Version trouble with IntervalTrees. Only able to install "BioAlignments" after removing package "Bio"

[kopperud]

I have a problem when installing the package. I realize the problem is constraining version for the IntervalTrees package (multi-package problem), but I don't know where better to post this issue.

If I understand correctly, BioAlignments requires version 0.5.0 of package IntervalTrees, however does it even exist? If I go to https://github.com/BioJulia/IntervalTrees.jl/releases, the latest is 0.4.1.

Also, package Bio has the following version requirements for package IntervalTrees: [0.0.1,0.1.1).

Code

Pkg.add("BioAlignments")

Then I get this error message:

julia> Pkg.add("BioAlignments")
ERROR: Unsatisfiable requirements detected for package IntervalTrees:
├─version range [0.0.0-,∞) set by an explicit requirement
├─version range [0.0.0-,∞) required by package Bio, whose allowed version range is [0.0.0-,∞):
│ └─version range [0.0.0-,∞) set by an explicit requirement
├─version range [0.0.0-,∞) required by package BioSequences, whose allowed version range is [0.5.0,∞):
│ ├─version range [0.0.0-,∞) set by an explicit requirement
│ └─version range [0.5.0,∞) required by package BioAlignments, whose allowed version range is [0.0.0-,∞):
  │ └─version range [0.0.0-,∞) set by an explicit requirement
├─version range [0.0.0-,∞) required by package BioAlignments, whose allowed version range is [0.0.0-,∞):
│ └─[see above for BioAlignments backtrace]
└─version range [0.2.0,∞) required by package GenomicFeatures, whose allowed version range is [0.1.0,∞):
  └─version range [0.1.0,∞) required by package BioAlignments, whose allowed version range is [0.0.0-,∞):
    └─[see above for BioAlignments backtrace]
The intersection of the requirements is empty.
filter_versions(::Dict{String,Base.Pkg.Types.VersionSet}, ::Dict{String,Dict{VersionNumber,Base.Pkg.Types.Available}}, ::Dict{AbstractString,Base.Pkg.Types.ResolveBacktraceItem}) at .\pkg\query.jl:299
prune_versions(::Dict{String,Base.Pkg.Types.VersionSet}, ::Dict{String,Dict{VersionNumber,Base.Pkg.Types.Available}}, ::Dict{AbstractString,Base.Pkg.Types.ResolveBacktraceItem}) at .\pkg\query.jl:328
prune_dependencies(::Dict{String,Base.Pkg.Types.VersionSet}, ::Dict{String,Dict{VersionNumber,Base.Pkg.Types.Available}}, ::Dict{AbstractString,Base.Pkg.Types.ResolveBacktraceItem}) at .\pkg\query.jl:546
resolve(::Dict{String,Base.Pkg.Types.VersionSet}, ::Dict{String,Dict{VersionNumber,Base.Pkg.Types.Available}}, ::Dict{String,Tuple{VersionNumber,Bool}}, ::Dict{String,Base.Pkg.Types.Fixed}, ::Dict{String,VersionNumber}, ::Set{String}) at .\pkg\entry.jl:498
resolve(::Dict{String,Base.Pkg.Types.VersionSet}, ::Dict{String,Dict{VersionNumber,Base.Pkg.Types.Available}}, ::Dict{String,Tuple{VersionNumber,Bool}}, ::Dict{String,Base.Pkg.Types.Fixed}) at .\pkg\entry.jl:479
edit(::Function, ::String, ::Base.Pkg.Types.VersionSet, ::Vararg{Base.Pkg.Types.VersionSet,N} where N) at .\pkg\entry.jl:30
(::Base.Pkg.Entry.##1#3{String,Base.Pkg.Types.VersionSet})() at .\task.jl:335
Stacktrace:
 [1] sync_end() at .\task.jl:287
 [2] macro expansion at .\task.jl:303 [inlined]
 [3] add(::String, ::Base.Pkg.Types.VersionSet) at .\pkg\entry.jl:51
 [4] (::Base.Pkg.Dir.##4#7{Array{Any,1},Base.Pkg.Entry.#add,Tuple{String}})() at .\pkg\dir.jl:36
 [5] cd(::Base.Pkg.Dir.##4#7{Array{Any,1},Base.Pkg.Entry.#add,Tuple{String}}, ::String) at .\file.jl:59
 [6] #cd#1(::Array{Any,1}, ::Function, ::Function, ::String, ::Vararg{String,N} where N) at .\pkg\dir.jl:36
 [7] add(::String) at .\pkg\pkg.jl:117

After removing package Bio, the installation works fine.

