Git failed to fetch [email protected]:BioJulia/BioAlignments.jl.git This can be caused by a DOCUMENTER_KEY variable that is not correctly set up. Make sure that the environment variable is properly set up as a Base64-encoded string of the SSH private key. You may need to re-generate the keys with DocumenterTools.

Failed to push: exception = failed process: Process(`git fetch upstream`, ProcessExited(128)) [128] Stacktrace: [1] pipeline_error @ ./process.jl:565 [inlined] [2] run(::Cmd; wait::Bool) @ Base ./process.jl:480 [3] run @ ./process.jl:477 [inlined] [4] (::Documenter.var"#git_commands#22"{String, String, SubString{String}, String, Vector{Any}, Bool, String, String})(sshconfig::String) @ Documenter ~/.julia/packages/Documenter/PLD7m/src/Documenter.jl:500 [5] (::Documenter.var"#21#27"{String})() @ Documenter ~/.julia/packages/Documenter/PLD7m/src/Documenter.jl:598 [6] cd(f::Documenter.var"#21#27"{String}, dir::String) @ Base.Filesystem ./file.jl:112 [7] #20 @ ~/.julia/packages/Documenter/PLD7m/src/Documenter.jl:598 [inlined] [8] withenv(f::Documenter.var"#20#26"{String, String}, keyvals::Pair{String, String}) @ Base ./env.jl:257 [9] (::Documenter.var"#19#25"{String, String, SubString{String}})(sshconfig::String, io::IOStream) @ Documenter ~/.julia/packages/Documenter/PLD7m/src/Documenter.jl:597 [10] mktemp(fn::Documenter.var"#19#25"{String, String, SubString{String}}, parent::String) @ Base.Filesystem ./file.jl:738 [11] mktemp(fn::Function) @ Base.Filesystem ./file.jl:736 [12] git_push(root::String, temp::String, repo::String; branch::String, dirname::String, target::String, sha::SubString{String}, devurl::String, versions::Vector{Any}, forcepush::Bool, deploy_config::Documenter.GitHubActions, subfolder::String) @ Documenter ~/.julia/packages/Documenter/PLD7m/src/Documenter.jl:582 [13] git_push @ ~/.julia/packages/Documenter/PLD7m/src/Documenter.jl:477 [inlined] [14] #13 @ ~/.julia/packages/Documenter/PLD7m/src/Documenter.jl:456 [inlined] [15] mktempdir(fn::Documenter.var"#13#15"{SubString{String}, String, String, String, String, String, String, Vector{Any}, Bool, Documenter.GitHubActions, String}, parent::String; prefix::String) @ Base.Filesystem ./file.jl:766 [16] mktempdir(fn::Function, parent::String) @ Base.Filesystem ./file.jl:762 [17] mktempdir @ ./file.jl:762 [inlined] [18] (::Documenter.var"#12#14"{String, String, String, String, String, Nothing, String, Vector{Any}, Bool, Documenter.GitHubActions, String})() @ Documenter ~/.julia/packages/Documenter/PLD7m/src/Documenter.jl:455 [19] cd(f::Documenter.var"#12#14"{String, String, String, String, String, Nothing, String, Vector{Any}, Bool, Documenter.GitHubActions, String}, dir::String) @ Base.Filesystem ./file.jl:112 [20] deploydocs(; root::String, target::String, dirname::String, repo::String, branch::String, deps::Nothing, make::Nothing, devbranch::String, devurl::String, versions::Vector{Any}, forcepush::Bool, deploy_config::Documenter.GitHubActions, push_preview::Bool) @ Documenter ~/.julia/packages/Documenter/PLD7m/src/Documenter.jl:432 [21] top-level scope @ ~/work/BioAlignments.jl/BioAlignments.jl/docs/make.jl:23 [22] include(fname::String) @ Base.MainInclude ./client.jl:489 [23] top-level scope @ none:8 [24] eval @ ./boot.jl:385 [inlined] [25] exec_options(opts::Base.JLOptions) @ Base ./client.jl:291 [26] _start() @ Base ./client.jl:552

no docs found for 'seq2ref(::PairwiseAlignment, ::Integer)' in `@docs` block in src/references.md:55-82 ```@docs PairwiseAlignment Base.count(::PairwiseAlignment, ::Operation) count_matches count_mismatches count_insertions count_deletions count_aligned GlobalAlignment SemiGlobalAlignment OverlapAlignment LocalAlignment EditDistance HammingDistance LevenshteinDistance AbstractScoreModel AffineGapScoreModel AbstractCostModel CostModel PairwiseAlignmentResult pairalign score distance alignment hasalignment seq2ref(::PairwiseAlignment, ::Integer) ref2seq(::PairwiseAlignment, ::Integer) ```

no docs found for 'ref2seq(::PairwiseAlignment, ::Integer)' in `@docs` block in src/references.md:55-82 ```@docs PairwiseAlignment Base.count(::PairwiseAlignment, ::Operation) count_matches count_mismatches count_insertions count_deletions count_aligned GlobalAlignment SemiGlobalAlignment OverlapAlignment LocalAlignment EditDistance HammingDistance LevenshteinDistance AbstractScoreModel AffineGapScoreModel AbstractCostModel CostModel PairwiseAlignmentResult pairalign score distance alignment hasalignment seq2ref(::PairwiseAlignment, ::Integer) ref2seq(::PairwiseAlignment, ::Integer) ```

8 docstrings potentially missing: BioAlignments.seq2aln :: Tuple{Alignment, Integer} BioAlignments.ismetaop :: Tuple{Operation} BioAlignments.aln2ref :: Tuple{Alignment, Integer} BioAlignments.sequence :: Tuple{PairwiseAlignment} BioAlignments.sequence :: Tuple{AlignedSequence} BioAlignments.sequence :: Tuple{PairwiseAlignmentResult} BioAlignments.aln2seq :: Tuple{Alignment, Integer} BioAlignments.ref2aln :: Tuple{Alignment, Integer}

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

The following actions uses Node.js version which is deprecated and will be forced to run on node20: actions/checkout@v2. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/