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kwsparks pbastide

phyloplots.jl's Issues

need Gadfly-based plots

For now, Gadfly-based functions have been commented out. Using both Gadfly and RCall causes compilation errors. Things run & test fine if using Gadfly only, or using RCall only (current choice). Using both works if we don't use PhyloNetworks also... These issues were with using:

- Gadfly                        0.6.5+ commit c778af59f9, tagged v0.7.0
- RCall                         0.10.3
- PhyloNetworks                 0.6.0+ commit 88b8ac5107

warning messages when using RCall (with or without Gadfly): many messages this one, with "R_NaString" replaced by various things from RCall

WARNING: eval from module Const to PhyloPlots:    
Expr(:block, Expr(:line, 73, Symbol("/Users/ane/.julia/v0.6/RCall/src/Const.jl"))::Any, Expr(:., :NaString, Expr(:quote, :p)::Any)::Any = Expr(:call, :unsafe_load, Expr(:call, :cglobal, "R_NaString", Expr(:call, :typeof, Expr(:., :NaString, Expr(:quote, :p)::Any)::Any)::Any)::Any)::Any)::Any
  ** incremental compilation may be broken for this module **

error messages when using all 3 packages, RCall, Gadfly, PhyloNetworks (the stacktrace looks useless):

ERROR: LoadError: MethodError: no method matching convert(::Type{AssertionError}, ::String)
Closest candidates are:
  convert(::Type{Any}, ::ANY) at essentials.jl:28
  convert(::Type{T}, ::T) where T at essentials.jl:29

and final error:

MethodError(Core.Inference.convert, (AssertionError, "invalid age range update"), 0x0000000000000ac6)

the net1 show the wrong topology

Hi

I am not perfectly familiar with SNaQ, and I run it for the first time for my data with 6 taxa (5 ingroups and one outgroup).

I have one question about comparing the trees; when I compare the astral tree and net0, there are no differences between them, as I expected.
The part that I can not understand is that net1 shows the different topology that is not true. How can I fix it?

Would you please let me know when the network's topology changed and why?

Thanks a lot
Niloo

Failed to compile errors

I installed PhyloPlots today, and I cannot load it:

