[INFO] cloning repository https://github.com/clinico-omics/omics-tools
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/clinico-omics/omics-tools" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fomics-tools", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fomics-tools'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 225d596d6872b010a31f9f8703e5294decfa73ef
[INFO] checking clinico-omics/omics-tools against try#9b06ec641f3d05c126a54ceadba42a64366f72b4 for pr-95755
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fclinico-omics%2Fomics-tools" "/workspace/builds/worker-23/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-23/source'...
[INFO] [stderr] done.
[INFO] validating manifest of git repo https://github.com/clinico-omics/omics-tools on toolchain 9b06ec641f3d05c126a54ceadba42a64366f72b4
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+9b06ec641f3d05c126a54ceadba42a64366f72b4" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] removed /workspace/builds/worker-23/source/.cargo/config.toml
[INFO] started tweaking git repo https://github.com/clinico-omics/omics-tools
[INFO] finished tweaking git repo https://github.com/clinico-omics/omics-tools
[INFO] tweaked toml for git repo https://github.com/clinico-omics/omics-tools written to /workspace/builds/worker-23/source/Cargo.toml
[INFO] crate git repo https://github.com/clinico-omics/omics-tools already has a lockfile, it will not be regenerated
[INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+9b06ec641f3d05c126a54ceadba42a64366f72b4" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr] warning: profiles for the non root package will be ignored, specify profiles at the workspace root:
[INFO] [stderr] package:   /workspace/builds/worker-23/source/bam-util/Cargo.toml
[INFO] [stderr] workspace: /workspace/builds/worker-23/source/Cargo.toml
[INFO] [stderr] warning: profiles for the non root package will be ignored, specify profiles at the workspace root:
[INFO] [stderr] package:   /workspace/builds/worker-23/source/vcf-util/Cargo.toml
[INFO] [stderr] workspace: /workspace/builds/worker-23/source/Cargo.toml
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-23/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-23/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:b0c94ce3c1162fcb8e57cac5b65ec2f72eabb1eebea4fcc35e269e823f681646" "/opt/rustwide/cargo-home/bin/cargo" "+9b06ec641f3d05c126a54ceadba42a64366f72b4" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] c65d627948227f877982184ffd6602a6a518dd708fd1f923144d623034ed9948
[INFO] running `Command { std: "docker" "start" "-a" "c65d627948227f877982184ffd6602a6a518dd708fd1f923144d623034ed9948", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "c65d627948227f877982184ffd6602a6a518dd708fd1f923144d623034ed9948", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "c65d627948227f877982184ffd6602a6a518dd708fd1f923144d623034ed9948", kill_on_drop: false }`
[INFO] [stdout] c65d627948227f877982184ffd6602a6a518dd708fd1f923144d623034ed9948
