Edge encoding #15
Annotations
10 errors
|
../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L44
failed to run `@setup` block in src/man/converting_coal2generation_units.md
```@setup converting
using PhyloNetworks, PhyloPlots, PhyloCoalSimulations, StableRNGs
figpath = joinpath("..", "assets", "figures"); mkpath(figpath)
figname(x) = joinpath(figpath, x)
net = readnewick("((C:0.9,(B:0.2)#H1:0.7::0.6)i1:0.6,(#H1:0.6::0.4,A:1.0)i2:0.5)i3;");
```
exception =
LoadError: The following 1 direct dependency failed to precompile:
PhyloPlots
Failed to precompile PhyloPlots [c0d5b6db-e3fc-52bc-a87d-1d050989ed3b] to "/home/runner/.julia/compiled/v1.11/PhyloPlots/jl_ustUWv".
ERROR: LoadError: UndefVarError: `TraitSubstitutionModel` not defined in `PhyloNetworks`
Suggestion: check for spelling errors or missing imports.
Stacktrace:
[1] getproperty(x::Module, f::Symbol)
@ Base ./Base.jl:42
[2] top-level scope
@ ~/.julia/packages/PhyloPlots/f3q9v/src/substitutionmodels.jl:1
[3] include(mod::Module, _path::String)
@ Base ./Base.jl:557
[4] include(x::String)
@ PhyloPlots ~/.julia/packages/PhyloPlots/f3q9v/src/PhyloPlots.jl:3
[5] top-level scope
@ ~/.julia/packages/PhyloPlots/f3q9v/src/PhyloPlots.jl:21
[6] include
@ ./Base.jl:557 [inlined]
[7] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
@ Base ./loading.jl:2790
[8] top-level scope
@ stdin:5
in expression starting at /home/runner/.julia/packages/PhyloPlots/f3q9v/src/substitutionmodels.jl:1
in expression starting at /home/runner/.julia/packages/PhyloPlots/f3q9v/src/PhyloPlots.jl:3
in expression starting at stdin:
in expression starting at string:1
|
|
../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L44
failed to run `@example` block in src/man/converting_coal2generation_units.md:92-104
```@example converting
using DataFrames, RCall
R"svg"(figname("net_genNe.svg"), width=3.5, height=3); # hide
R"par"(mar=[.5,1,.0,.1]); # hide
plot(net_gen, tipoffset=0.1, showedgelength=true, edgelabelcolor="red4",
edgelabel=DataFrame(n=[e.number for e in net_gen.edge],
l=[Ne[e.number] for e in net_gen.edge]));
R"text"(x=1, y=2.5, Ne[rootedgenumber], adj=1, col="red4");
R"mtext"("red: Ne values", side=1, line=-1.5, col="red4");
R"mtext"("black: edge lengths", side=1, line=-0.5);
R"dev.off()" # hide
nothing # hide
```
exception =
UndefVarError: `figname` not defined in `Main.__atexample__named__converting`
Suggestion: check for spelling errors or missing imports.
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/RCall/0ggIQ/src/macros.jl:74
[2] eval
@ ./boot.jl:430 [inlined]
[3] #60
@ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [inlined]
[4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:802
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState)
@ Base.CoreLogging ./logging/logging.jl:522
[8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger)
@ Base.CoreLogging ./logging/logging.jl:632
[9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:801
|
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../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L44
failed to run `@setup` block in src/man/correlated_inheritance.md
```@setup correlated
using PhyloNetworks, PhyloPlots, PhyloCoalSimulations
figpath = joinpath("..", "assets", "figures"); mkpath(figpath)
figname(x) = joinpath(figpath, x)
```
exception =
LoadError: The following 1 direct dependency failed to precompile:
PhyloPlots
Failed to precompile PhyloPlots [c0d5b6db-e3fc-52bc-a87d-1d050989ed3b] to "/home/runner/.julia/compiled/v1.11/PhyloPlots/jl_N9aRAf".