julia> using PhyloPlots
[ Info: Precompiling PhyloPlots [c0d5b6db-e3fc-52bc-a87d-1d050989ed3b]
ERROR: LoadError: LoadError: LoadError: UndefVarError: @printf not defined
Stacktrace:
 [1] top-level scope
 [2] include(::Function, ::Module, ::String) at ./Base.jl:380
 [3] include at ./Base.jl:368 [inlined]
 [4] include(::String) at /Users/Clauberry/.julia/packages/Optim/5JqO8/src/Optim.jl:18
 [5] top-level scope at /Users/Clauberry/.julia/packages/Optim/5JqO8/src/Optim.jl:106
 [6] include(::Function, ::Module, ::String) at ./Base.jl:380
 [7] include(::Module, ::String) at ./Base.jl:368
 [8] top-level scope at none:2
 [9] eval at ./boot.jl:331 [inlined]
 [10] eval(::Expr) at ./client.jl:467
 [11] top-level scope at ./none:3
in expression starting at /Users/Clauberry/.julia/packages/Optim/5JqO8/src/types.jl:66
in expression starting at /Users/Clauberry/.julia/packages/Optim/5JqO8/src/types.jl:64
in expression starting at /Users/Clauberry/.julia/packages/Optim/5JqO8/src/Optim.jl:106
ERROR: LoadError: Failed to precompile Optim [429524aa-4258-5aef-a3af-852621145aeb] to /Users/Clauberry/.julia/compiled/v1.5/Optim/R5uoh_TiTLt.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1305
 [3] _require(::Base.PkgId) at ./loading.jl:1030
 [4] require(::Base.PkgId) at ./loading.jl:928
 [5] require(::Module, ::Symbol) at ./loading.jl:923
 [6] include(::Function, ::Module, ::String) at ./Base.jl:380
 [7] include(::Module, ::String) at ./Base.jl:368
 [8] top-level scope at none:2
 [9] eval at ./boot.jl:331 [inlined]
 [10] eval(::Expr) at ./client.jl:467
 [11] top-level scope at ./none:3
in expression starting at /Users/Clauberry/.julia/packages/KernelDensity/JfNeR/src/KernelDensity.jl:5
ERROR: LoadError: LoadError: Failed to precompile KernelDensity [5ab0869b-81aa-558d-bb23-cbf5423bbe9b] to /Users/Clauberry/.julia/compiled/v1.5/KernelDensity/4QyGx_TiTLt.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1305
 [3] _require(::Base.PkgId) at ./loading.jl:1030
 [4] require(::Base.PkgId) at ./loading.jl:928
 [5] require(::Module, ::Symbol) at ./loading.jl:923
 [6] include(::Function, ::Module, ::String) at ./Base.jl:380
 [7] include at ./Base.jl:368 [inlined]
 [8] include(::String) at /Users/Clauberry/.julia/packages/Gadfly/cqMtH/src/Gadfly.jl:1
 [9] top-level scope at /Users/Clauberry/.julia/packages/Gadfly/cqMtH/src/Gadfly.jl:1111
 [10] include(::Function, ::Module, ::String) at ./Base.jl:380
 [11] include(::Module, ::String) at ./Base.jl:368
 [12] top-level scope at none:2
 [13] eval at ./boot.jl:331 [inlined]
 [14] eval(::Expr) at ./client.jl:467
 [15] top-level scope at ./none:3
in expression starting at /Users/Clauberry/.julia/packages/Gadfly/cqMtH/src/statistics.jl:22
in expression starting at /Users/Clauberry/.julia/packages/Gadfly/cqMtH/src/Gadfly.jl:1111
ERROR: LoadError: Failed to precompile Gadfly [c91e804a-d5a3-530f-b6f0-dfbca275c004] to /Users/Clauberry/.julia/compiled/v1.5/Gadfly/DvECm_TiTLt.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1305
 [3] _require(::Base.PkgId) at ./loading.jl:1030
 [4] require(::Base.PkgId) at ./loading.jl:928
 [5] require(::Module, ::Symbol) at ./loading.jl:923
 [6] include(::Function, ::Module, ::String) at ./Base.jl:380
 [7] include(::Module, ::String) at ./Base.jl:368
 [8] top-level scope at none:2
 [9] eval at ./boot.jl:331 [inlined]
 [10] eval(::Expr) at ./client.jl:467
 [11] top-level scope at ./none:3
in expression starting at /Users/Clauberry/.julia/packages/PhyloPlots/CBmgP/src/PhyloPlots.jl:12
ERROR: Failed to precompile PhyloPlots [c0d5b6db-e3fc-52bc-a87d-1d050989ed3b] to /Users/Clauberry/.julia/compiled/v1.5/PhyloPlots/Pfae6_TiTLt.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1305
 [3] _require(::Base.PkgId) at ./loading.jl:1030
 [4] require(::Base.PkgId) at ./loading.jl:928
 [5] require(::Module, ::Symbol) at ./loading.jl:923

I am working on Julia 1.5.1 and these are the packages that I have

(@v1.5) pkg> status
Status `~/.julia/environments/v1.5/Project.toml`
  [a93c6f00] DataFrames v0.20.2
  [31c24e10] Distributions v0.23.12
  [634d3b9d] DrWatson v1.16.6
  [7073ff75] IJulia v1.23.1
  [ff71e718] MixedModels v3.1.1
  [33ad39ac] PhyloNetworks v0.11.0
  [c0d5b6db] PhyloPlots v0.2.2
  [b98c9c47] Pipe v1.3.0
  [6f49c342] RCall v0.13.6
  [2913bbd2] StatsBase v0.33.2
  [44d3d7a6] Weave v0.10.6

I later tracked the master branch, but I get the same errors:

(@v1.5) pkg> status
Status `~/.julia/environments/v1.5/Project.toml`
  [a93c6f00] DataFrames v0.20.2
  [31c24e10] Distributions v0.23.12
  [634d3b9d] DrWatson v1.16.6
  [7073ff75] IJulia v1.23.1
  [ff71e718] MixedModels v3.1.1
  [33ad39ac] PhyloNetworks v0.11.0
  [c0d5b6db] PhyloPlots v0.2.2 `https://github.com/cecileane/PhyloPlots.jl.git#master`
  [b98c9c47] Pipe v1.3.0
  [6f49c342] RCall v0.13.6
  [2913bbd2] StatsBase v0.33.2
  [44d3d7a6] Weave v0.10.6

the progress bar keeps getting stuck

When installing PhyloPlots using the Julia package, the system does not report an error, but the progress bar keeps getting stuck and I don't know what the problem is.
image

