Hello! i have a situation installation Biotools and idk even what is about. A screenshoot of my problem
Can you please post the error again as text, enclosed in triple back-ticks, like ``` ?
The screenshot is hardly readable.
In addition, can you please post the output of
using Pkg
Pkg.status()
?
A few things going on here.
First, if you have a lot of packages in your global environment, you can end up with a lot of conflicts. If you can, pare down what’s installed in the global environment and use more temporary environments, invoked with ]activate --temp.
Second, it’s likely that an indirect dependency which is used by many packages had a breaking version (likely Adapt.jl v3 vs. v4, I’m guessing), and some of your packages support it and others don’t. Pkg (right now) doesn’t do a great job with conflicts deep in the dependency tree.
BioTools declares a dependency on BioAlignments v1 and BioSequences v1, which are way out of date (both are currently v3). So that likely is the immediate issue.
(@v1.10) pkg> add BioTools@*
Resolving package versions…
ERROR: Unsatisfiable requirements detected for package MLJModels [d491faf4]:
MLJModels [d491faf4] log:
├─possible versions are: 0.1.0-0.16.16 or uninstalled
├─restricted to versions * by an explicit requirement, leaving only versions: 0.1.0-0.16.16
├─restricted by compatibility requirements with MLJ [add582a8] to versions: [0.1.0-0.11.3, 0.12.1-0.16.16]
│ └─MLJ [add582a8] log:
│ ├─possible versions are: 0.1.0-0.20.3 or uninstalled
│ ├─restricted to versions * by an explicit requirement, leaving only versions: 0.1.0-0.20.3
│ └─restricted by compatibility requirements with MLJModels [d491faf4] to versions: 0.1.0-0.18.6 or uninstalled, leaving only versions: 0.1.0-0.18.6
│ └─MLJModels [d491faf4] log: see above
├─restricted by compatibility requirements with Combinatorics [861a8166] to versions: 0.1.0-0.15.11 or uninstalled, leaving only versions: [0.1.0-0.11.3, 0.12.1-0.15.11]
│ └─Combinatorics [861a8166] log:
│ ├─possible versions are: 0.7.0-1.0.2 or uninstalled
│ └─restricted by compatibility requirements with BioSequences [7e6ae17a] to versions: 0.7.0
│ └─BioSequences [7e6ae17a] log:
│ ├─possible versions are: 1.0.0-3.1.6 or uninstalled
│ ├─restricted to versions * by an explicit requirement, leaving only versions: 1.0.0-3.1.6
│ └─restricted by compatibility requirements with BioTools [fa51a905] to versions: 1.0.0-1.1.0
│ └─BioTools [fa51a905] log:
│ ├─possible versions are: 1.0.0-1.1.0 or uninstalled
│ └─restricted to versions * by an explicit requirement, leaving only versions: 1.0.0-1.1.0
├─restricted by compatibility requirements with Distributions [31c24e10] to versions: 0.1.0-0.7.2 or uninstalled, leaving only versions: 0.1.0-0.7.2
│ └─Distributions [31c24e10] log:
│ ├─possible versions are: 0.16.0-0.25.107 or uninstalled
│ ├─restricted by compatibility requirements with SpecialFunctions [276daf66] to versions: 0.16.0-0.25.45 or uninstalled, leaving only versions: 0.16.0-0.25.45
│ │ └─SpecialFunctions [276daf66] log:
│ │ ├─possible versions are: 0.7.0-2.3.1 or uninstalled
│ │ ├─restricted by compatibility requirements with PhyloNetworks [33ad39ac] to versions: 0.7.0-0.10.3
│ │ │ └─PhyloNetworks [33ad39ac] log:
│ │ │ ├─possible versions are: 0.9.0-0.16.3 or uninstalled
│ │ │ ├─restricted to versions * by an explicit requirement, leaving only versions: 0.9.0-0.16.3
│ │ │ ├─restricted by compatibility requirements with BioSequences [7e6ae17a] to versions: 0.9.0-0.11.0 or uninstalled, leaving only versions: 0.9.0-0.11.0
