[INFO] fetching crate atg 0.2.0... [INFO] testing atg-0.2.0 against master#a77da2d454e6caa227a85b16410b95f93495e7e0 for pr-91031 [INFO] extracting crate atg 0.2.0 into /workspace/builds/worker-94/source [INFO] validating manifest of crates.io crate atg 0.2.0 on toolchain a77da2d454e6caa227a85b16410b95f93495e7e0 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+a77da2d454e6caa227a85b16410b95f93495e7e0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] started tweaking crates.io crate atg 0.2.0 [INFO] finished tweaking crates.io crate atg 0.2.0 [INFO] tweaked toml for crates.io crate atg 0.2.0 written to /workspace/builds/worker-94/source/Cargo.toml [INFO] crate crates.io crate atg 0.2.0 already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+a77da2d454e6caa227a85b16410b95f93495e7e0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-94/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-94/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@sha256:5736fa189c1c60b01babf4b8b698fe57b6ecc41933a7ff2e0b8d7a221459412b" "/opt/rustwide/cargo-home/bin/cargo" "+a77da2d454e6caa227a85b16410b95f93495e7e0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 86dbdeac75c4965edc0dc5414e241de759eee0537f2e2b6e0775a78227c769e6 [INFO] running `Command { std: "docker" "start" "-a" "86dbdeac75c4965edc0dc5414e241de759eee0537f2e2b6e0775a78227c769e6", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "86dbdeac75c4965edc0dc5414e241de759eee0537f2e2b6e0775a78227c769e6", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "86dbdeac75c4965edc0dc5414e241de759eee0537f2e2b6e0775a78227c769e6", kill_on_drop: false }` [INFO] [stdout] 86dbdeac75c4965edc0dc5414e241de759eee0537f2e2b6e0775a78227c769e6 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-94/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-94/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@sha256:5736fa189c1c60b01babf4b8b698fe57b6ecc41933a7ff2e0b8d7a221459412b" "/opt/rustwide/cargo-home/bin/cargo" "+a77da2d454e6caa227a85b16410b95f93495e7e0" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 96174805821f865d537ac52c44cd0987c609164071d4aa91fbcc9d1c87e52900 [INFO] running `Command { std: "docker" "start" "-a" "96174805821f865d537ac52c44cd0987c609164071d4aa91fbcc9d1c87e52900", kill_on_drop: false }` [INFO] [stderr] Compiling libc v0.2.102 [INFO] [stderr] Compiling log v0.4.14 [INFO] [stderr] Compiling cfg-if v1.0.0 [INFO] [stderr] Compiling unicode-width v0.1.9 [INFO] [stderr] Compiling ansi_term v0.12.1 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling strsim v0.8.0 [INFO] [stderr] Compiling bitflags v1.3.2 [INFO] [stderr] Compiling ansi_term v0.11.0 [INFO] [stderr] Compiling textwrap v0.11.0 [INFO] [stderr] Compiling atty v0.2.14 [INFO] [stderr] Compiling clap v2.33.3 [INFO] [stderr] Compiling loggerv v0.7.2 [INFO] [stderr] Compiling atg v0.2.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: field is never read: `message` [INFO] [stdout] --> src/utils/errors.rs:121:5 [INFO] [stdout] | [INFO] [stdout] 121 | message: String, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 1 warning emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 17.17s [INFO] running `Command { std: "docker" "inspect" "96174805821f865d537ac52c44cd0987c609164071d4aa91fbcc9d1c87e52900", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "96174805821f865d537ac52c44cd0987c609164071d4aa91fbcc9d1c87e52900", kill_on_drop: false }` [INFO] [stdout] 96174805821f865d537ac52c44cd0987c609164071d4aa91fbcc9d1c87e52900 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-94/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-94/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@sha256:5736fa189c1c60b01babf4b8b698fe57b6ecc41933a7ff2e0b8d7a221459412b" "/opt/rustwide/cargo-home/bin/cargo" "+a77da2d454e6caa227a85b16410b95f93495e7e0" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 1b61a5c68f192f65d3ef6b4c53e56e1f85963f02034df64f17339318bbc49d59 [INFO] running `Command { std: "docker" "start" "-a" "1b61a5c68f192f65d3ef6b4c53e56e1f85963f02034df64f17339318bbc49d59", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] Compiling atg v0.2.