa08b4a1ba59c17404 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0/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@sha256:34b6a614d2c27851fe6cbf88fbd1137609cefab8b10d0615aaeb6fd47975d74e" "/opt/rustwide/cargo-home/bin/cargo" "+5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] e2afb148d17af7049797c65415d07f14df314bb30c4cb979950e9ad7d78bd360 [INFO] running `Command { std: "docker" "start" "-a" "e2afb148d17af7049797c65415d07f14df314bb30c4cb979950e9ad7d78bd360", 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 memchr v2.3.4 [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] Checking cfg-if v0.1.10 [INFO] [stderr] Compiling cfg-if v1.0.0 [INFO] [stderr] Compiling regex-syntax v0.6.21 [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] Checking tinyvec_macros v0.1.0 [INFO] [stderr] Checking matches v0.1.8 [INFO] [stderr] Compiling serde_derive v1.0.117 [INFO] [stderr] Compiling syn v0.15.44 [INFO] [stderr] Compiling serde v1.0.117 [INFO] [stderr] Checking quick-error v1.2.3 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Compiling maybe-uninit v2.0.0 [INFO] [stderr] Compiling ndarray v0.13.1 [INFO] [stderr] Checking unicode-width v0.1.8 [INFO] [stderr] Compiling log v0.4.11 [INFO] [stderr] Compiling crc32fast v1.2.1 [INFO] [stderr] Compiling unicode-segmentation v1.7.0 [INFO] [stderr] Checking scopeguard v1.1.0 [INFO] [stderr] Checking smallvec v1.5.0 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Checking rustc-serialize v0.3.24 [INFO] [stderr] Checking ascii v1.0.0 [INFO] [stderr] Compiling hdf5 v0.7.0 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking termcolor v1.1.2 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Checking ieee754 v0.2.6 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling libloading v0.6.5 [INFO] [stderr] Checking tinyvec v1.1.0 [INFO] [stderr] Compiling thread_local v1.0.1 [INFO] [stderr] Checking textwrap v0.11.0 [INFO] [stderr] Checking matrixmultiply v0.2.3 [INFO] [stderr] Checking unicode-bidi v0.3.4 [INFO] [stderr] Checking form_urlencoded v1.0.0 [INFO] [stderr] Checking humantime v1.3.0 [INFO] [stderr] Checking lock_api v0.3.4 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling jobserver v0.1.21 [INFO] [stderr] Checking parking_lot_core v0.7.2 [INFO] [stderr] Checking rand v0.4.6 [INFO] [stderr] Checking hdf5-types v0.7.0 [INFO] [stderr] Checking clap v2.33.3 [INFO] [stderr] Checking unicode-normalization v0.1.16 [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 num-integer v0.1.44 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling crossbeam-utils v0.7.2 [INFO] [stderr] Compiling miniz_oxide v0.4.3 [INFO] [stderr] Compiling cc v1.0.65 [INFO] [stderr] Compiling heck v0.3.1 [INFO] [stderr] Checking parking_lot v0.10.2 [INFO] [stderr] Checking rand v0.3.23 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling aho-corasick v0.7.15 [INFO] [stderr] Compiling quote v1.0.7 [INFO] [stderr] Compiling openssl-src v111.12.0+1.1.1h [INFO] [stderr] Compiling quote v0.6.13 [INFO] [stderr] Checking crossbeam-channel v0.4.4 [INFO] [stderr] Compiling openssl-sys v0.9.58 [INFO] [stderr] Compiling libz-sys v1.1.2 [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 flate2 v1.0.19 [INFO] [stderr] Checking idna v0.2.0 [INFO] [stderr] Checking regex v1.4.2 [INFO] [stderr] Checking pbr v1.0.3 [INFO] [stderr] Checking url v2.2.0 [INFO] [stderr] Checking memrange v0.1.3 [INFO] [stderr] Checking theban_interval_tree v0.7.1 [INFO] [stderr] Checking env_logger v0.7.1 [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-3a856165a084bfe8/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: 0x55ef94f9f9b0 - std::backtrace_rs::backtrace::libunwind::trace::h0f5cd2ee8b0d7274 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/../../backtrace/src/backtrace/libunwind.rs:90:5 [INFO] [stderr] 1: 0x55ef94f9f9b0 - std::backtrace_rs::backtrace::trace_unsynchronized::h06905b5aeda069a1 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5 [INFO] [stderr] 2: 0x55ef94f9f9b0 - std::sys_common::backtrace::_print_fmt::h4fe4c7c875072f30 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/sys_common/backtrace.rs:67:5 [INFO] [stderr] 3: 0x55ef94f9f9b0 - ::fmt::hcc0746f004a9b7ef [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/sys_common/backtrace.rs:46:22 [INFO] [stderr] 4: 0x55ef94fbdf1c - core::fmt::write::h9a6d9c74526a6c1b [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/core/src/fmt/mod.rs:1115:17 [INFO] [stderr] 5: 