Build #360116 2021-03-09T22:27:51.893138+00:00
# rustc version
rustc 1.52.0-nightly (8f349be27 2021-03-08)
# docs.rs version
docsrs 0.6.0 (918ee5d 2021-03-06)
# build log
[INFO] running `Command { std: "docker" "create" "-v" "/home/cratesfyi/workspace/builds/bio-0.33.0/target:/opt/rustwide/target:rw,Z" "-v" "/home/cratesfyi/workspace/builds/bio-0.33.0/source:/opt/rustwide/workdir:ro,Z" "-v" "/home/cratesfyi/workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/home/cratesfyi/workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "DOCS_RS=1" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "3221225472" "--cpus" "2" "--user" "1001:1001" "--network" "none" "rustops/crates-build-env@sha256:f2f6bcd4b43ebee4e173f653a26493129bdb64017c85f916b780ca7fbdbaa79d" "/opt/rustwide/cargo-home/bin/cargo" "+nightly" "rustdoc" "--lib" "-Zrustdoc-map" "-Zunstable-options" "--config=doc.extern-map.registries.crates-io=\"https://docs.rs\"" "-j2" "--" "-Z" "unstable-options" "--resource-suffix" "-20210308-1.52.0-nightly-8f349be27" "--static-root-path" "/" "--cap-lints" "warn" "--disable-per-crate-search", kill_on_drop: false }`
[INFO] [stdout] 565c027850d7ae89028d7a5fad6331c3ca9d055c9f48a9da534dcb0f5f9f104e
[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" "565c027850d7ae89028d7a5fad6331c3ca9d055c9f48a9da534dcb0f5f9f104e", kill_on_drop: false }`
[INFO] [stderr] /opt/crates-build-env/entrypoint.sh: line 7: /etc/hosts: Permission denied
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[INFO] [stderr] Documenting bio v0.33.0 (/opt/rustwide/workdir)
[INFO] [stderr] warning: could not parse code block as Rust code
[INFO] [stderr] --> /opt/rustwide/cargo-home/registry/src/github.com-1ecc6299db9ec823/nalgebra-0.19.0/src/base/storage.rs:61:9
[INFO] [stderr] |
[INFO] [stderr] 61 | /// ```.ignore
[INFO] [stderr] | _________^
[INFO] [stderr] 62 | | /// let lindex = self.linear_index(irow, icol);
[INFO] [stderr] 63 | | /// assert!(*self.get_unchecked(irow, icol) == *self.get_unchecked_linear(lindex)
[INFO] [stderr] 64 | | /// ```
[INFO] [stderr] | |___________^
[INFO] [stderr] |
[INFO] [stderr] = note: error from rustc: this file contains an unclosed delimiter
[INFO] [stderr] help: `ignore` code blocks require valid Rust code for syntax highlighting. Mark blocks that do not contain Rust code as text
[INFO] [stderr] |
[INFO] [stderr] 61 | /// ```text,.ignore
[INFO] [stderr] | ^^^^^^^^
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/alignment/poa.rs:15:5
[INFO] [stderr] |
[INFO] [stderr] 15 | //! https://github.com/ljdursi/poapy
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/ljdursi/poapy>`
[INFO] [stderr] |
[INFO] [stderr] = note: `#[warn(rustdoc::non_autolinks)]` on by default
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/alignment/sparse.rs:51:17
[INFO] [stderr] |
[INFO] [stderr] 51 | /// Paper here :https://arxiv.org/abs/1407.2407. Original implementation here:
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://arxiv.org/abs/1407.2407.>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/alignment/sparse.rs:52:5
[INFO] [stderr] |
[INFO] [stderr] 52 | /// https://github.com/fpavetic/lcskpp
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/fpavetic/lcskpp>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/data_structures/bit_tree.rs:8:35
[INFO] [stderr] |
[INFO] [stderr] 8 | //! Implementation outlined here: https://www.topcoder.com/community/data-science/data-science-tutorials/binary-indexed-trees/
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://www.topcoder.com/community/data-science/data-science-tutorials/binary-indexed-trees/>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/data_structures/interval_tree/array_backed_interval_tree.rs:4:5
[INFO] [stderr] |
[INFO] [stderr] 4 | //! https://github.com/lh3/cgranges / https://github.com/lh3/cgranges/blob/master/cpp/IITree.h
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/lh3/cgranges>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/data_structures/interval_tree/array_backed_interval_tree.rs:4:39
[INFO] [stderr] |
[INFO] [stderr] 4 | //! https://github.com/lh3/cgranges / https://github.com/lh3/cgranges/blob/master/cpp/IITree.h
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/lh3/cgranges/blob/master/cpp/IITree.h>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/data_structures/suffix_array.rs:181:5
[INFO] [stderr] |
[INFO] [stderr] 181 | /// http://ls11-www.cs.tu-dortmund.de/people/rahmann/algoseq.pdf
