[INFO] cloning repository https://github.com/swemeshy/counts_to_csv [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/swemeshy/counts_to_csv" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fswemeshy%2Fcounts_to_csv", kill_on_drop: false }` [INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fswemeshy%2Fcounts_to_csv'... [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] fcac3c11d1d1d65496d2c996355ef02f87ebef7b [INFO] checking swemeshy/counts_to_csv against master#3aedcf06b73fc36feeebca3d579e1d2a6c40acc5 for pr-65819 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fswemeshy%2Fcounts_to_csv" "/workspace/builds/worker-3/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-3/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/swemeshy/counts_to_csv on toolchain 3aedcf06b73fc36feeebca3d579e1d2a6c40acc5 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+3aedcf06b73fc36feeebca3d579e1d2a6c40acc5" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/swemeshy/counts_to_csv [INFO] finished tweaking git repo https://github.com/swemeshy/counts_to_csv [INFO] tweaked toml for git repo https://github.com/swemeshy/counts_to_csv written to /workspace/builds/worker-3/source/Cargo.toml [INFO] crate git repo https://github.com/swemeshy/counts_to_csv already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+3aedcf06b73fc36feeebca3d579e1d2a6c40acc5" "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-3/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3/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:c46a2d1a26fb48b37929c74ca49dd9409f2375a0a3bdb8fe07617f3ffccaa889" "/opt/rustwide/cargo-home/bin/cargo" "+3aedcf06b73fc36feeebca3d579e1d2a6c40acc5" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] cc709af38fafc718ae9de731837c7c49797df53f1b7a04d7e2b9b5924109ce95 [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" "cc709af38fafc718ae9de731837c7c49797df53f1b7a04d7e2b9b5924109ce95", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "cc709af38fafc718ae9de731837c7c49797df53f1b7a04d7e2b9b5924109ce95", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "cc709af38fafc718ae9de731837c7c49797df53f1b7a04d7e2b9b5924109ce95", kill_on_drop: false }` [INFO] [stdout] cc709af38fafc718ae9de731837c7c49797df53f1b7a04d7e2b9b5924109ce95 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3/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:c46a2d1a26fb48b37929c74ca49dd9409f2375a0a3bdb8fe07617f3ffccaa889" "/opt/rustwide/cargo-home/bin/cargo" "+3aedcf06b73fc36feeebca3d579e1d2a6c40acc5" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 216c962f8f3d58e2b6612601e4dbc89c0b5bf437c979d40c3f847269e7956e31 [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" "216c962f8f3d58e2b6612601e4dbc89c0b5bf437c979d40c3f847269e7956e31", kill_on_drop: false }` [INFO] [stderr] Compiling memchr v2.3.4 [INFO] [stderr] Compiling syn v1.0.63 [INFO] [stderr] Compiling version_check v0.9.3 [INFO] [stderr] Compiling regex-syntax v0.6.23 [INFO] [stderr] Compiling serde_derive v1.0.124 [INFO] [stderr] Checking rawpointer v0.2.1 [INFO] [stderr] Compiling serde v1.0.124 [INFO] [stderr] Checking smallvec v1.6.1 [INFO] [stderr] Compiling ndarray v0.14.0 [INFO] [stderr] Compiling ndarray v0.13.1 [INFO] [stderr] Compiling unicode-segmentation v1.7.1 [INFO] [stderr] Checking byteorder v1.4.3 [INFO] [stderr] Compiling anyhow v1.0.38 [INFO] [stderr] Compiling hdf5 v0.7.1 [INFO] [stderr] Checking ascii v1.0.0 [INFO] [stderr] Checking os_str_bytes v2.4.0 [INFO] [stderr] Checking termcolor v1.1.2 [INFO] [stderr] Checking strsim v0.10.0 [INFO] [stderr] Compiling num-traits v0.2.14 [INFO] [stderr] Compiling crossbeam-utils v0.8.3 [INFO] [stderr] Compiling num-integer v0.1.44 [INFO] [stderr] Compiling num-complex v0.2.4 [INFO] [stderr] Compiling indexmap v1.6.2 [INFO] [stderr] Compiling libloading v0.6.7 [INFO] [stderr] Checking instant v0.1.9 [INFO] [stderr] Checking lock_api v0.4.2 [INFO] [stderr] Checking textwrap v0.12.1 [INFO] [stderr] Checking matrixmultiply v0.2.4 [INFO] [stderr] Checking regex-automata v0.1.9 [INFO] [stderr] Checking log v0.4.14 [INFO] [stderr] Compiling heck v0.3.2 [INFO] [stderr] Checking atty v0.2.14 [INFO] [stderr] Checking num_cpus v1.13.0 [INFO] [stderr] Checking parking_lot_core v0.8.3 [INFO] [stderr] Checking terminal_size v0.1.16 [INFO] [stderr] Checking hdf5-types v0.7.1 [INFO] [stderr] Compiling quote v1.0.9 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Checking colored v1.9.3 [INFO] [stderr] Checking aho-corasick v0.7.15 [INFO] [stderr] Checking parking_lot v0.11.1 [INFO] [stderr] Checking csv-core v0.1.10 [INFO] [stderr] Checking crossbeam-epoch v0.9.3 [INFO] [stderr] Checking crossbeam-channel v0.5.0 [INFO] [stderr] Checking crossbeam-deque v0.8.0 [INFO] [stderr] Checking rayon-core v1.9.0 [INFO] [stderr] Checking regex v1.4.4 [INFO] [stderr] Checking approx v0.3.2 [INFO] [stderr] Checking num-complex v0.3.1 [INFO] [stderr] Checking chrono v0.4.19 [INFO] [stderr] Checking rayon v1.5.0 [INFO] [stderr] Checking alga v0.9.3 [INFO] [stderr] Checking console v0.14.1 [INFO] [stderr] Checking simple_logger v1.11.0 [INFO] [stderr] Checking indicatif v0.15.0 [INFO] [stderr] Checking sprs