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-23/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-23/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:b0c94ce3c1162fcb8e57cac5b65ec2f72eabb1eebea4fcc35e269e823f681646" "/opt/rustwide/cargo-home/bin/cargo" "+9b06ec641f3d05c126a54ceadba42a64366f72b4" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 0c5b92cb62fd23a00df0d96000bb0b2559fa3d3744916ce9e4b815d69b83ebb7
[INFO] running `Command { std: "docker" "start" "-a" "0c5b92cb62fd23a00df0d96000bb0b2559fa3d3744916ce9e4b815d69b83ebb7", kill_on_drop: false }`
[INFO] [stderr] warning: profiles for the non root package will be ignored, specify profiles at the workspace root:
[INFO] [stderr] package:   /opt/rustwide/workdir/bam-util/Cargo.toml
[INFO] [stderr] workspace: /opt/rustwide/workdir/Cargo.toml
[INFO] [stderr] warning: profiles for the non root package will be ignored, specify profiles at the workspace root:
[INFO] [stderr] package:   /opt/rustwide/workdir/vcf-util/Cargo.toml
[INFO] [stderr] workspace: /opt/rustwide/workdir/Cargo.toml
[INFO] [stderr]    Compiling libc v0.2.94
[INFO] [stderr]    Compiling autocfg v1.0.1
[INFO] [stderr]    Compiling pkg-config v0.3.19
[INFO] [stderr]    Compiling proc-macro2 v1.0.26
[INFO] [stderr]    Compiling unicode-xid v0.2.2
[INFO] [stderr]    Compiling syn v1.0.72
[INFO] [stderr]    Compiling version_check v0.9.3
[INFO] [stderr]     Checking cfg-if v1.0.0
[INFO] [stderr]    Compiling memchr v2.4.0
[INFO] [stderr]    Compiling bitflags v1.2.1
[INFO] [stderr]    Compiling unicode-segmentation v1.7.1
[INFO] [stderr]     Checking lazy_static v1.4.0
[INFO] [stderr]     Checking regex-syntax v0.6.25
[INFO] [stderr]     Checking void v1.0.2
[INFO] [stderr]    Compiling log v0.4.14
[INFO] [stderr]     Checking unicode-width v0.1.8
[INFO] [stderr]     Checking strsim v0.8.0
[INFO] [stderr]     Checking lazy_static v0.2.11
[INFO] [stderr]     Checking ansi_term v0.11.0
[INFO] [stderr]    Compiling proc-macro2 v0.4.30
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]    Compiling semver v0.1.20
[INFO] [stderr]     Checking matches v0.1.8
[INFO] [stderr]     Checking termcolor v1.1.2
[INFO] [stderr]     Checking tinyvec_macros v0.1.0
[INFO] [stderr]    Compiling unicode-xid v0.1.0
[INFO] [stderr]    Compiling ryu v1.0.5
[INFO] [stderr]    Compiling lexical-core v0.7.6
[INFO] [stderr]    Compiling syn v0.15.44
[INFO] [stderr]     Checking adler v1.0.2
[INFO] [stderr]     Checking exitcode v1.1.2
[INFO] [stderr]    Compiling glob v0.3.0
[INFO] [stderr]     Checking gimli v0.24.0
[INFO] [stderr]    Compiling failure_derive v0.1.8
[INFO] [stderr]     Checking rustc-demangle v0.1.19
[INFO] [stderr]     Checking object v0.24.0
[INFO] [stderr]     Checking static_assertions v1.1.0
[INFO] [stderr]     Checking arrayvec v0.5.2
[INFO] [stderr]     Checking ahash v0.4.7
[INFO] [stderr]     Checking percent-encoding v2.1.0
[INFO] [stderr]    Compiling crc32fast v1.2.1
[INFO] [stderr]     Checking fallible-iterator v0.2.0
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]     Checking smallvec v1.6.1
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking fallible-streaming-iterator v0.1.9
[INFO] [stderr]     Checking hashbrown v0.9.1
