[INFO] updating cached repository https://github.com/chfi/rs-gfa-utils [INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "-c" "remote.origin.fetch=refs/heads/*:refs/heads/*" "fetch" "origin" "--force" "--prune", kill_on_drop: false }` [INFO] [stderr] From https://github.com/chfi/rs-gfa-utils [INFO] [stderr] 8e6b180..ebd427e master -> master [INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }` [INFO] [stdout] ebd427e8b7759ff54179c7a408030e750e9f5b7c [INFO] checking chfi/rs-gfa-utils against master#e22b61bff0bdd08be7665607cb7be3748c8a35d2 for pr-74627 [INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fchfi%2Frs-gfa-utils" "/workspace/builds/worker-9/source", kill_on_drop: false }` [INFO] [stderr] Cloning into '/workspace/builds/worker-9/source'... [INFO] [stderr] done. [INFO] validating manifest of git repo https://github.com/chfi/rs-gfa-utils on toolchain e22b61bff0bdd08be7665607cb7be3748c8a35d2 [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+e22b61bff0bdd08be7665607cb7be3748c8a35d2" "read-manifest" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] started tweaking git repo https://github.com/chfi/rs-gfa-utils [INFO] removed path dependency gfa from git repo https://github.com/chfi/rs-gfa-utils [INFO] removed path dependency handlegraph from git repo https://github.com/chfi/rs-gfa-utils [INFO] finished tweaking git repo https://github.com/chfi/rs-gfa-utils [INFO] tweaked toml for git repo https://github.com/chfi/rs-gfa-utils written to /workspace/builds/worker-9/source/Cargo.toml [INFO] crate git repo https://github.com/chfi/rs-gfa-utils already has a lockfile, it will not be regenerated [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+e22b61bff0bdd08be7665607cb7be3748c8a35d2" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] warning: dependency (gfa) specified without providing a local path, Git repository, or version to use. This will be considered an error in future versions [INFO] [stderr] warning: dependency (handlegraph) specified without providing a local path, Git repository, or version to use. This will be considered an error in future versions [INFO] [stderr] Updating crates.io index [INFO] [stderr] error: the lock file /workspace/builds/worker-9/source/Cargo.lock needs to be updated but --locked was passed to prevent this [INFO] [stderr] If you want to try to generate the lock file without accessing the network, use the --offline flag. [INFO] the lockfile is outdated, regenerating it [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+e22b61bff0bdd08be7665607cb7be3748c8a35d2" "generate-lockfile" "--manifest-path" "Cargo.toml" "-Zno-index-update", kill_on_drop: false }` [INFO] running `Command { std: "/workspace/cargo-home/bin/cargo" "+e22b61bff0bdd08be7665607cb7be3748c8a35d2" "fetch" "--locked" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] warning: dependency (gfa) specified without providing a local path, Git repository, or version to use. This will be considered an error in future versions [INFO] [stderr] warning: dependency (handlegraph) specified without providing a local path, Git repository, or version to use. This will be considered an error in future versions [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-9/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-9/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" "MAP_USER_ID=0" "-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" "--network" "none" "rustops/crates-build-env@sha256:a636fd89d022f18117e1dc8fb37a0a009933cdbbe082814857f0e2024962d47c" "/opt/rustwide/cargo-home/bin/cargo" "+e22b61bff0bdd08be7665607cb7be3748c8a35d2" "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] f07a45fb8936404074c88cbd1e0c1c1dbf94608272e34259576cd77205804ffd [INFO] running `Command { std: "docker" "start" "-a" "f07a45fb8936404074c88cbd1e0c1c1dbf94608272e34259576cd77205804ffd", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "f07a45fb8936404074c88cbd1e0c1c1dbf94608272e34259576cd77205804ffd", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "f07a45fb8936404074c88cbd1e0c1c1dbf94608272e34259576cd77205804ffd", kill_on_drop: false }` [INFO] [stdout] f07a45fb8936404074c88cbd1e0c1c1dbf94608272e34259576cd77205804ffd [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-9/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-9/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" "MAP_USER_ID=0" "-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" "--network" "none" "rustops/crates-build-env@sha256:a636fd89d022f18117e1dc8fb37a0a009933cdbbe082814857f0e2024962d47c" "/opt/rustwide/cargo-home/bin/cargo" "+e22b61bff0bdd08be7665607cb7be3748c8a35d2" "check" "--frozen" "--all" "--all-targets" "--message-format=json", 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] 5510054a1ecd27a580cfdb3b056708c4eaf4befcb092d64aeb2f62c81c21e785 [INFO] running `Command { std: "docker" "start" "-a" "5510054a1ecd27a580cfdb3b056708c4eaf4befcb092d64aeb2f62c81c21e785", kill_on_drop: false }` [INFO] [stderr] warning: dependency (gfa) specified without providing a local path, Git repository, or version to use. This will be considered an error in future versions [INFO] [stderr] warning: dependency (handlegraph) specified without providing a local path, Git repository, or version to use. This will be considered an error in future versions [INFO] [stderr] Compiling autocfg v1.0.0 [INFO] [stderr] Compiling maybe-uninit v2.0.0 [INFO] [stderr] Compiling syn v1.0.36 [INFO] [stderr] Compiling lexical-core v0.7.4 [INFO] [stderr] Compiling byteorder v1.3.4 [INFO] [stderr] Checking regex-syntax v0.6.18 [INFO] [stderr] Compiling rayon-core v1.7.1 [INFO] [stderr] Checking arrayvec v0.5.1 [INFO] [stderr] Checking static_assertions v1.1.0 [INFO] [stderr] Checking scopeguard v1.1.0 [INFO] [stderr] Compiling serde_derive v1.0.114 [INFO] [stderr] Compiling unicode-segmentation v1.6.0 [INFO] [stderr] Checking ansi_term v0.11.0 [INFO] [stderr] Compiling serde v1.0.114 [INFO] [stderr] Checking strsim v0.8.0 [INFO] [stderr] Checking vec_map v0.8.2 [INFO] [stderr] Checking either v1.5.3 [INFO] [stderr] Checking thread_local v1.0.1 [INFO] [stderr] Compiling proc-macro-error-attr v1.0.4 [INFO] [stderr] Compiling nom v5.1.2 [INFO] [stderr] Compiling proc-macro-error v1.0.4 [INFO] [stderr] Checking atty v0.2.14 [INFO] [stderr] Checking aho-corasick v0.7.13 [INFO] [stderr] Checking clap v2.33.1 [INFO] [stderr] Compiling crossbeam-utils v0.7.2 [INFO] [stderr] Compiling memoffset v0.5.5 [INFO] [stderr] Compiling crossbeam-epoch v0.8.2 [INFO] [stderr] Compiling rayon v1.3.1 [INFO] [stderr] Compiling heck v0.3.1 [INFO] [stderr] Checking regex-automata v0.1.9 [INFO] [stderr] Checking bstr v0.2.13 [INFO] [stderr] Checking crossbeam-queue v0.2.3 [INFO] [stderr] Checking crossbeam-deque v0.7.3 [INFO] [stderr] Checking regex v1.3.9 [INFO] [stderr] Checking gfa v0.5.0 [INFO] [stderr] Checking gfa v0.2.3 [INFO] [stderr] Checking handlegraph v0.2.0 [INFO] [stderr] Compiling structopt-derive v0.4.8 [INFO] [stderr] Checking structopt v0.3.15 [INFO] [stderr] Checking gfautil v0.1.0 (/opt/rustwide/workdir) [INFO] [stdout] error[E0432]: unresolved imports `gfa::gafpaf::CIGAROp`, `gfa::gafpaf::GAFPath`, `gfa::gafpaf::GAFStep`, `gfa::gafpaf::CIGAR` [INFO] [stdout] --> src/gaf_convert.rs:11:25 [INFO] [stdout] | [INFO] [stdout] 11 | gafpaf::{parse_gaf, CIGAROp, GAFPath, GAFStep, CIGAR}, [INFO] [stdout] | ^^^^^^^ ^^^^^^^ ^^^^^^^ ^^^^^ no `CIGAR` in `gafpaf` [INFO] [stdout] | | | | [INFO] [stdout] | | | no `GAFStep` in `gafpaf` [INFO] [stdout] | | no `GAFPath` in `gafpaf` [INFO] [stdout] | no `CIGAROp` in `gafpaf` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `prelude::*` [INFO] [stdout] --> src/gaf_convert.rs:4:10 [INFO] [stdout] | [INFO] [stdout] 4 | io::{prelude::*, BufReader}, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `BStr` [INFO] [stdout] --> src/gaf_convert.rs:8:19 [INFO] [stdout] | [INFO] [stdout] 8 | use bstr::{io::*, BStr, BString, ByteSlice, ByteVec}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `BStr` [INFO] [stdout] --> src/subgraph.rs:7:12 [INFO] [stdout] | [INFO] [stdout] 7 | use bstr::{BStr, BString}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0432]: unresolved imports `gfa::gafpaf::CIGAROp`, `gfa::gafpaf::GAFPath`, `gfa::gafpaf::GAFStep`, `gfa::gafpaf::CIGAR` [INFO] [stdout] --> src/gaf_convert.rs:11:25 [INFO] [stdout] | [INFO] [stdout] 11 | gafpaf::{parse_gaf, CIGAROp, GAFPath, GAFStep, CIGAR}, [INFO] [stdout] | ^^^^^^^ ^^^^^^^ ^^^^^^^ ^^^^^ no `CIGAR` in `gafpaf` [INFO] [stdout] | | | | [INFO] [stdout] | | | no `GAFStep` in `gafpaf` [INFO] [stdout] | | no `GAFPath` in `gafpaf` [INFO] [stdout] | no `CIGAROp` in `gafpaf` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `prelude::*` [INFO] [stdout] --> src/gaf_convert.rs:4:10 [INFO] [stdout] | [INFO] [stdout] 4 | io::{prelude::*, BufReader}, [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `BStr` [INFO] [stdout] --> src/gaf_convert.rs:8:19 [INFO] [stdout] | [INFO] [stdout] 8 | use bstr::{io::*, BStr, BString, ByteSlice, ByteVec}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `BStr` [INFO] [stdout] --> src/subgraph.rs:7:12 [INFO] [stdout] | [INFO] [stdout] 7 | use bstr::{BStr, BString}; [INFO] [stdout] | ^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `handles_iter` found for reference `&T` in the current scope [INFO] [stdout] --> src/edges.rs:10:10 [INFO] [stdout] | [INFO] [stdout] 10 | .handles_iter() [INFO] [stdout] | ^^^^^^^^^^^^ method not found in `&T` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0609]: no field `0` on type `std::ops::Range` [INFO] [stdout] --> src/gaf_convert.rs:143:49 [INFO] [stdout] | [INFO] [stdout] 143 | let mut query_index = gaf.seq_range.0; [INFO] [stdout] | ^ unknown field [INFO] [stdout] | [INFO] [stdout] = note: available fields are: `start`, `end` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0609]: no field `0` on type `std::ops::Range` [INFO] [stdout] --> src/gaf_convert.rs:144:49 [INFO] [stdout] | [INFO] [stdout] 144 | let mut tgt_offset = gaf.path_range.0; [INFO] [stdout] | ^ unknown field [INFO] [stdout] | [INFO] [stdout] = note: available fields are: `start`, `end` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0599]: no method named `handles_iter` found for reference `&T` in the current scope [INFO] [stdout] --> src/edges.rs:10:10 [INFO] [stdout] | [INFO] [stdout] 10 | .handles_iter() [INFO] [stdout] | ^^^^^^^^^^^^ method not found in `&T` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0308]: mismatched types [INFO] [stdout] --> src/gaf_convert.rs:189:38 [INFO] [stdout] | [INFO] [stdout] 189 | query_seq_range: (query_start, query_end), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ expected