│ │ │ │ └─BioSequences [7e6ae17a] log: see above
│ │ │ └─restricted by compatibility requirements with StatsModels [3eaba693] to versions: 0.10.0-0.16.3 or uninstalled, leaving only versions: 0.10.0-0.11.0
│ │ │ └─StatsModels [3eaba693] log:
│ │ │ ├─possible versions are: 0.3.0-0.7.3 or uninstalled
│ │ │ ├─restricted by compatibility requirements with PhyloNetworks [33ad39ac] to versions: 0.3.0-0.6.33
│ │ │ │ └─PhyloNetworks [33ad39ac] log: see above
│ │ │ ├─restricted by compatibility requirements with MixedModels [ff71e718] to versions: 0.6.0-0.7.3, leaving only versions: 0.6.0-0.6.33
│ │ │ │ └─MixedModels [ff71e718] log:
│ │ │ │ ├─possible versions are: 0.18.1-4.23.1 or uninstalled
│ │ │ │ ├─restricted to versions * by an explicit requirement, leaving only versions: 0.18.1-4.23.1
│ │ │ │ ├─restricted by compatibility requirements with NLopt [76087f3c] to versions: 2.3.1-4.23.1 or uninstalled, leaving only versions: 2.3.1-4.23.1
│ │ │ │ │ └─NLopt [76087f3c] log:
│ │ │ │ │ ├─possible versions are: 0.5.0-1.0.2 or uninstalled
│ │ │ │ │ ├─restricted by compatibility requirements with PhyloNetworks [33ad39ac] to versions: 0.5.1-1.0.2
│ │ │ │ │ │ └─PhyloNetworks [33ad39ac] log: see above
│ │ │ │ │ ├─restricted by julia compatibility requirements to versions: 0.6.0-1.0.2 or uninstalled, leaving only versions: 0.6.0-1.0.2
│ │ │ │ │ └─restricted by compatibility requirements with PhyloNetworks [33ad39ac] to versions: 0.5.1-0.6.5, leaving only versions: 0.6.0-0.6.5
│ │ │ │ │ └─PhyloNetworks [33ad39ac] log: see above
│ │ │ │ ├─restricted by compatibility requirements with StatsModels [3eaba693] to versions: 2.0.0-4.8.2 or uninstalled, leaving only versions: 2.3.1-4.8.2
│ │ │ │ │ └─StatsModels [3eaba693] log: see above
│ │ │ │ └─restricted by compatibility requirements with GLM [38e38edf] to versions: 0.18.1-3.8.0 or uninstalled, leaving only versions: 2.3.1-3.8.0
│ │ │ │ └─GLM [38e38edf] log:
│ │ │ │ ├─possible versions are: 1.0.0-1.9.0 or uninstalled
│ │ │ │ ├─restricted to versions * by an explicit requirement, leaving only versions: 1.0.0-1.9.0
│ │ │ │ ├─restricted by compatibility requirements with StatsModels [3eaba693] to versions: 1.3.0-1.8.3 or uninstalled, leaving only versions: 1.3.0-1.8.3
│ │ │ │ │ └─StatsModels [3eaba693] log: see above
│ │ │ │ └─restricted by compatibility requirements with StatsBase [2913bbd2] to versions: 1.0.0-1.4.2 or uninstalled, leaving only versions: 1.3.0-1.4.2
│ │ │ │ └─StatsBase [2913bbd2] log:
│ │ │ │ ├─possible versions are: 0.24.0-0.34.2 or uninstalled
│ │ │ │ ├─restricted by compatibility requirements with PhyloNetworks [33ad39ac] to versions: 0.26.0-0.34.2
│ │ │ │ │ └─PhyloNetworks [33ad39ac] log: see above
│ │ │ │ ├─restricted by compatibility requirements with PhyloNetworks [33ad39ac] to versions: 0.26.0-0.33.21
│ │ │ │ │ └─PhyloNetworks [33ad39ac] log: see above
│ │ │ │ ├─restricted by compatibility requirements with HypothesisTests [09f84164] to versions: 0.24.0-0.32.2, leaving only versions: 0.26.0-0.32.2
│ │ │ │ │ └─HypothesisTests [09f84164] log:
│ │ │ │ │ ├─possible versions are: 0.7.0-0.11.0 or uninstalled
│ │ │ │ │ ├─restricted to versions * by an explicit requirement, leaving only versions: 0.7.0-0.11.0
│ │ │ │ │ └─restricted by compatibility requirements with Combinatorics [861a8166] to versions: 0.7.0-0.8.0 or uninstalled, leaving only versions: 0.7.0-0.8.0
│ │ │ │ │ └─Combinatorics [861a8166] log: see above