[INFO] [stderr]     Checking tinyvec v1.2.0
[INFO] [stderr]     Checking unicode-bidi v0.3.5
[INFO] [stderr]     Checking unreachable v1.0.0
[INFO] [stderr]     Checking textwrap v0.11.0
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]     Checking form_urlencoded v1.0.1
[INFO] [stderr]    Compiling rustc_version v0.1.7
[INFO] [stderr]     Checking thread_local v0.3.4
[INFO] [stderr]    Compiling num-traits v0.2.14
[INFO] [stderr]    Compiling num-integer v0.1.44
[INFO] [stderr]    Compiling miniz_oxide v0.4.4
[INFO] [stderr]    Compiling heck v0.3.2
[INFO] [stderr]     Checking hashlink v0.6.0
[INFO] [stderr]    Compiling proc-macro-error-attr v1.0.4
[INFO] [stderr]    Compiling proc-macro-error v1.0.4
[INFO] [stderr]    Compiling nom v5.1.2
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking atty v0.2.11
[INFO] [stderr]     Checking time v0.1.44
[INFO] [stderr]     Checking aho-corasick v0.7.18
[INFO] [stderr]    Compiling quote v1.0.9
[INFO] [stderr]     Checking unicode-normalization v0.1.17
[INFO] [stderr]     Checking clap v2.33.3
[INFO] [stderr]    Compiling quote v0.6.13
[INFO] [stderr]    Compiling jobserver v0.1.22
[INFO] [stderr]    Compiling cc v1.0.67
[INFO] [stderr]     Checking idna v0.2.3
[INFO] [stderr]    Compiling openssl-src v111.15.0+1.1.1k
[INFO] [stderr]     Checking chrono v0.4.19
[INFO] [stderr]     Checking regex v1.5.4
[INFO] [stderr]     Checking url v2.2.2
[INFO] [stderr]     Checking addr2line v0.15.1
[INFO] [stderr]    Compiling openssl-sys v0.9.63
[INFO] [stderr]    Compiling libz-sys v1.1.3
[INFO] [stderr]    Compiling lzma-sys v0.1.17
[INFO] [stderr]    Compiling bzip2-sys v0.1.10+1.0.8
[INFO] [stderr]    Compiling curl-sys v0.4.43+curl-7.76.0
[INFO] [stderr]    Compiling backtrace v0.3.59
[INFO] [stderr]    Compiling libsqlite3-sys v0.20.1
[INFO] [stderr]    Compiling cloudflare-zlib-sys v0.2.0
[INFO] [stderr]    Compiling hts-sys v1.11.1-fix1
[INFO] [stderr]     Checking stderrlog v0.4.3
[INFO] [stderr]    Compiling derefable v0.1.0
[INFO] [stderr]     Checking flate2 v1.0.20
[INFO] [stderr]    Compiling synstructure v0.12.4
[INFO] [stderr]    Compiling structopt-derive v0.4.14
[INFO] [stderr]    Compiling thiserror-impl v1.0.24
[INFO] [stderr]    Compiling strum_macros v0.20.1
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]     Checking failure v0.1.8
[INFO] [stderr]     Checking vcf v0.5.0
[INFO] [stderr] The following warnings were emitted during compilation:
[INFO] [stderr] 
[INFO] [stderr] warning: cc: fatal error: Killed signal terminated program cc1
[INFO] [stderr] warning: compilation terminated.
[INFO] [stderr] 
[INFO] [stderr] error: failed to run custom build command for `libsqlite3-sys v0.20.1`
[INFO] [stderr] 
[INFO] [stderr] Caused by:
[INFO] [stderr]   process didn't exit successfully: `/opt/rustwide/target/debug/build/libsqlite3-sys-de0c5d9b63f4b621/build-script-build` (exit status: 1)
[INFO] [stderr]   --- stdout
[INFO] [stderr]   cargo:rerun-if-changed=sqlite3/sqlite3.c
[INFO] [stderr]   cargo:rerun-if-changed=sqlite3/wasm32-wasi-vfs.c
[INFO] [stderr]   cargo:rerun-if-env-changed=SQLITE_MAX_VARIABLE_NUMBER