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: field is never read: `message` [INFO] [stdout] --> src/utils/errors.rs:121:5 [INFO] [stdout] | [INFO] [stdout] 121 | message: String, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 1 warning emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field is never read: `message` [INFO] [stdout] --> src/utils/errors.rs:121:5 [INFO] [stdout] | [INFO] [stdout] 121 | message: String, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: 1 warning emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 20.71s [INFO] running `Command { std: "docker" "inspect" "1b61a5c68f192f65d3ef6b4c53e56e1f85963f02034df64f17339318bbc49d59", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "1b61a5c68f192f65d3ef6b4c53e56e1f85963f02034df64f17339318bbc49d59", kill_on_drop: false }` [INFO] [stdout] 1b61a5c68f192f65d3ef6b4c53e56e1f85963f02034df64f17339318bbc49d59 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-94/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-94/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@sha256:5736fa189c1c60b01babf4b8b698fe57b6ecc41933a7ff2e0b8d7a221459412b" "/opt/rustwide/cargo-home/bin/cargo" "+a77da2d454e6caa227a85b16410b95f93495e7e0" "test" "--frozen", kill_on_drop: false }` [INFO] [stdout] 81f5c6462e9ad2a8208e9f772e97e5c0e3653fcb278607a1e4ec4fde11445c22 [INFO] running `Command { std: "docker" "start" "-a" "81f5c6462e9ad2a8208e9f772e97e5c0e3653fcb278607a1e4ec4fde11445c22", kill_on_drop: false }` [INFO] [stderr] Blocking waiting for file lock on package cache [INFO] [stderr] warning: field is never read: `message` [INFO] [stderr] --> src/utils/errors.rs:121:5 [INFO] [stderr] | [INFO] [stderr] 121 | message: String, [INFO] [stderr] | ^^^^^^^^^^^^^^^ [INFO] [stderr] | [INFO] [stderr] = note: `#[warn(dead_code)]` on by default [INFO] [stderr] [INFO] [stderr] warning: `atg` (lib) generated 1 warning [INFO] [stderr] warning: `atg` (lib test) generated 1 warning (1 duplicate) [INFO] [stderr] Finished test [unoptimized + debuginfo] target(s) in 0.23s [INFO] [stderr] Running unittests (/opt/rustwide/target/debug/deps/atg-0ca595e56a4ea911) [INFO] [stdout] [INFO] [stdout] running 66 tests [INFO] [stdout] test gtf::reader::test_ighm::test_read ... ok [INFO] [stdout] test gtf::reader::test_nm_201550::test_read ... ok [INFO] [stdout] test gtf::reader::test_nm_001385228::test_read ... ok [INFO] [stdout] test gtf::record::tests::test_attributes_parsing ... ok [INFO] [stdout] test gtf::record::tests::test_single_attribute_parsing ... ok [INFO] [stdout] test gtf::reader::tests::test_nm_001365057 ... ok [INFO] [stdout] test gtf::reader::tests::test_nm_001371720 ... ok [INFO] [stdout] test gtf::reader::tests::test_nm_201550 ... ok [INFO] [stdout] test models::test_codon::test_codon_builder ... ok [INFO] [stdout] test gtf::reader::tests::test_nm_001365408 ... ok [INFO] [stdout] test models::test_start_codon::case_1 ... ok [INFO] [stdout] test gtf::writer::tests::test_nm_001371720 ... ok [INFO] [stdout] test gtf::writer::tests::test_nm_001365057 ... ok [INFO] [stdout] test gtf::writer::tests::test_nm_201550 ... ok [INFO] [stdout] test models::test_start_codon::case_4 ... ok [INFO] [stdout] test models::test_start_codon::case_2 ... ok [INFO] [stdout] test models::test_start_codon::case_3 ... ok [INFO] [stdout] test gtf::writer::tests::test_nm_001365408 ... ok [INFO] [stdout] test models::test_start_codon::case_5 ... ok [INFO] [stdout] test models::test_start_codon::case_6 ... ok [INFO] [stdout] test models::test_stop_codon::case_1 ... ok [INFO] [stdout] test models::test_stop_codon::case_2 ... ok [INFO] [stdout] test models::test_stop_codon::case_3 ... ok [INFO] [stdout] test models::test_stop_codon::case_4 ... ok [INFO] [stdout] test models::test_stop_codon::case_6 ... ok [INFO] [stdout] test models::test_stop_codon::case_5 ... ok [INFO] [stdout] test models::tests::test_exon_downstream_frame ... ok [INFO] [stdout] test models::tests::test_frame_addition ... ok [INFO] [stdout] test models::tests::test_special_transcripts ... ok [INFO] [stdout] test models::tests::test_transcript ... ok [INFO] [stdout] test refgene::reader::tests::test_missing_exon_frame ... ok [INFO] [stdout] test refgene::reader::tests::test_missing_exon_start ... ok [INFO] [stdout] test refgene::reader::tests::test_missing_exon_stop ... ok [INFO] [stdout] test refgene::reader::tests::test_nm_001365057 ... ok [INFO] [stdout] test refgene::reader::tests::test_nm_001365408 ... ok [INFO] [stdout] test refgene::reader::tests::test_nm_001371720 ... ok [INFO] [stdout] test refgene::reader::tests::test_nm_201550 ... ok [INFO] [stdout] test refgene::reader::tests::test_parse_exons_no_cds ... ok [INFO] [stdout] test refgene::reader::tests::test_wrong_exon_frame ... ok [INFO] [stdout] test refgene::tests::test_parse_exons_with_cds ... ok [INFO] [stdout] test refgene::tests::test_transcript_building ... ok [INFO] [stdout] test refgene::writer::tests::test_nm_001365057 ... ok [INFO] [stdout] test refgene::writer::tests::test_nm_001365408 ... ok [INFO] [stdout] test refgene::tests::test_parsing_and_composing ... ok [INFO] [stdout] test refgene::writer::tests::test_nm_201550 ... ok [INFO] [stdout] test utils::genomic_relations::test_intersect::test_a_fully_in_b ... ok [INFO] [stdout] test refgene::writer::tests::test_nm_001371720 ... ok [INFO] [stdout] test utils::genomic_relations::test_intersect::test_left_overlap ... ok [INFO] [stdout] test utils::genomic_relations::test_intersect::test_b_fully_in_a ... ok [INFO] [stdout] test utils::genomic_relations::test_intersect::test_no_overlap ... ok [INFO] [stdout] test utils::genomic_relations::test_intersect::test_right_overlap ... ok [INFO] [stdout] test utils::genomic_relations::test_overlap::test_cds_overlap ... ok [INFO] [stdout] test utils::genomic_relations::test_relation::test_downstream ... ok [INFO] [stdout] test utils::genomic_relations::test_relation::test_inside ... ok [INFO] [stdout] test utils::genomic_relations::test_relation::test_left ... ok [INFO] [stdout] test utils::genomic_relations::test_relation::test_match ... ok [INFO] [stdout] test utils::genomic_relations::test_relation::test_overlaps ... ok [INFO] [stdout] test utils::genomic_relations::test_relation::test_upstream ... ok [INFO] [stdout] test utils::genomic_relations::test_relation::test_right ... ok [INFO] [stdout] test utils::genomic_relations::test_subtraction::test_case_1 ... ok [INFO] [stdout] test utils::genomic_relations::test_subtraction::test_case_2 ... ok [INFO] [stdout] test utils::genomic_relations::test_subtraction::test_case_3 ... ok [INFO] [stdout] test utils::genomic_relations::test_subtraction::test_case_4 ... ok [INFO] [stdout] test utils::genomic_relations::test_subtraction::test_case_5 ... ok [INFO] [stdout] test utils::genomic_relations::test_subtraction::test_case_6 ... ok [INFO] [stdout] test utils::genomic_relations::test_subtraction::test_case_7 ... ok [INFO] [stdout] [INFO] [stdout] test result: ok. 66 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.01s [INFO] [stdout] [INFO] [stderr] Running unittests (/opt/rustwide/target/debug/deps/atg-5781541b1f3dfbbe) [INFO] [stdout] [INFO] [stdout] running 0 tests [INFO] [stdout] [INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s [INFO] [stdout] [INFO] [stderr] Doc-tests atg [INFO] [stdout] [INFO] [stdout] running 32 tests [INFO] [stdout] test src/lib.rs - (line 41) - compile ... ok [INFO] [stdout] test src/gtf/reader.rs - gtf::reader::Reader::from_file (line 50) ... FAILED [INFO] [stdout] test src/gtf/reader.rs - gtf::reader::Reader::transcripts (line 126) ... FAILED [INFO] [stdout] test src/models/exon.rs - models::exon::Exon (line 