v0.9.3 [INFO] [stderr] Compiling hdf5-sys v0.7.1 [INFO] [stderr] error: failed to run custom build command for `hdf5-sys v0.7.1` [INFO] [stderr] [INFO] [stderr] Caused by: [INFO] [stderr] process didn't exit successfully: `/opt/rustwide/target/debug/build/hdf5-sys-18bbfbf014f6c69c/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-0.7.1/build.rs:549:13 [INFO] [stderr] stack backtrace: [INFO] [stderr] 0: 0x555802a171a0 - std::backtrace_rs::backtrace::libunwind::trace::h4dee703919bfd40a [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/../../backtrace/src/backtrace/libunwind.rs:90:5 [INFO] [stderr] 1: 0x555802a171a0 - std::backtrace_rs::backtrace::trace_unsynchronized::h457e839f1a563e20 [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/../../backtrace/src/backtrace/mod.rs:66:5 [INFO] [stderr] 2: 0x555802a171a0 - std::sys_common::backtrace::_print_fmt::h86a55fb30f8393c8 [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/sys_common/backtrace.rs:67:5 [INFO] [stderr] 3: 0x555802a171a0 - ::fmt::h7b3d6cac46d277e1 [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/sys_common/backtrace.rs:46:22 [INFO] [stderr] 4: 0x555802a321bf - core::fmt::write::h127419eb46f2ecc9 [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/core/src/fmt/mod.rs:1094:17 [INFO] [stderr] 5: 0x555802a143b5 - std::io::Write::write_fmt::h6010cfbb4726588b [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/io/mod.rs:1578:15 [INFO] [stderr] 6: 0x555802a1913b - std::sys_common::backtrace::_print::h79b4f9652330cc9d [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/sys_common/backtrace.rs:49:5 [INFO] [stderr] 7: 0x555802a1913b - std::sys_common::backtrace::print::h330bb326a76af8cf [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/sys_common/backtrace.rs:36:9 [INFO] [stderr] 8: 0x555802a1913b - std::panicking::default_hook::{{closure}}::heb6a42a7d50a472e [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/panicking.rs:208:50 [INFO] [stderr] 9: 0x555802a18c03 - std::panicking::default_hook::h17e521ba6d68d6e1 [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/panicking.rs:225:9 [INFO] [stderr] 10: 0x555802a196ed - std::panicking::rust_panic_with_hook::h70db735e3a6e70cb [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/panicking.rs:591:17 [INFO] [stderr] 11: 0x55580294f7c3 - std::panicking::begin_panic::{{closure}}::h64762824ab10c536 [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/panicking.rs:520:9 [INFO] [stderr] 12: 0x5558029772a9 - std::sys_common::backtrace::__rust_end_short_backtrace::h4a41408138580013 [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/sys_common/backtrace.rs:141:18 [INFO] [stderr] 13: 0x55580294f6f9 - std::panicking::begin_panic::h15f8eab1a48fda24 [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/panicking.rs:519:12 [INFO] [stderr] 14: 0x555802812029 - build_script_build::LibrarySearcher::try_locate_hdf5_library::h24adc7e1965aa63a [INFO] [stderr] at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.1/build.rs:549:13 [INFO] [stderr] 15: 0x555802813841 - build_script_build::main::h15cde601d3fb1652 [INFO] [stderr] at /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/hdf5-sys-0.7.1/build.rs:647:9 [INFO] [stderr] 16: 0x55580281cf3b - core::ops::function::FnOnce::call_once::h39531d5de042c35c [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/core/src/ops/function.rs:227:5 [INFO] [stderr] 17: 0x55580282059e - std::sys_common::backtrace::__rust_begin_short_backtrace::h0da64ec1d243aecb [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/sys_common/backtrace.rs:125:18 [INFO] [stderr] 18: 0x55580281ce81 - std::rt::lang_start::{{closure}}::hfd5a75f5c45b6b82 [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/rt.rs:66:18 [INFO] [stderr] 19: 0x555802a19aea - core::ops::function::impls:: for &F>::call_once::hbcc915e668c7ca11 [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/core/src/ops/function.rs:259:13 [INFO] [stderr] 20: 0x555802a19aea - std::panicking::try::do_call::h6b0f430d48122ddf [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/panicking.rs:379:40 [INFO] [stderr] 21: 0x555802a19aea - std::panicking::try::h6ba420e2e21b5afa [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/panicking.rs:343:19 [INFO] [stderr] 22: 0x555802a19aea - std::panic::catch_unwind::h8366719d1f615eee [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/panic.rs:431:14 [INFO] [stderr] 23: 0x555802a19aea - std::rt::lang_start_internal::h965c28c9ce06ee73 [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/rt.rs:51:25 [INFO] [stderr] 24: 0x55580281ce60 - std::rt::lang_start::ha3c513a3f2809ed3 [INFO] [stderr] at /rustc/3aedcf06b73fc36feeebca3d579e1d2a6c40acc5/library/std/src/rt.rs:65:5 [INFO] [stderr] 25: 0x555802814d3c - main [INFO] [stderr] 26: 0x7f82c0ea70b3 - __libc_start_main [INFO] [stderr] 27: 0x55580280cece - _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" "216c962f8f3d58e2b6612601e4dbc89c0b5bf437c979d40c3f847269e7956e31", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "216c962f8f3d58e2b6612601e4dbc89c0b5bf437c979d40c3f847269e7956e31", kill_on_drop: false }` [INFO] [stdout] 216c962f8f3d58e2b6612601e4dbc89c0b5bf437c979d40c3f847269e7956e31