ERROR: LoadError: UndefVarError: `TraitSubstitutionModel` not defined in `PhyloNetworks`
Suggestion: check for spelling errors or missing imports.
Stacktrace:
[1] getproperty(x::Module, f::Symbol)
@ Base ./Base.jl:42
[2] top-level scope
@ ~/.julia/packages/PhyloPlots/f3q9v/src/substitutionmodels.jl:1
[3] include(mod::Module, _path::String)
@ Base ./Base.jl:557
[4] include(x::String)
@ PhyloPlots ~/.julia/packages/PhyloPlots/f3q9v/src/PhyloPlots.jl:3
[5] top-level scope
@ ~/.julia/packages/PhyloPlots/f3q9v/src/PhyloPlots.jl:21
[6] include
@ ./Base.jl:557 [inlined]
[7] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
@ Base ./loading.jl:2790
[8] top-level scope
@ stdin:5
in expression starting at /home/runner/.julia/packages/PhyloPlots/f3q9v/src/substitutionmodels.jl:1
in expression starting at /home/runner/.julia/packages/PhyloPlots/f3q9v/src/PhyloPlots.jl:3
in expression starting at stdin:
in expression starting at string:1
|
|
../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L44
failed to run `@example` block in src/man/correlated_inheritance.md:61-69
```@example correlated
net = readnewick("((A:0.0)#H1:3::0.6,#H1:3)root;")
using RCall # hide
R"svg"(figname("net1taxon.svg"), width=3, height=2); # hide
R"par"(mar=[0,0,0,0]); # hide
plot(net, shownodelabel=true, showgamma=true, showedgenumber=true, tipoffset=0.1);
R"dev.off()" # hide
nothing # hide
```
exception =
UndefVarError: `figname` not defined in `Main.__atexample__named__correlated`
Suggestion: check for spelling errors or missing imports.
Stacktrace:
[1] top-level scope
@ ~/.julia/packages/RCall/0ggIQ/src/macros.jl:74
[2] eval
@ ./boot.jl:430 [inlined]
[3] #60
@ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [inlined]
[4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:802
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState)
@ Base.CoreLogging ./logging/logging.jl:522
[8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger)
@ Base.CoreLogging ./logging/logging.jl:632
[9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:801
|
|
../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L44
failed to run `@example` block in src/man/correlated_inheritance.md:76-98
```@example correlated
using Random; Random.seed!(12);
gt1 = simulatecoalescent(net, 1, 6; inheritancecorrelation=0, nodemapping=true)[1];
gt2 = simulatecoalescent(net, 1, 6; inheritancecorrelation=0.5, nodemapping=true)[1];
gt3 = simulatecoalescent(net, 1, 6; inheritancecorrelation=0.99, nodemapping=true)[1];
# build data frames to label each edge with the species lineage it evolved in
using DataFrames
speciespath(phy) = DataFrame(
number = [e.number for e in phy.edge],
label = [e.inte1 for e in phy.edge]
)
el1 = speciespath(gt1); el2 = speciespath(gt2); el3 = speciespath(gt3);
R"svg"(figname("net1taxon_3genetrees.svg"), width=8, height=3); # hide
R"par"(mar=[0,0,0,0], oma=[0,0,2,0]); R"layout"([1 2 3])# hide
plot(gt1, shownodelabel=true, edgelabel=el1, edgelabelcolor=el1.label, tipoffset=0.1);
plot(gt2, shownodelabel=true, edgelabel=el2, edgelabelcolor=el2.label, tipoffset=0.1);
plot(gt3, shownodelabel=true, edgelabel=el3, edgelabelcolor=el3.label, tipoffset=0.1);
R"mtext"("gene tree " .* ["1","2","3"] .* "\n(r=" .* ["0","0.5","0.99"] .* ")", side=3, line=-1.1, outer=true, at=[0.2,0.5,0.8]); # hide
R"dev.off()" # hide
nothing # hide
```
exception =
UndefVarError: `simulatecoalescent` not defined in `Main.__atexample__named__correlated`
Suggestion: check for spelling errors or missing imports.