10) ... ok [INFO] [stdout] test src/gtf/reader.rs - gtf::reader::Reader (line 22) ... FAILED [INFO] [stdout] test src/utils/genomic_relations.rs - utils::genomic_relations::exon_cds_overlap (line 171) ... ok [INFO] [stdout] test src/models/codon.rs - models::codon::Codon::from_transcript (line 41) ... ok [INFO] [stdout] test src/models/frame.rs - models::frame::Frame (line 15) ... ok [INFO] [stdout] test src/models/exon.rs - models::exon::Exon::new (line 38) ... ok [INFO] [stdout] test src/models/exon.rs - models::exon::Exon::is_coding (line 124) ... ok [INFO] [stdout] test src/models/transcript.rs - models::transcript::TranscriptBuilder (line 329) ... ok [INFO] [stdout] test src/gtf/record.rs - gtf::record::GtfRecordBuilder (line 368) ... ok [INFO] [stdout] test src/models/frame.rs - models::frame::Frame::to_gtf (line 108) ... ok [INFO] [stdout] test src/models/frame.rs - models::frame::Frame::to_refgene (line 127) ... ok [INFO] [stdout] test src/utils/genomic_relations.rs - utils::genomic_relations::subtract (line 91) ... ok [INFO] [stdout] test src/models/utils.rs - models::utils::parse_chrom (line 136) ... ok [INFO] [stdout] test src/models/transcript.rs - models::transcript::TranscriptBuilder::new (line 365) ... ok [INFO] [stdout] test src/utils/genomic_relations.rs - utils::genomic_relations::relation (line 142) ... ok [INFO] [stdout] test src/models/frame.rs - models::frame::Frame::from_gtf (line 65) ... ok [INFO] [stdout] test src/models/transcripts.rs - models::transcripts::Transcripts::by_name (line 63) ... ok [INFO] [stdout] test src/models/transcripts.rs - models::transcripts::Transcripts::by_gene (line 94) ... ok [INFO] [stdout] test src/gtf/writer.rs - gtf::writer::Writer (line 17) ... ok [INFO] [stdout] test src/utils/genomic_relations.rs - utils::genomic_relations::union (line 66) ... ok [INFO] [stdout] test src/refgene/reader.rs - refgene::reader::Reader::from_file (line 54) ... ok [INFO] [stdout] test src/refgene/writer.rs - refgene::writer::Writer (line 14) ... ok [INFO] [stdout] test src/refgene/reader.rs - refgene::reader::Reader (line 26) ... ok [INFO] [stdout] test src/refgene/reader.rs - refgene::reader::Reader::transcripts (line 131) ... ok [INFO] [stdout] test src/models/transcripts.rs - models::transcripts::Transcripts (line 11) ... ok [INFO] [stdout] test src/utils/genomic_relations.rs - utils::genomic_relations::intersect (line 42) ... ok [INFO] [stdout] test src/models/utils.rs - models::utils::Strand (line 57) ... ok [INFO] [stdout] test src/models/frame.rs - models::frame::Frame::from_refgene (line 84) ... ok [INFO] [stdout] test src/models/transcripts.rs - models::transcripts::Transcripts::push (line 125) ... ok [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] [INFO] [stdout] ---- src/gtf/reader.rs - gtf::reader::Reader::from_file (line 50) stdout ---- [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/gtf/reader.rs - gtf::reader::Reader::transcripts (line 126) stdout ---- [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] ---- src/gtf/reader.rs - gtf::reader::Reader (line 22) stdout ---- [INFO] [stdout] Couldn't compile the test. [INFO] [stdout] [INFO] [stdout] failures: [INFO] [stdout] src/gtf/reader.rs - gtf::reader::Reader (line 22) [INFO] [stdout] src/gtf/reader.rs - gtf::reader::Reader::from_file (line 50) [INFO] [stdout] src/gtf/reader.rs - gtf::reader::Reader::transcripts (line 126) [INFO] [stdout] [INFO] [stdout] test result: FAILED. 29 passed; 3 failed; 0 ignored; 0 measured; 0 filtered out; finished in 8.82s [INFO] [stdout] [INFO] [stderr] error: test failed, to rerun pass '--doc' [INFO] running `Command { std: "docker" "inspect" "81f5c6462e9ad2a8208e9f772e97e5c0e3653fcb278607a1e4ec4fde11445c22", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "81f5c6462e9ad2a8208e9f772e97e5c0e3653fcb278607a1e4ec4fde11445c22", kill_on_drop: false }` [INFO] [stdout] 81f5c6462e9ad2a8208e9f772e97e5c0e3653fcb278607a1e4ec4fde11445c22