Trouble precompiling PhyloPlots

I had no trouble precompiling PhyloPlots on my MacBook Plus. My identically configured Mac Mini yields the following:

julia> import PhyloPlots
[ Info: Precompiling PhyloPlots [c0d5b6db-e3fc-52bc-a87d-1d050989ed3b]
FATAL ERROR: Symbol "ccalllib_libR.dylib574"not found
signal (6): Abort trap: 6
in expression starting at /Users/roth9lab/.julia/packages/PhyloPlots/CBmgP/src/PhyloPlots.jl:14
__pthread_kill at /usr/lib/system/libsystem_kernel.dylib (unknown line)
Allocations: 24212978 (Pool: 24204272; Big: 8706); GC: 18
ERROR: Failed to precompile PhyloPlots [c0d5b6db-e3fc-52bc-a87d-1d050989ed3b] to /Users/roth9lab/.julia/compiled/v1.5/PhyloPlots/Pfae6_BC6hT.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1290
 [3] _require(::Base.PkgId) at ./loading.jl:1030
 [4] require(::Base.PkgId) at ./loading.jl:928
 [5] require(::Module, ::Symbol) at ./loading.jl:923

I can't find ccalllib_libR.dylib574 on either machine. I have reinstalled R and am using the same version Julia on both (1.5.0). I always work from a conda environment running Python 2.7.15, well isolated from the rest of the machine.

Any suggestions would be greatly appreciated.

plot on remove server: window doesn't open

Hi

I want to do network analyses for my dataset.

I am working on the server (EVE), and I install both packages, "PhyloNetworks" and "PhyloPlots" in julia.

when I type:

using PhyloNet
the julia doesn't complain,

and when I type plot, it shows me:

plot (generic function with 11 methods)

Everything looks good, but when I use the plot (e.g., plot(genetrees[3], :R);), it doesn't show me anything, no result, no error,.....

Is it possible that the plot doesn't work on the server?

Would you please let me have your idea to solve my problem?

With the best
Niloo

error in documentation?

Hi Cecile, I am running the steps in the documentation, and I get one error:

julia> using RCall

julia> using PhyloNetworks

julia> net = readTopology("(((A:.2,(B:.1)#H1:.1::0.9):.1,(C:.11,#H1:.01::0.1):.19):.1,D:.4);");

julia> using PhyloPlots

julia> @rput net
PhyloNetworks.HybridNetwork, Rooted Network
9 edges
9 nodes: 4 tips, 1 hybrid nodes, 4 internal tree nodes.
tip labels: A, B, C, D
(((A:0.2,(B:0.1)#H1:0.1::0.9):0.1,(C:0.11,#H1:0.01::0.1):0.19):0.1,D:0.4);


R> str(net)
List of 7
 $ edge               : int [1:8, 1:2] 5 5 6 6 7 8 8 9 6 4 ...
 $ reticulation.length: num 0.01
 $ Nnode              : int 5
 $ edge.length        : num [1:8] 0.1 0.4 0.1 0.19 0.11 0.2 0.1 0.1
 $ reticulation       : int [1, 1:2] 7 9
 $ reticulation.gamma : num 0.1
 $ tip.label          : chr [1:4] "A" "B" "C" "D"
 - attr(*, "class")= chr [1:2] "evonet" "phylo"

R> plot(net)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'

I am able to plot with plot(net,:RCall) without problems.
I just did Pkg.update() yesterday, could that be the problem?

This is my info:

julia> versioninfo()
Julia Version 0.6.2
Commit d386e40c17 (2017-12-13 18:08 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin14.5.0)
  CPU: Intel(R) Core(TM) i5-7267U CPU @ 3.10GHz
  WORD_SIZE: 64
  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Prescott)
  LAPACK: libopenblas64_
  LIBM: libopenlibm
  LLVM: libLLVM-3.9.1 (ORCJIT, broadwell)

julia> Pkg.status()
 - CSV                           0.2.2
 - DataFrames                    0.11.5
 - PhyloNetworks                 0.7.0+             master
 - PhyloPlots                    0.1.0
 - RCall                         0.10.5

Thanks!

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