[INFO] fetching crate genomic_interval_pipeline 0.1.3... [INFO] checking genomic_interval_pipeline-0.1.3 against master#36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923 for pr-81863 [INFO] extracting crate genomic_interval_pipeline 0.1.3 into /workspace/builds/worker-11/source [INFO] validating manifest of crates.io crate genomic_interval_pipeline 0.1.3 on toolchain 36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923" "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-11/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" "+36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/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@sha256:21f1ed92105a0ef9b0d27ad8bdeb7f36f9f01ac17fffe3a3f3dc5241fc25d8f4" "/opt/rustwide/cargo-home/bin/cargo" "+36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923" "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] f6a32ceec5d80027ad39b64a46dbf996b50d3de61d3fadd1d438a0b35f66c7aa [INFO] running `Command { std: "docker" "start" "-a" "f6a32ceec5d80027ad39b64a46dbf996b50d3de61d3fadd1d438a0b35f66c7aa", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "f6a32ceec5d80027ad39b64a46dbf996b50d3de61d3fadd1d438a0b35f66c7aa", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f6a32ceec5d80027ad39b64a46dbf996b50d3de61d3fadd1d438a0b35f66c7aa", kill_on_drop: false }` [INFO] [stdout] f6a32ceec5d80027ad39b64a46dbf996b50d3de61d3fadd1d438a0b35f66c7aa [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-11/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" "rustops/crates-build-env@sha256:21f1ed92105a0ef9b0d27ad8bdeb7f36f9f01ac17fffe3a3f3dc5241fc25d8f4" "/opt/rustwide/cargo-home/bin/cargo" "+36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 49e42f7207f790934b43935de072a88dfa1ff68679f9328dc6d6d805aab04e02 [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" "49e42f7207f790934b43935de072a88dfa1ff68679f9328dc6d6d805aab04e02", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [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 syn v1.0.50 [INFO] [stderr] Checking lazy_static v1.4.0 [INFO] [stderr] Checking cfg-if v0.1.10 [INFO] [stderr] Compiling version_check v0.9.2 [INFO] [stderr] Compiling proc-macro2 v0.4.30 [INFO] [stderr] Compiling regex-syntax v0.6.21 [INFO] [stderr] Compiling cfg-if v1.0.0 [INFO] [stderr] Compiling bitflags v1.2.1 [INFO] [stderr] Compiling unicode-xid v0.1.0 [INFO] [stderr] Checking tinyvec_macros v0.1.0 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling maybe-uninit v2.0.0 [INFO] [stderr] Compiling serde_derive v1.0.117 [INFO] [stderr] Compiling syn v0.15.44 [INFO] [stderr] Compiling glob v0.3.0 [INFO] [stderr] Compiling log v0.4.11 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Checking scopeguard v1.1.0 [INFO] [stderr] Compiling ndarray v0.13.1 [INFO] [stderr] Checking unicode-width v0.1.8 [INFO] [stderr] Checking strsim v0.8.0 [INFO] [stderr] Checking adler v0.2.3 [INFO] [stderr] Checking rustc-serialize v0.3.24 [INFO] [stderr] Compiling hdf5 v0.7.0 [INFO] [stderr] Checking ascii v1.0.0 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking ansi_term v0.11.0 [INFO] [stderr] Checking custom_derive v0.1.7 [INFO] [stderr] Checking linear-map v1.2.0 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling libloading v0.6.5 [INFO] [stderr] Checking tinyvec v1.1.0 [INFO] [stderr] Checking thread_local v1.0.1 [INFO] [stderr] Checking matrixmultiply v0.2.3 [INFO] [stderr] Checking lock_api v0.3.4 [INFO] [stderr] Checking form_urlencoded v1.0.0 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Checking textwrap v0.11.0 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Compiling memchr v2.3.4 [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] Checking crc32fast v1.2.1 [INFO] [stderr] Compiling quote v1.0.7 [INFO] [stderr] Compiling aho-corasick v0.7.15 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Checking unicode-normalization v0.1.16 [INFO] [stderr] Compiling quote v0.6.13 [INFO] [stderr] Checking crossbeam-channel v0.4.4 [INFO] [stderr] Compiling jobserver v0.1.21 [INFO] [stderr] Checking atty v0.2.14 [INFO] [stderr] Checking parking_lot_core v0.7.2 [INFO] [stderr] Checking time v0.1.44 [INFO] [stderr] Checking rand v0.4.6 [INFO] [stderr] Checking hdf5-types v0.7.0 [INFO] [stderr] Checking flate2 v1.0.19 [INFO] [stderr] Checking clap v2.33.3 [INFO] [stderr] Compiling cc v1.0.65 [INFO] [stderr] Checking parking_lot v0.10.2 [INFO] [stderr] Checking pbr v1.0.3 [INFO] [stderr] Checking memrange v0.1.3 [INFO] [stderr] Checking idna v0.2.0 [INFO] [stderr] Checking regex v1.4.2 [INFO] [stderr] Compiling openssl-src v111.12.0+1.1.1h [INFO] [stderr] Checking rand v0.3.23 [INFO] [stderr] Checking theban_interval_tree v0.7.1 [INFO] [stderr] Checking 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 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 