Hint: a global variable of this name also exists in PhyloCoalSimulations.
Stacktrace:
[1] top-level scope
@ correlated_inheritance.md:77
[2] eval
@ ./boot.jl:430 [inlined]
[3] #60
@ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [inlined]
[4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:802
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState)
@ Base.CoreLogging ./logging/logging.jl:522
[8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger)
@ Base.CoreLogging ./logging/logging.jl:632
[9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:801
|
|
../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L44
failed to run `@example` block in src/man/getting_started.md:39-51
```@example getting_started
using PhyloNetworks
net = readnewick("((C:0.9,(B:0.2)#H1:0.7::0.6):0.6,(#H1:0.6,A:1):0.5);");
using PhyloPlots
R"svg"(figname("net3taxa.svg"), width=6, height=3); # hide
R"par"(mar=[.1,.1,.1,.1]); R"layout"([1 2]); # hide
plot(net, showedgenumber=true, shownodelabel=true, showgamma=true, tipoffset=0.1);
R"mtext"("in grey: edge numbers", side=1, line=-1); # hide
plot(net, showedgelength=true, useedgelength=true, tipoffset=0.1);
R"mtext"("in black: edge lengths", side=1, line=-1); # hide
R"dev.off()" # hide
nothing # hide
```
exception =
The following 1 direct dependency failed to precompile:
PhyloPlots
Failed to precompile PhyloPlots [c0d5b6db-e3fc-52bc-a87d-1d050989ed3b] to "/home/runner/.julia/compiled/v1.11/PhyloPlots/jl_V5iCVQ".
ERROR: LoadError: UndefVarError: `TraitSubstitutionModel` not defined in `PhyloNetworks`
Suggestion: check for spelling errors or missing imports.
Stacktrace:
[1] getproperty(x::Module, f::Symbol)
@ Base ./Base.jl:42
[2] top-level scope
@ ~/.julia/packages/PhyloPlots/f3q9v/src/substitutionmodels.jl:1
[3] include(mod::Module, _path::String)
@ Base ./Base.jl:557
[4] include(x::String)
@ PhyloPlots ~/.julia/packages/PhyloPlots/f3q9v/src/PhyloPlots.jl:3
[5] top-level scope
@ ~/.julia/packages/PhyloPlots/f3q9v/src/PhyloPlots.jl:21
[6] include
@ ./Base.jl:557 [inlined]
[7] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
@ Base ./loading.jl:2790
[8] top-level scope
@ stdin:5
in expression starting at /home/runner/.julia/packages/PhyloPlots/f3q9v/src/substitutionmodels.jl:1
in expression starting at /home/runner/.julia/packages/PhyloPlots/f3q9v/src/PhyloPlots.jl:3
in expression starting at stdin:
|
|
../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L44
failed to run `@example` block in src/man/getting_started.md:100-114
```@example getting_started
R"svg"(figname("genetrees_gettingstarted_1.svg"), width=6, height=3); # hide
R"par"(mar=[.1,.1,.1,.1]); R"layout"([1 2]); # hide
using DataFrames
for i in 1:2
gt = trees[i]
plot(gt, tipoffset=0.1,
edgelabel=DataFrame(number = [e.number for e in gt.edge],
label = [e.inte1 for e in gt.edge]));
R"mtext"("gene $i", line=-1) # hide
end
R"mtext"("numbers: network edge each gene lineage maps to, at time of coalescence.\n8 = number of edge above the network root", side=1, line=-1, outer=true); # hide
R"dev.off()" # hide
nothing # hide
```
exception =
UndefVarError: `plot` not defined in `Main.__atexample__named__getting_started`
Suggestion: check for spelling errors or missing imports.