struct `std::ops::Range`, found tuple [INFO] [stdout] | [INFO] [stdout] = note: expected struct `std::ops::Range` [INFO] [stdout] found tuple `(_, _)` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0609]: no field `0` on type `std::ops::Range` [INFO] [stdout] --> src/gaf_convert.rs:143:49 [INFO] [stdout] | [INFO] [stdout] 143 | let mut query_index = gaf.seq_range.0; [INFO] [stdout] | ^ unknown field [INFO] [stdout] | [INFO] [stdout] = note: available fields are: `start`, `end` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0609]: no field `0` on type `std::ops::Range` [INFO] [stdout] --> src/gaf_convert.rs:144:49 [INFO] [stdout] | [INFO] [stdout] 144 | let mut tgt_offset = gaf.path_range.0; [INFO] [stdout] | ^ unknown field [INFO] [stdout] | [INFO] [stdout] = note: available fields are: `start`, `end` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0308]: mismatched types [INFO] [stdout] --> src/gaf_convert.rs:193:21 [INFO] [stdout] | [INFO] [stdout] 193 | target_seq_range, [INFO] [stdout] | ^^^^^^^^^^^^^^^^ expected struct `std::ops::Range`, found tuple [INFO] [stdout] | [INFO] [stdout] = note: expected struct `std::ops::Range` [INFO] [stdout] found tuple `(_, _)` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ByteVec` [INFO] [stdout] --> src/gaf_convert.rs:8:45 [INFO] [stdout] | [INFO] [stdout] 8 | use bstr::{io::*, BStr, BString, ByteSlice, ByteVec}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error[E0308]: mismatched types [INFO] [stdout] --> src/gaf_convert.rs:189:38 [INFO] [stdout] | [INFO] [stdout] 189 | query_seq_range: (query_start, query_end), [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^ expected struct `std::ops::Range`, found tuple [INFO] [stdout] | [INFO] [stdout] = note: expected struct `std::ops::Range` [INFO] [stdout] found tuple `(_, _)` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 6 previous errors; 4 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0308, E0432, E0599, E0609. [INFO] [stdout] [INFO] [stdout] For more information about an error, try `rustc --explain E0308`. [INFO] [stdout] [INFO] [stderr] error: could not compile `gfautil`. [INFO] [stderr] [INFO] [stderr] To learn more, run the command again with --verbose. [INFO] [stderr] warning: build failed, waiting for other jobs to finish... [INFO] [stdout] error[E0308]: mismatched types [INFO] [stdout] --> src/gaf_convert.rs:193:21 [INFO] [stdout] | [INFO] [stdout] 193 | target_seq_range, [INFO] [stdout] | ^^^^^^^^^^^^^^^^ expected struct `std::ops::Range`, found tuple [INFO] [stdout] | [INFO] [stdout] = note: expected struct `std::ops::Range` [INFO] [stdout] found tuple `(_, _)` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `ByteVec` [INFO] [stdout] --> src/gaf_convert.rs:8:45 [INFO] [stdout] | [INFO] [stdout] 8 | use bstr::{io::*, BStr, BString, ByteSlice, ByteVec}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] error: aborting due to 6 previous errors; 4 warnings emitted [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] Some errors have detailed explanations: E0308, E0432, E0599, E0609. [INFO] [stdout] [INFO] [stdout] For more information about an error, try `rustc --explain E0308`. [INFO] [stdout] [INFO] [stderr] error: build failed [INFO] running `Command { std: "docker" "inspect" "5510054a1ecd27a580cfdb3b056708c4eaf4befcb092d64aeb2f62c81c21e785", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "5510054a1ecd27a580cfdb3b056708c4eaf4befcb092d64aeb2f62c81c21e785", kill_on_drop: false }` [INFO] [stdout] 5510054a1ecd27a580cfdb3b056708c4eaf4befcb092d64aeb2f62c81c21e785