julia> Pkg.rm("Bio")
INFO: Upgrading IntervalTrees: v0.1.0 => v0.4.1
INFO: Removing BGZFStreams v0.2.0
INFO: Removing Bio v0.4.7
INFO: Removing Calculus v0.4.0
INFO: Removing CodecZlib v0.4.3
INFO: Removing ColorTypes v0.6.7
INFO: Removing Colors v0.8.2
INFO: Removing CommonSubexpressions v0.1.0
INFO: Removing DiffResults v0.0.3
INFO: Removing DiffRules v0.0.5
INFO: Removing Distributions v0.15.0
INFO: Removing FixedPointNumbers v0.4.6
INFO: Removing ForwardDiff v0.7.5
INFO: Removing Iterators v0.3.1
INFO: Removing LibExpat v0.4.2
INFO: Removing Libz v0.2.4
INFO: Removing LightGraphs v0.12.0
INFO: Removing LightXML v0.6.0
INFO: Removing MacroTools v0.4.2
INFO: Removing Missings v0.2.10
INFO: Removing NaNMath v0.3.1
INFO: Removing PDMats v0.8.0
INFO: Removing QuadGK v0.2.1
INFO: Removing Reexport v0.1.0
INFO: Removing Rmath v0.4.0
INFO: Removing Roots v0.6.0
INFO: Removing SimpleTraits v0.6.0
INFO: Removing SortingAlgorithms v0.2.1
INFO: Removing SpecialFunctions v0.6.0
INFO: Removing StaticArrays v0.7.2
INFO: Removing StatsBase v0.23.1
INFO: Removing StatsFuns v0.6.0
INFO: Removing WinRPM v0.3.2
WARNING: The following packages have been updated but were already imported:
- IntervalTrees
Restart Julia to use the updated versions.
INFO: Package database updated

julia> Pkg.add("BioAlignments")
INFO: Cloning cache of BioAlignments from https://github.com/BioJulia/BioAlignments.jl.git
INFO: Cloning cache of GenomicFeatures from https://github.com/BioJulia/GenomicFeatures.jl.git
INFO: Installing BGZFStreams v0.2.0
INFO: Installing BioAlignments v0.3.0
INFO: Installing ColorTypes v0.6.7
INFO: Installing FixedPointNumbers v0.4.6
INFO: Installing GenomicFeatures v0.2.1
INFO: Installing Libz v0.2.4
INFO: Package database updated

Your Environment

• 0.6.0 (same error on 0.6.3)
• Windows 10

Installed packages:

show(STDOUT, "text/plain", sort(collect(Pkg.installed())))
57-element Array{Pair{String,VersionNumber},1}:
 "Automa"=>v"0.6.1"
 "BGZFStreams"=>v"0.2.0"
 "BinDeps"=>v"0.8.8"
 "BinaryProvider"=>v"0.3.2"
 "Bio"=>v"0.4.7"
 "BioCore"=>v"1.4.0"
 "BioSequences"=>v"0.8.3"
 "BioSymbols"=>v"2.0.0"
 "BufferedStreams"=>v"0.4.0"
 "Calculus"=>v"0.4.0"
 "CodecZlib"=>v"0.4.3"
 "ColorTypes"=>v"0.6.7"
 "Colors"=>v"0.8.2"
 "Combinatorics"=>v"0.6.0"
 "CommonSubexpressions"=>v"0.1.0"
 "Compat"=>v"0.69.0"
 "Conda"=>v"0.8.1"
 "DataStructures"=>v"0.8.3"
 "DiffResults"=>v"0.0.3"
 "DiffRules"=>v"0.0.5"
 "Distributions"=>v"0.15.0"
 "FixedPointNumbers"=>v"0.4.6"
 "ForwardDiff"=>v"0.7.5"
 "IJulia"=>v"1.8.0"
 "IndexableBitVectors"=>v"0.1.2"
 "IntervalTrees"=>v"0.1.0"
 "IterTools"=>v"0.2.1"
 "Iterators"=>v"0.3.1"
 "JSON"=>v"0.17.2"
 "LibExpat"=>v"0.4.2"
 "Libz"=>v"0.2.4"
 "LightGraphs"=>v"0.12.0"
 "LightXML"=>v"0.6.0"
 "MacroTools"=>v"0.4.2"
 "MbedTLS"=>v"0.5.11"
 "Missings"=>v"0.2.10"
 "NaNMath"=>v"0.3.1"
 "Nullables"=>v"0.0.5"
 "PDMats"=>v"0.8.0"
 "Polynomials"=>v"0.3.2"
 "QuadGK"=>v"0.2.1"
 "Reexport"=>v"0.1.0"
 "Rmath"=>v"0.4.0"
 "Roots"=>v"0.6.0"
 "SHA"=>v"0.5.7"
 "SimpleTraits"=>v"0.6.0"
 "SortingAlgorithms"=>v"0.2.1"
 "SpecialFunctions"=>v"0.6.0"
 "StaticArrays"=>v"0.7.2"
 "StatsBase"=>v"0.23.1"
 "StatsFuns"=>v"0.6.0"
 "TranscodingStreams"=>v"0.5.2"
 "Twiddle"=>v"0.4.0"
 "URIParser"=>v"0.3.1"
 "VersionParsing"=>v"1.1.1"
 "WinRPM"=>v"0.3.2"
 "ZMQ"=>v"0.6.2"

[TransGirlCodes]

The last release of Bio is kindof out of date with other packages like IntervalTrees, but I'm working on getting a more modern release of it out by JuliaCon. Likewise with IntervalTrees, there are a few issues that need to be worked out over there and a newer version released. But BioAlignments should be fine with IntervalTrees 0.4.1, the REQUIRE file on the master branch specifies IntervalTrees 0.4.1.