│ │ │ │ └─restricted by compatibility requirements with GLM [38e38edf] to versions: 0.30.0-0.33.21, leaving only versions: 0.30.0-0.32.2
│ │ │ │ └─GLM [38e38edf] log: see above
│ │ │ └─restricted by compatibility requirements with StatsBase [2913bbd2] to versions: 0.3.0-0.6.21 or uninstalled, leaving only versions: 0.6.0-0.6.21
│ │ │ └─StatsBase [2913bbd2] log: see above
│ │ └─restricted by compatibility requirements with Distributions [31c24e10] to versions: 0.7.0-0.9.0
│ │ └─Distributions [31c24e10] log: see above
│ └─restricted by compatibility requirements with HypothesisTests [09f84164] to versions: 0.16.0-0.21.12
│ └─HypothesisTests [09f84164] log: see above
└─restricted by compatibility requirements with Distances [b4f34e82] to versions: 0.11.0-0.16.16 or uninstalled — no versions left
└─Distances [b4f34e82] log:
├─possible versions are: 0.7.0-0.10.11 or uninstalled
├─restricted by compatibility requirements with ImageDistances [51556ac3] to versions: [0.7.0-0.8.2, 0.9.2-0.10.11]
│ └─ImageDistances [51556ac3] log:
│ ├─possible versions are: 0.1.0-0.2.17 or uninstalled
│ ├─restricted by compatibility requirements with ProgressMeter [92933f4c] to versions: 0.2.2-0.2.17 or uninstalled, leaving only versions: 0.2.2-0.2.17
│ │ └─ProgressMeter [92933f4c] log:
│ │ ├─possible versions are: 0.6.0-1.10.0 or uninstalled
│ │ ├─restricted by compatibility requirements with TSne [24678dba] to versions: [0.6.0-0.9.0, 1.3.2-1.10.0]
│ │ │ └─TSne [24678dba] log:
│ │ │ ├─possible versions are: 1.2.0-1.3.0 or uninstalled
│ │ │ ├─restricted to versions * by an explicit requirement, leaving only versions: 1.2.0-1.3.0
│ │ │ └─restricted by compatibility requirements with ProgressMeter [92933f4c] to versions: 1.3.0 or uninstalled, leaving only versions: 1.3.0
│ │ │ └─ProgressMeter [92933f4c] log: see above
│ │ └─restricted by compatibility requirements with MixedModels [ff71e718] to versions: 1.0.0-1.10.0, leaving only versions: 1.3.2-1.10.0
│ │ └─MixedModels [ff71e718] log: see above
│ ├─restricted by compatibility requirements with ImageCore [a09fc81d] to versions: 0.1.0-0.2.13 or uninstalled, leaving only versions: 0.2.2-0.2.13
│ │ └─ImageCore [a09fc81d] log:
│ │ ├─possible versions are: 0.7.0-0.10.2 or uninstalled
│ │ ├─restricted by compatibility requirements with Images [916415d5] to versions: [0.7.0-0.8.22, 0.9.3-0.10.2]
│ │ │ └─Images [916415d5] log:
│ │ │ ├─possible versions are: 0.17.3-0.26.0 or uninstalled
│ │ │ ├─restricted to versions * by an explicit requirement, leaving only versions: 0.17.3-0.26.0
│ │ │ ├─restricted by compatibility requirements with ImageDistances [51556ac3] to versions: 0.18.0-0.26.0 or uninstalled, leaving only versions: 0.18.0-0.26.0
│ │ │ │ └─ImageDistances [51556ac3] log: see above
│ │ │ └─restricted by compatibility requirements with Reexport [189a3867] to versions: 0.17.3-0.24.1 or uninstalled, leaving only versions: 0.18.0-0.24.1
│ │ │ └─Reexport [189a3867] log:
│ │ │ ├─possible versions are: 0.2.0-1.2.2 or uninstalled
│ │ │ └─restricted by compatibility requirements with DataFrames [a93c6f00] to versions: 0.2.0
│ │ │ └─DataFrames [a93c6f00] log:
│ │ │ ├─possible versions are: 0.11.7-1.6.1 or uninstalled
│ │ │ ├─restricted to versions * by an explicit requirement, leaving only versions: 0.11.7-1.6.1
│ │ │ ├─restricted by compatibility requirements with PhyloNetworks [33ad39ac] to versions: 0.13.0-1.6.1
│ │ │ │ └─PhyloNetworks [33ad39ac] log: see above
│ │ │ ├─restricted by compatibility requirements with PhyloNetworks [33ad39ac] to versions: 0.13.0-0.21.8
