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Remove strict documentation requirement #199

Remove strict documentation requirement

Remove strict documentation requirement #199

Triggered via push January 17, 2024 08:07
Status Success
Total duration 2m 0s
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6 warnings and 1 notice
Documentation: ../../../.julia/packages/Documenter/bYYzK/src/Utilities/Utilities.jl#L34
no docs found for 'XAM' in `@docs` block in src/man/records.md:3-5 ```@docs XAM ```
Documentation: ../../../.julia/packages/Documenter/bYYzK/src/Utilities/Utilities.jl#L34
80 docstrings not included in the manual: XAM.SAM.quality :: Tuple{Type{String}, XAM.SAM.Record} XAM.SAM.quality :: Tuple{XAM.SAM.Record} XAM.SAM.tag :: Tuple{XAM.SAM.MetaInfo} XAM.isqcfail :: Tuple{XAM.XAMRecord} XAM.SAM.MetaInfo :: Tuple{AbstractString, Any} XAM.SAM.MetaInfo :: Tuple{AbstractString} XAM.FLAG_QCFAIL XAM.FLAG_DUP XAM.BAM.alignment :: Tuple{XAM.BAM.Record} XAM.SAM.tempname :: Tuple{XAM.SAM.Record} XAM.FLAG_READ2 XAM.FLAG_MREVERSE XAM.SAM.value :: Tuple{XAM.SAM.MetaInfo} XAM.issupplementaryalignment :: Tuple{XAM.XAMRecord} XAM.BAM.mappingquality :: Tuple{XAM.BAM.Record} XAM.SAM.sequence :: Tuple{Type{String}, XAM.SAM.Record} XAM.SAM.sequence :: Tuple{XAM.SAM.Record} XAM.isproperpair :: Tuple{XAM.XAMRecord} XAM.ismatereverse :: Tuple{XAM.XAMRecord} XAM.FLAG_SECONDARY XAM.SAM.iscomment :: Tuple{XAM.SAM.MetaInfo} XAM.isduplicate :: Tuple{XAM.XAMRecord} XAM.SAM.position :: Tuple{XAM.SAM.Record} XAM.BAM.tempname :: Tuple{XAM.BAM.Record} XAM.isread1 :: Tuple{XAM.XAMRecord} XAM.BAM.nextrefid :: Tuple{XAM.BAM.Record} XAM.isnegativestrand :: Tuple{XAM.XAMRecord} XAM.BAM.position :: Tuple{XAM.BAM.Record} XAM.BAM.auxdata :: Tuple{XAM.BAM.Record} XAM.SAM.alignment :: Tuple{XAM.SAM.Record} XAM.FLAG_MUNMAP XAM.SAM.keyvalues :: Tuple{XAM.SAM.MetaInfo} XAM.isforward :: Tuple{XAM.XAMRecord} XAM.isunmapped :: Tuple{XAM.XAMRecord} XAM.SAM.rightposition :: Tuple{XAM.SAM.Record} XAM.issecondaryalignment :: Tuple{XAM.XAMRecord} XAM.FLAG_SUPPLEMENTARY XAM.FLAG_UNMAP XAM.SAM.Header :: Tuple{} XAM.BAM.n_cigar_op :: Union{Tuple{XAM.BAM.Record}, Tuple{XAM.BAM.Record, Bool}} XAM.FLAG_PAIRED XAM.SAM.refname :: Tuple{XAM.SAM.Record} XAM.BAM.quality :: Tuple{XAM.BAM.Record} XAM.FLAG_READ1 XAM.BAM.nextposition :: Tuple{XAM.BAM.Record} XAM.ismateunmapped :: Tuple{XAM.XAMRecord} XAM.SAM.seqlength :: Tuple{XAM.SAM.Record} XAM.BAM.nextrefname :: Tuple{XAM.BAM.Record} XAM.FLAG_REVERSE XAM.SAM.cigar :: Tuple{XAM.SAM.Record} BioGenerics.header :: Tuple{XAM.BAM.Reader} XAM.FLAG_PROPER_PAIR XAM.BAM.BAI :: Tuple{IO} XAM.BAM.BAI :: Tuple{AbstractString} XAM.SAM.nextposition :: Tuple{XAM.SAM.Record} XAM.BAM.templength :: Tuple{XAM.BAM.Record} XAM.isread2 :: Tuple{XAM.XAMRecord} XAM.BAM.rightposition :: Tuple{XAM.BAM.Record} XAM.SAM.nextrefname :: Tuple{XAM.SAM.Record} XAM.SAM.alignlength :: Tuple{XAM.SAM.Record} XAM.isreverse :: Tuple{XAM.XAMRecord} XAM.isprimaryalignment :: Tuple{XAM.XAMRecord} XAM.BAM.seqlength :: Tuple{XAM.BAM.Record} XAM.BAM.refid :: Tuple{XAM.BAM.Record} XAM.BAM.sequence :: Tuple{XAM.BAM.Record} XAM.ismapped :: Tuple{XAM.XAMRecord} XAM.BAM.alignlength :: Tuple{XAM.BAM.Record} XAM.SAM.mappingquality :: Tuple{XAM.SAM.Record} XAM.ispositivestrand :: Tuple{XAM.XAMRecord} Base.read! :: Tuple{XAM.SAM.Reader, XAM.SAM.Record} XAM.BAM.refname :: Tuple{XAM.BAM.Record} XAM.ispaired :: Tuple{XAM.XAMRecord} Base.findall :: Tuple{XAM.SAM.Header, AbstractString} XAM.BAM.reflen :: Tuple{XAM.BAM.Record} XAM.SAM.auxdata :: Tuple{XAM.SAM.Record} XAM.isprimary :: Tuple{XAM.XAMRecord} XAM.BAM.cigar :: Union{Tuple{XAM.BAM.Record}, Tuple{XAM.BAM.Record, Bool}} XAM.SAM.templength :: Tuple{XAM.SAM.Record} XAM.BAM.cigar_rle :: Union{Tuple{XAM.BAM.Record}, Tuple{XAM.BAM.Record, Bool}} XAM.isnextmapped :: Tuple{XAM.XAMRecord} These are docstrings in the checked modules (configured with the modules keyword) that are not included in @docs or @autodocs blocks.
Documentation: ../../../.julia/packages/Documenter/bYYzK/src/DocChecks.jl#L248
linkcheck 'https://biojulia.github.io/XAM.jl/stable' status: 301, redirects to 'https://biojulia.dev/XAM.jl/stable'
Documentation: ../../../.julia/packages/Documenter/bYYzK/src/DocChecks.jl#L248
linkcheck 'https://biojulia.github.io/XAM.jl/dev/' status: 301, redirects to 'https://biojulia.dev/XAM.jl/dev/'
Documentation: ../../../.julia/packages/Documenter/bYYzK/src/DocChecks.jl#L248
linkcheck 'https://julialang.slack.com/channels/biology' status: 301, redirects to 'https://julialang.slack.com/archives/biology'
Documentation: ../../../.julia/packages/Documenter/bYYzK/src/DocChecks.jl#L248
linkcheck 'https://discourse.julialang.org/c/domain/bio' status: 301, redirects to 'https://discourse.julialang.org/c/domain/bio/15'
[julia-buildpkg] Caching of the julia depot was not detected
Consider using `julia-actions/cache` to speed up runs https://github.com/julia-actions/cache. To ignore, set input `ignore-no-cache: true`