0x55ef94f9cdc5 - std::io::Write::write_fmt::h23dab4cc9ce72ee2 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/io/mod.rs:1665:15 [INFO] [stderr] 6: 0x55ef94fa1a2b - std::sys_common::backtrace::_print::h173dc702502d65d2 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/sys_common/backtrace.rs:49:5 [INFO] [stderr] 7: 0x55ef94fa1a2b - std::sys_common::backtrace::print::h61bd27c4742ba817 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/sys_common/backtrace.rs:36:9 [INFO] [stderr] 8: 0x55ef94fa1a2b - std::panicking::default_hook::{{closure}}::hcaae87f0495ae613 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/panicking.rs:208:50 [INFO] [stderr] 9: 0x55ef94fa1501 - std::panicking::default_hook::h0538e728ee080db0 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/panicking.rs:225:9 [INFO] [stderr] 10: 0x55ef94fa20f4 - std::panicking::rust_panic_with_hook::h3039e236b6ca482c [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/panicking.rs:622:17 [INFO] [stderr] 11: 0x55ef94dce6c3 - std::panicking::begin_panic::{{closure}}::hdf9983629aba2c6d [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/panicking.rs:542:9 [INFO] [stderr] 12: 0x55ef94dce319 - std::sys_common::backtrace::__rust_end_short_backtrace::hd0c0fb69c8479bc7 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/sys_common/backtrace.rs:141:18 [INFO] [stderr] 13: 0x55ef94dce5f9 - std::panicking::begin_panic::hcdc9c5aff13791e2 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/panicking.rs:541:12 [INFO] [stderr] 14: 0x55ef94d9edb7 - build_script_build::LibrarySearcher::try_locate_hdf5_library::h01eef2fa5fffdee3 [INFO] [stderr] at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.0/build.rs:549:13 [INFO] [stderr] 15: 0x55ef94da05db - build_script_build::main::h66f7b633d3ff0d4e [INFO] [stderr] at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.0/build.rs:647:9 [INFO] [stderr] 16: 0x55ef94da434b - core::ops::function::FnOnce::call_once::h0fea7572554ead72 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/core/src/ops/function.rs:227:5 [INFO] [stderr] 17: 0x55ef94daaa5e - std::sys_common::backtrace::__rust_begin_short_backtrace::h9c487c5e3b281228 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/sys_common/backtrace.rs:125:18 [INFO] [stderr] 18: 0x55ef94da8f51 - std::rt::lang_start::{{closure}}::hfb468abe1addcd90 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/rt.rs:63:18 [INFO] [stderr] 19: 0x55ef94fa25fa - core::ops::function::impls:: for &F>::call_once::h61bcc1dec5918b7e [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/core/src/ops/function.rs:259:13 [INFO] [stderr] 20: 0x55ef94fa25fa - std::panicking::try::do_call::h672d24f85ce22db4 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/panicking.rs:401:40 [INFO] [stderr] 21: 0x55ef94fa25fa - std::panicking::try::he383e7ef11604e58 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/panicking.rs:365:19 [INFO] [stderr] 22: 0x55ef94fa25fa - std::panic::catch_unwind::h502ac6058961e393 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/panic.rs:434:14 [INFO] [stderr] 23: 0x55ef94fa25fa - std::rt::lang_start_internal::{{closure}}::h851ee37bb5d99fdf [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/rt.rs:45:48 [INFO] [stderr] 24: 0x55ef94fa25fa - std::panicking::try::do_call::h84f41bb3453bbd14 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/panicking.rs:401:40 [INFO] [stderr] 25: 0x55ef94fa25fa - std::panicking::try::h969c45dbbf2e4c94 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/panicking.rs:365:19 [INFO] [stderr] 26: 0x55ef94fa25fa - std::panic::catch_unwind::he40b1a4614f73e03 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/panic.rs:434:14 [INFO] [stderr] 27: 0x55ef94fa25fa - std::rt::lang_start_internal::h0fbab25cccdb30d8 [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/rt.rs:45:20 [INFO] [stderr] 28: 0x55ef94da8f20 - std::rt::lang_start::h980a34e54b36185a [INFO] [stderr] at /rustc/5a8a44196b3cf099f8c9b0156bd902eaec0b4e5f/library/std/src/rt.rs:62:5 [INFO] [stderr] 29: 0x55ef94da1acc - main [INFO] [stderr] 30: 0x7f88650980b3 - __libc_start_main [INFO] [stderr] 31: 0x55ef94d99f2e - _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" "e2afb148d17af7049797c65415d07f14df314bb30c4cb979950e9ad7d78bd360", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "e2afb148d17af7049797c65415d07f14df314bb30c4cb979950e9ad7d78bd360", kill_on_drop: false }` [INFO] [stdout] e2afb148d17af7049797c65415d07f14df314bb30c4cb979950e9ad7d78bd360