│ │ │ │ └─PhyloNetworks [33ad39ac] log: see above
│ │ │ └─restricted by compatibility requirements with RCall [6f49c342] to versions: 0.19.0-1.6.1, leaving only versions: 0.19.0-0.21.8
│ │ │ └─RCall [6f49c342] log:
│ │ │ ├─possible versions are: 0.12.0-0.14.1 or uninstalled
│ │ │ ├─restricted to versions * by an explicit requirement, leaving only versions: 0.12.0-0.14.1
│ │ │ ├─restricted by compatibility requirements with PhyloPlots [c0d5b6db] to versions: 0.12.0-0.13.18
│ │ │ │ └─PhyloPlots [c0d5b6db] log:
│ │ │ │ ├─possible versions are: 0.2.0-1.0.0 or uninstalled
│ │ │ │ └─restricted to versions * by an explicit requirement, leaving only versions: 0.2.0-1.0.0
│ │ │ └─restricted by compatibility requirements with StatsModels [3eaba693] to versions: 0.13.4-0.14.1 or uninstalled, leaving only versions: 0.13.4-0.13.18
│ │ │ └─StatsModels [3eaba693] log: see above
│ │ └─restricted by compatibility requirements with FixedPointNumbers [53c48c17] to versions: 0.7.0-0.8.22 or uninstalled, leaving only versions: 0.7.0-0.8.22
│ │ └─FixedPointNumbers [53c48c17] log:
│ │ ├─possible versions are: 0.5.0-0.8.4 or uninstalled
│ │ └─restricted by compatibility requirements with GenomicFeatures [899a7d2d] to versions: 0.5.2-0.7.1
│ │ └─GenomicFeatures [899a7d2d] log:
│ │ ├─possible versions are: 1.0.0-3.0.0 or uninstalled
│ │ └─restricted by compatibility requirements with BioAlignments [00701ae9] to versions: 1.0.0-1.0.4
│ │ └─BioAlignments [00701ae9] log:
│ │ ├─possible versions are: 1.0.0-3.1.0 or uninstalled
│ │ ├─restricted to versions * by an explicit requirement, leaving only versions: 1.0.0-3.1.0
│ │ └─restricted by compatibility requirements with BioTools [fa51a905] to versions: 1.0.0-1.0.1
│ │ └─BioTools [fa51a905] log: see above
│ └─restricted by compatibility requirements with Distances [b4f34e82] to versions: 0.2.8-0.2.17 or uninstalled, leaving only versions: 0.2.8-0.2.13
│ └─Distances [b4f34e82] log: see above
├─restricted by compatibility requirements with NearestNeighborDescent [dd2c4c9e] to versions: 0.7.0-0.9.2, leaving only versions: [0.7.0-0.8.2, 0.9.2]
│ └─NearestNeighborDescent [dd2c4c9e] log:
│ ├─possible versions are: 0.1.0-0.3.6 or uninstalled
│ ├─restricted by compatibility requirements with UMAP [c4f8c510] to versions: 0.1.4-0.3.6
│ │ └─UMAP [c4f8c510] log:
│ │ ├─possible versions are: 0.1.0-0.1.11 or uninstalled
│ │ ├─restricted to versions * by an explicit requirement, leaving only versions: 0.1.0-0.1.11
│ │ └─restricted by compatibility requirements with Distances [b4f34e82] to versions: 0.1.6-0.1.11 or uninstalled, leaving only versions: 0.1.6-0.1.11
│ │ └─Distances [b4f34e82] log: see above
│ └─restricted by compatibility requirements with DataStructures [864edb3b] to versions: 0.1.0-0.3.1 or uninstalled, leaving only versions: 0.1.4-0.3.1
│ └─DataStructures [864edb3b] log:
│ ├─possible versions are: 0.9.0-0.18.18 or uninstalled
│ ├─restricted by compatibility requirements with NearestNeighborDescent [dd2c4c9e] to versions: [0.15.0, 0.17.0-0.18.18]
│ │ └─NearestNeighborDescent [dd2c4c9e] log: see above
│ └─restricted by compatibility requirements with GenomicFeatures [899a7d2d] to versions: 0.11.0-0.17.20, leaving only versions: [0.15.0, 0.17.0-0.17.20]
│ └─GenomicFeatures [899a7d2d] log: see above
└─restricted by compatibility requirements with TSne [24678dba] to versions: 0.9.0-0.10.11, leaving only versions: 0.9.2
└─TSne [24678dba] log: see above
this is the error
klo weno
you are rigth, the enviroment problem was the deal. Ty