Stacktrace:
[1] top-level scope
@ getting_started.md:106
[2] eval
@ ./boot.jl:430 [inlined]
[3] #60
@ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [inlined]
[4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:802
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState)
@ Base.CoreLogging ./logging/logging.jl:522
[8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger)
@ Base.CoreLogging ./logging/logging.jl:632
[9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:801
|
|
../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L44
failed to run `@setup` block in src/man/mapping_genetree_to_network.md
```@setup mapping
using PhyloNetworks, PhyloPlots, PhyloCoalSimulations, RCall, DataFrames, StableRNGs
figpath = joinpath("..", "assets", "figures"); mkpath(figpath)
figname(x) = joinpath(figpath, x)
```
exception =
LoadError: The following 1 direct dependency failed to precompile:
PhyloPlots
Failed to precompile PhyloPlots [c0d5b6db-e3fc-52bc-a87d-1d050989ed3b] to "/home/runner/.julia/compiled/v1.11/PhyloPlots/jl_eHttFH".
ERROR: LoadError: UndefVarError: `TraitSubstitutionModel` not defined in `PhyloNetworks`
Suggestion: check for spelling errors or missing imports.
Stacktrace:
[1] getproperty(x::Module, f::Symbol)
@ Base ./Base.jl:42
[2] top-level scope
@ ~/.julia/packages/PhyloPlots/f3q9v/src/substitutionmodels.jl:1
[3] include(mod::Module, _path::String)
@ Base ./Base.jl:557
[4] include(x::String)
@ PhyloPlots ~/.julia/packages/PhyloPlots/f3q9v/src/PhyloPlots.jl:3
[5] top-level scope
@ ~/.julia/packages/PhyloPlots/f3q9v/src/PhyloPlots.jl:21
[6] include
@ ./Base.jl:557 [inlined]
[7] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
@ Base ./loading.jl:2790
[8] top-level scope
@ stdin:5
in expression starting at /home/runner/.julia/packages/PhyloPlots/f3q9v/src/substitutionmodels.jl:1
in expression starting at /home/runner/.julia/packages/PhyloPlots/f3q9v/src/PhyloPlots.jl:3
in expression starting at stdin:
in expression starting at string:1
|
|
../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L44
failed to run `@example` block in src/man/mapping_genetree_to_network.md:51-65
```@example mapping
R"svg"(figname("genetree_example1.svg"), width=7.5, height=3); # hide
R"par"(mar=[.1,.2,.1,.2], oma=[0,0,0,0.8]); R"layout"([1 2]); # hide
plot(net, showedgenumber=true, shownodelabel=true, tipoffset=0.1);
R"mtext"("species network", side=3, line=-1); # hide
R"mtext"("grey: population edge number", side=1, line=-1, cex=0.9); # hide
plot(tree, edgelabel=DataFrame(number=[e.number for e in tree.edge],
label=[e.inte1 for e in tree.edge]),
edgelabelcolor="red4", shownodelabel=true, tipoffset=0.1);
R"mtext"("gene tree", side=3, line=-1); # hide
R"mtext"("red (edge inte1 value): population a gene edge maps into", side=1, line=-2, cex=0.9); # hide
R"mtext"("black (node names): speciation/reticulation a node maps to", side=1, line=-1, cex=0.9); # hide
R"dev.off()" # hide
nothing # hide
```
exception =
LoadError: UndefVarError: `@R_str` not defined in `Main.__atexample__named__mapping`
Suggestion: check for spelling errors or missing imports.
Hint: a global variable of this name may be made accessible by importing RCall in the current active module Main
Stacktrace:
[1] top-level scope
@ :0
[2] eval
@ ./boot.jl:430 [inlined]
[3] #60
@ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [inlined]
[4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:802
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState)
@ Base.CoreLogging ./logging/logging.jl:522
[8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger)
@ Base.CoreLogging ./logging/logging.jl:632
[9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:801
in expression starting at mapping_genetree_to_network.md:52
|
|
../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L44
invalid local link/image: file does not exist in src/man/mapping_genetree_to_network.md
link =
@ast MarkdownAST.Image("../assets/figures/genetree_example1.svg", "") do
MarkdownAST.Text("example 1: degree-2 node names in gene tree")
end
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