[INFO] [stderr]   cargo:rerun-if-env-changed=SQLITE_MAX_EXPR_DEPTH
[INFO] [stderr]   cargo:rerun-if-env-changed=LIBSQLITE3_FLAGS
[INFO] [stderr]   TARGET = Some("x86_64-unknown-linux-gnu")
[INFO] [stderr]   OPT_LEVEL = Some("0")
[INFO] [stderr]   HOST = Some("x86_64-unknown-linux-gnu")
[INFO] [stderr]   CC_x86_64-unknown-linux-gnu = None
[INFO] [stderr]   CC_x86_64_unknown_linux_gnu = None
[INFO] [stderr]   HOST_CC = None
[INFO] [stderr]   CC = None
[INFO] [stderr]   CFLAGS_x86_64-unknown-linux-gnu = None
[INFO] [stderr]   CFLAGS_x86_64_unknown_linux_gnu = None
[INFO] [stderr]   HOST_CFLAGS = None
[INFO] [stderr]   CFLAGS = None
[INFO] [stderr]   CRATE_CC_NO_DEFAULTS = None
[INFO] [stderr]   DEBUG = Some("true")
[INFO] [stderr]   CARGO_CFG_TARGET_FEATURE = Some("fxsr,llvm14-builtins-abi,sse,sse2")
[INFO] [stderr]   running: "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-DSQLITE_CORE" "-DSQLITE_DEFAULT_FOREIGN_KEYS=1" "-DSQLITE_ENABLE_API_ARMOR" "-DSQLITE_ENABLE_COLUMN_METADATA" "-DSQLITE_ENABLE_DBSTAT_VTAB" "-DSQLITE_ENABLE_FTS3" "-DSQLITE_ENABLE_FTS3_PARENTHESIS" "-DSQLITE_ENABLE_FTS5" "-DSQLITE_ENABLE_JSON1" "-DSQLITE_ENABLE_LOAD_EXTENSION=1" "-DSQLITE_ENABLE_MEMORY_MANAGEMENT" "-DSQLITE_ENABLE_RTREE" "-DSQLITE_ENABLE_STAT2" "-DSQLITE_ENABLE_STAT4" "-DSQLITE_SOUNDEX" "-DSQLITE_THREADSAFE=1" "-DSQLITE_USE_URI" "-DHAVE_USLEEP=1" "-D_POSIX_THREAD_SAFE_FUNCTIONS" "-DHAVE_ISNAN" "-DHAVE_LOCALTIME_R" "-o" "/opt/rustwide/target/debug/build/libsqlite3-sys-cf85303bd995648f/out/sqlite3/sqlite3.o" "-c" "sqlite3/sqlite3.c"
[INFO] [stderr]   cargo:warning=cc: fatal error: Killed signal terminated program cc1
[INFO] [stderr]   cargo:warning=compilation terminated.
[INFO] [stderr]   exit status: 1
[INFO] [stderr] 
[INFO] [stderr]   --- stderr
[INFO] [stderr] 
[INFO] [stderr] 
[INFO] [stderr]   error occurred: Command "cc" "-O0" "-ffunction-sections" "-fdata-sections" "-fPIC" "-g" "-fno-omit-frame-pointer" "-m64" "-DSQLITE_CORE" "-DSQLITE_DEFAULT_FOREIGN_KEYS=1" "-DSQLITE_ENABLE_API_ARMOR" "-DSQLITE_ENABLE_COLUMN_METADATA" "-DSQLITE_ENABLE_DBSTAT_VTAB" "-DSQLITE_ENABLE_FTS3" "-DSQLITE_ENABLE_FTS3_PARENTHESIS" "-DSQLITE_ENABLE_FTS5" "-DSQLITE_ENABLE_JSON1" "-DSQLITE_ENABLE_LOAD_EXTENSION=1" "-DSQLITE_ENABLE_MEMORY_MANAGEMENT" "-DSQLITE_ENABLE_RTREE" "-DSQLITE_ENABLE_STAT2" "-DSQLITE_ENABLE_STAT4" "-DSQLITE_SOUNDEX" "-DSQLITE_THREADSAFE=1" "-DSQLITE_USE_URI" "-DHAVE_USLEEP=1" "-D_POSIX_THREAD_SAFE_FUNCTIONS" "-DHAVE_ISNAN" "-DHAVE_LOCALTIME_R" "-o" "/opt/rustwide/target/debug/build/libsqlite3-sys-cf85303bd995648f/out/sqlite3/sqlite3.o" "-c" "sqlite3/sqlite3.c" with args "cc" did not execute successfully (status code exit status: 1).
[INFO] [stderr] 
[INFO] [stderr] 
[INFO] [stderr] warning: build failed, waiting for other jobs to finish...
[INFO] running `Command { std: "docker" "inspect" "0c5b92cb62fd23a00df0d96000bb0b2559fa3d3744916ce9e4b815d69b83ebb7", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "0c5b92cb62fd23a00df0d96000bb0b2559fa3d3744916ce9e4b815d69b83ebb7", kill_on_drop: false }`
[INFO] [stdout] 0c5b92cb62fd23a00df0d96000bb0b2559fa3d3744916ce9e4b815d69b83ebb7