[INFO] fetching crate genomic_interval_pipeline 0.1.3... [INFO] testing genomic_interval_pipeline-0.1.3 against master#b70888601af92f6cdc0364abab3446e418b91d36 for pr-86479 [INFO] extracting crate genomic_interval_pipeline 0.1.3 into /workspace/builds/worker-6/source [INFO] validating manifest of crates.io crate genomic_interval_pipeline 0.1.3 on toolchain b70888601af92f6cdc0364abab3446e418b91d36 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+b70888601af92f6cdc0364abab3446e418b91d36" "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-6/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" "+b70888601af92f6cdc0364abab3446e418b91d36" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/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" "+b70888601af92f6cdc0364abab3446e418b91d36" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 955610b861997677c78628d2dc8754a33dd98c49162b7205b40f2367409a8273 [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" "955610b861997677c78628d2dc8754a33dd98c49162b7205b40f2367409a8273", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "955610b861997677c78628d2dc8754a33dd98c49162b7205b40f2367409a8273", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "955610b861997677c78628d2dc8754a33dd98c49162b7205b40f2367409a8273", kill_on_drop: false }` [INFO] [stdout] 955610b861997677c78628d2dc8754a33dd98c49162b7205b40f2367409a8273 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6/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" "+b70888601af92f6cdc0364abab3446e418b91d36" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 37af54f6a87b997b87d51de38b273f9053a854384d33202824036d4d62543485 [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" "37af54f6a87b997b87d51de38b273f9053a854384d33202824036d4d62543485", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.80 [INFO] [stderr] Compiling autocfg v1.0.1 [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 quick-error v1.2.3 [INFO] [stderr] Compiling cfg-if v1.0.0 [INFO] [stderr] Compiling proc-macro2 v0.4.30 [INFO] [stderr] Compiling tinyvec_macros v0.1.0 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling unicode-xid v0.1.0 [INFO] [stderr] Compiling matches v0.1.8 [INFO] [stderr] Compiling syn v0.15.44 [INFO] [stderr] Compiling maybe-uninit v2.0.0 [INFO] [stderr] Compiling serde v1.0.117 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Compiling scopeguard v1.1.0 [INFO] [stderr] Compiling smallvec v1.5.0 [INFO] [stderr] Compiling percent-encoding v2.1.0 [INFO] [stderr] Compiling rawpointer v0.2.1 [INFO] [stderr] Compiling crc32fast v1.2.1 [INFO] [stderr] Compiling ndarray v0.13.1 [INFO] [stderr] Compiling adler v0.2.3 [INFO] [stderr] Compiling ascii v1.0.0 [INFO] [stderr] Compiling rustc-serialize v0.3.24 [INFO] [stderr] Compiling hdf5 v0.7.0 [INFO] [stderr] Compiling termcolor v1.1.2 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling libloading v0.6.5 [INFO] [stderr] Compiling thread_local v1.0.1 [INFO] [stderr] Compiling unicode-bidi v0.3.4 [INFO] [stderr] Compiling tinyvec v1.1.0 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling humantime v1.3.0 [INFO] [stderr] Compiling matrixmultiply v0.2.3 [INFO] [stderr] Compiling lock_api v0.3.4 [INFO] [stderr] Compiling heck v0.3.1 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling form_urlencoded v1.0.0 [INFO] [stderr] Compiling log v0.4.11 [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 proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling aho-corasick v0.7.15 [INFO] [stderr] Compiling quote v0.6.13 [INFO] [stderr] Compiling unicode-normalization v0.1.16 [INFO] [stderr] Compiling jobserver v0.1.21 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling parking_lot_core v0.7.2 [INFO] [stderr] Compiling rand v0.4.6 [INFO] [stderr] Compiling time v0.1.44 [INFO] [stderr] Compiling hdf5-types v0.7.0 [INFO] [stderr] Compiling flate2 v1.0.19 [INFO] [stderr] Compiling crossbeam-channel v0.4.4 [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 memrange v0.1.3 [INFO] [stderr] Compiling idna v0.2.0 [INFO] [stderr] Compiling regex v1.4.2 [INFO] [stderr] Compiling rand v0.3.23 [INFO] [stderr] Compiling pbr v1.0.3 [INFO] [stderr] Compiling openssl-src v111.12.0+1.1.1h [INFO] [stderr] Compiling theban_interval_tree v0.7.1 [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 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 proc-macro-error v1.0.4 [INFO] [stderr] Compiling derefable v0.1.0 [INFO] [stderr] Compiling hdf5-sys v0.7.0 [INFO] [stderr] Compiling derive-new v0.5.8 [INFO] [stderr] Compiling serde_derive v1.0.117 [INFO] [stderr] Compiling thiserror-impl v1.0.22 [INFO] [stderr] Compiling structopt-derive v0.4.13 [INFO] [stderr] Compiling hdf5-derive 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-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: 0x5581d9130a10 - std::backtrace_rs::backtrace::libunwind::trace::h99dbb39dca18857d [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/../../backtrace/src/backtrace/libunwind.rs:90:5 [INFO] [stderr] 1: 0x5581d9130a10 - std::backtrace_rs::backtrace::trace_unsynchronized::h832861927e9cfedf [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5 [INFO] [stderr] 2: 0x5581d9130a10 - std::sys_common::backtrace::_print_fmt::h3d18154c77dcf310 [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/sys_common/backtrace.rs:67:5 [INFO] [stderr] 3: 0x5581d9130a10 - ::fmt::he312f4ad5b9bb346 [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/sys_common/backtrace.rs:46:22 [INFO] [stderr] 4: 0x5581d914efdc - core::fmt::write::h9a6d9c74526a6c1b [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/core/src/fmt/mod.rs:1115:17 [INFO] [stderr] 5: 0x5581d912dfb5 - std::io::Write::write_fmt::h6aced00850e8186f [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/io/mod.rs:1665:15 [INFO] [stderr] 6: 0x5581d9132a8b - std::sys_common::backtrace::_print::h65d996766de40da4 [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/sys_common/backtrace.rs:49:5 [INFO] [stderr] 7: 0x5581d9132a8b - std::sys_common::backtrace::print::h40df9727e635f303 [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/sys_common/backtrace.rs:36:9 [INFO] [stderr] 8: 0x5581d9132a8b - std::panicking::default_hook::{{closure}}::hd2da4327dea91a51 [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/panicking.rs:208:50 [INFO] [stderr] 9: 0x5581d9132561 - std::panicking::default_hook::h3d55120ad6ada158 [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/panicking.rs:225:9 [INFO] [stderr] 10: 0x5581d9133154 - std::panicking::rust_panic_with_hook::hf85dd0bb545e3b55 [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/panicking.rs:622:17 [INFO] [stderr] 11: 0x5581d8f5f6d3 - std::panicking::begin_panic::{{closure}}::h9e0601c718203d46 [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/panicking.rs:542:9 [INFO] [stderr] 12: 0x5581d8f5f329 - std::sys_common::backtrace::__rust_end_short_backtrace::h5e8a50bcd73cb3e8 [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/sys_common/backtrace.rs:141:18 [INFO] [stderr] 13: 0x5581d8f5f609 - std::panicking::begin_panic::h65aac921296e9d25 [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/panicking.rs:541:12 [INFO] [stderr] 14: 0x5581d8f2fd97 - 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: 0x5581d8f315bb - 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: 0x5581d8f3537b - core::ops::function::FnOnce::call_once::h0fea7572554ead72 [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/core/src/ops/function.rs:227:5 [INFO] [stderr] 17: 0x5581d8f3ba3e - std::sys_common::backtrace::__rust_begin_short_backtrace::hbefb527344a68cd7 [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/sys_common/backtrace.rs:125:18 [INFO] [stderr] 18: 0x5581d8f39f31 - std::rt::lang_start::{{closure}}::hacf4fdae77ad98ea [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/rt.rs:63:18 [INFO] [stderr] 19: 0x5581d913365a - core::ops::function::impls:: for &F>::call_once::h5a0483c8d4e9c15d [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/core/src/ops/function.rs:259:13 [INFO] [stderr] 20: 0x5581d913365a - std::panicking::try::do_call::h6ad7918f175f6ddd [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/panicking.rs:401:40 [INFO] [stderr] 21: 0x5581d913365a - std::panicking::try::hcd5af58f52320690 [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/panicking.rs:365:19 [INFO] [stderr] 22: 0x5581d913365a - std::panic::catch_unwind::hf1ae33ba67228f1e [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/panic.rs:434:14 [INFO] [stderr] 23: 0x5581d913365a - std::rt::lang_start_internal::{{closure}}::h4a87bc0aa1312dc5 [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/rt.rs:45:48 [INFO] [stderr] 24: 0x5581d913365a - std::panicking::try::do_call::h1ade2a52932fc900 [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/panicking.rs:401:40 [INFO] [stderr] 25: 0x5581d913365a - std::panicking::try::h6f4a87ad169e174b [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/panicking.rs:365:19 [INFO] [stderr] 26: 0x5581d913365a - std::panic::catch_unwind::h043c7f08019f9e2a [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/panic.rs:434:14 [INFO] [stderr] 27: 0x5581d913365a - std::rt::lang_start_internal::h82825699ebfd70bd [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/rt.rs:45:20 [INFO] [stderr] 28: 0x5581d8f39f00 - std::rt::lang_start::hd5cc95aeab1216de [INFO] [stderr] at /rustc/b70888601af92f6cdc0364abab3446e418b91d36/library/std/src/rt.rs:62:5 [INFO] [stderr] 29: 0x5581d8f32aac - main [INFO] [stderr] 30: 0x7fa9d06ad0b3 - __libc_start_main [INFO] [stderr] 31: 0x5581d8f2af0e - _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" "37af54f6a87b997b87d51de38b273f9053a854384d33202824036d4d62543485", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "37af54f6a87b997b87d51de38b273f9053a854384d33202824036d4d62543485", kill_on_drop: false }` [INFO] [stdout] 37af54f6a87b997b87d51de38b273f9053a854384d33202824036d4d62543485