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://ls11-www.cs.tu-dortmund.de/people/rahmann/algoseq.pdf>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/io/bed.rs:120:6
[INFO] [stderr] |
[INFO] [stderr] 120 | /// (http://bedtools.readthedocs.org/en/latest/content/general-usage.html)
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://bedtools.readthedocs.org/en/latest/content/general-usage.html>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/io/gff.rs:8:23
[INFO] [stderr] |
[INFO] [stderr] 8 | //! GFF2 definition : http://gmod.org/wiki/GFF2#The_GFF2_File_Format (not yet support)
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://gmod.org/wiki/GFF2#The_GFF2_File_Format>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/io/gff.rs:9:23
[INFO] [stderr] |
[INFO] [stderr] 9 | //! GTF2 definition : http://mblab.wustl.edu/GTF2.html (not yet support)
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://mblab.wustl.edu/GTF2.html>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/io/gff.rs:10:23
[INFO] [stderr] |
[INFO] [stderr] 10 | //! GFF3 definition : http://gmod.org/wiki/GFF3#GFF3_Format
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://gmod.org/wiki/GFF3#GFF3_Format>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/pattern_matching/mod.rs:18:79
[INFO] [stderr] |
[INFO] [stderr] 18 | //! Another fast pattern matching algorithm is available in the twoway crate: https://crates.io/crates/twoway
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://crates.io/crates/twoway>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/pattern_matching/pssm/dnamotif.rs:31:9
[INFO] [stderr] |
[INFO] [stderr] 31 | /// https://github.com/rust-lang/rust/issues/42863
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/rust-lang/rust/issues/42863>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/pattern_matching/pssm/protmotif.rs:31:9
[INFO] [stderr] |
[INFO] [stderr] 31 | /// https://github.com/rust-lang/rust/issues/42863
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://github.com/rust-lang/rust/issues/42863>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/pattern_matching/pssm/mod.rs:231:11
[INFO] [stderr] |
[INFO] [stderr] 231 | /// https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169193/
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169193/>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/pattern_matching/pssm/mod.rs:280:12
[INFO] [stderr] |
[INFO] [stderr] 280 | /// https://en.wikipedia.org/wiki/Sequence_logo#Logo_creation
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://en.wikipedia.org/wiki/Sequence_logo#Logo_creation>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/stats/pairhmm/mod.rs:3:45
[INFO] [stderr] |
[INFO] [stderr] 3 | //! Current Topics in Genome Analysis 2008. http://doi.org/10.1017/CBO9780511790492.
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://doi.org/10.1017/CBO9780511790492.>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/stats/pairhmm/homopolypairhmm.rs:170:45
[INFO] [stderr] |
[INFO] [stderr] 170 | /// Current Topics in Genome Analysis 2008. http://doi.org/10.1017/CBO9780511790492.
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://doi.org/10.1017/CBO9780511790492.>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/stats/pairhmm/pairhmm.rs:46:45
[INFO] [stderr] |
[INFO] [stderr] 46 | /// Current Topics in Genome Analysis 2008. http://doi.org/10.1017/CBO9780511790492.
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<http://doi.org/10.1017/CBO9780511790492.>`
[INFO] [stderr]
[INFO] [stderr] warning: this URL is not a hyperlink
[INFO] [stderr] --> src/utils/fastexp.rs:32:9
[INFO] [stderr] |
[INFO] [stderr] 32 | /// https://eldorado.tu-dortmund.de/bitstream/2003/36203/1/Dissertation_Kopczynski.pdf
[INFO] [stderr] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ help: use an automatic link instead: `<https://eldorado.tu-dortmund.de/bitstream/2003/36203/1/Dissertation_Kopczynski.pdf>`
[INFO] [stderr]
[INFO] [stderr] warning: 21 warnings emitted
[INFO] [stderr]
[INFO] [stderr] Finished dev [unoptimized + debuginfo] target(s) in 1m 05s
[INFO] running `Command { std: "docker" "inspect" "565c027850d7ae89028d7a5fad6331c3ca9d055c9f48a9da534dcb0f5f9f104e", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "565c027850d7ae89028d7a5fad6331c3ca9d055c9f48a9da534dcb0f5f9f104e", kill_on_drop: false }`
[INFO] [stdout] 565c027850d7ae89028d7a5fad6331c3ca9d055c9f48a9da534dcb0f5f9f104e