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-d9fc9792c8caac7a/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: 0x562142242930 - std::backtrace_rs::backtrace::libunwind::trace::hb4de9797f80b7b8c [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/../../backtrace/src/backtrace/libunwind.rs:90:5 [INFO] [stderr] 1: 0x562142242930 - std::backtrace_rs::backtrace::trace_unsynchronized::h59566d0bd20efff7 [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5 [INFO] [stderr] 2: 0x562142242930 - std::sys_common::backtrace::_print_fmt::hcfa5ce6be50275d4 [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/sys_common/backtrace.rs:67:5 [INFO] [stderr] 3: 0x562142242930 - ::fmt::hd8c307a38b9bab04 [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/sys_common/backtrace.rs:46:22 [INFO] [stderr] 4: 0x56214225ea5c - core::fmt::write::h3868db8542c90941 [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/core/src/fmt/mod.rs:1096:17 [INFO] [stderr] 5: 0x56214223f1d2 - std::io::Write::write_fmt::hab90295d5a0f197d [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/io/mod.rs:1568:15 [INFO] [stderr] 6: 0x5621422449b5 - std::sys_common::backtrace::_print::h19224910b8700cf1 [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/sys_common/backtrace.rs:49:5 [INFO] [stderr] 7: 0x5621422449b5 - std::sys_common::backtrace::print::h25dedfa68c5fb84a [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/sys_common/backtrace.rs:36:9 [INFO] [stderr] 8: 0x5621422449b5 - std::panicking::default_hook::{{closure}}::h12c5765653a72a42 [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/panicking.rs:208:50 [INFO] [stderr] 9: 0x562142244513 - std::panicking::default_hook::he65cee71c4209f0c [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/panicking.rs:225:9 [INFO] [stderr] 10: 0x562142245151 - std::panicking::rust_panic_with_hook::h01a674d863fe0d8a [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/panicking.rs:591:17 [INFO] [stderr] 11: 0x56214212358e - std::panicking::begin_panic::{{closure}}::h19b4184239818cad [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/panicking.rs:520:9 [INFO] [stderr] 12: 0x562142144e59 - std::sys_common::backtrace::__rust_end_short_backtrace::hd415cf9fb3b30a90 [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/sys_common/backtrace.rs:141:18 [INFO] [stderr] 13: 0x5621421234bb - std::panicking::begin_panic::h0b86ee9f5681340d [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/panicking.rs:519:12 [INFO] [stderr] 14: 0x56214201e07b - build_script_build::LibrarySearcher::try_locate_hdf5_library::hb16737d5107ad56a [INFO] [stderr] at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.0/build.rs:549:13 [INFO] [stderr] 15: 0x56214201f8d5 - build_script_build::main::h1726a79c93d28cdd [INFO] [stderr] at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.0/build.rs:647:9 [INFO] [stderr] 16: 0x562142029f6b - core::ops::function::FnOnce::call_once::h87ed3503f2ede79f [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/core/src/ops/function.rs:227:5 [INFO] [stderr] 17: 0x5621420239ce - std::sys_common::backtrace::__rust_begin_short_backtrace::ha05fb1b5bc8bd968 [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/sys_common/backtrace.rs:125:18 [INFO] [stderr] 18: 0x56214202bde1 - std::rt::lang_start::{{closure}}::hd672ed9ac884c53a [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/rt.rs:66:18 [INFO] [stderr] 19: 0x562142245577 - core::ops::function::impls:: for &F>::call_once::h2c4fd7d4128112a8 [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/core/src/ops/function.rs:259:13 [INFO] [stderr] 20: 0x562142245577 - std::panicking::try::do_call::h41fb7dbbbe7bece6 [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/panicking.rs:379:40 [INFO] [stderr] 21: 0x562142245577 - std::panicking::try::hd38008ccba72bce1 [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/panicking.rs:343:19 [INFO] [stderr] 22: 0x562142245577 - std::panic::catch_unwind::h057e765cd60f2d13 [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/panic.rs:431:14 [INFO] [stderr] 23: 0x562142245577 - std::rt::lang_start_internal::hdb9d0b9d2cdcda8b [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/rt.rs:51:25 [INFO] [stderr] 24: 0x56214202bdb7 - std::rt::lang_start::h744f60e49d5fe9a4 [INFO] [stderr] at /rustc/36ecbc94eb6be90bc38b2d0fdd4bfac3f34d9923/library/std/src/rt.rs:65:5 [INFO] [stderr] 25: 0x562142020f1a - main [INFO] [stderr] 26: 0x7f40998fb0b3 - __libc_start_main [INFO] [stderr] 27: 0x5621420190be - _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" "49e42f7207f790934b43935de072a88dfa1ff68679f9328dc6d6d805aab04e02", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "49e42f7207f790934b43935de072a88dfa1ff68679f9328dc6d6d805aab04e02", kill_on_drop: false }` [INFO] [stdout] 49e42f7207f790934b43935de072a88dfa1ff68679f9328dc6d6d805aab04e02