wrong warning readTableCF

[crsl4]

I am reading a table produced by readTrees2CF and I get a warning that the column names do not match, when they do.
I will come back to debug this, but I don't have time right now, and wanted to document it.

julia> cf = readTableCF("1_astral_cf.txt")
┌ Warning: Column names for quartet concordance factors (CFs) were not recognized.
│ Was expecting CF12_34, CF13_24 and CF14_23 for the columns with CF values,
│ or CF12.34 or obsCF12, etc.
│ Will assume that the first 4 columns give the taxon names, and that columns 5-7 give the CFs.
└ @ PhyloNetworks ~/.julia/packages/PhyloNetworks/zeoh2/src/readData.jl:115
Object DataCF
number of quartets: 15


shell> head 1_astral_cf.txt
t1,t2,t3,t4,CF12_34,CF13_24,CF14_23,ngenes
1,2,3,4,1.0,0.0,0.0,30.0
1,2,3,5,1.0,0.0,0.0,30.0
1,2,3,6,1.0,0.0,0.0,30.0
1,2,4,5,1.0,0.0,0.0,30.0
1,2,4,6,1.0,0.0,0.0,30.0
1,2,5,6,1.0,0.0,0.0,30.0
1,3,4,5,0.0,0.13333333333333333,0.8666666666666667,30.0
1,3,4,6,0.0,0.13333333333333333,0.8666666666666667,30.0
1,3,5,6,0.5333333333333333,0.13333333333333333,0.3333333333333333,30.0

[cecileane]

I think this is due to an update to DataFrames. What version of DataFrames do you use? Can you try pinning DataFrames to 0.20 and see if the error goes away?

Fixing this is on my to-do list. names returns a vector of Strings with DataFrames 0.21. It used to return a vector of Symbols. We need to change DataFrames.names to DataFrames.propertynames.

For now, the master version of PhyloNetworks has upper bounds for all dependencies, in Project.toml. We will need to have these upper bounds anyway, for registering the next version.

[crsl4]

Agh! For some reason, I missed your reply, and since this error, I updated Julia and PhyloNetworks, so I don't know which version of DataFrames I was using. I do not get this warning anymore with Julia 1.4.2 and PhyloNetworks v0.11.0#master.
I am happy to close this issue, but we can leave it open if you prefer since you mention you have something in your to-do list

[cecileane]

Let's close this. There are 3 PRs in the queue, and then I'll take care of updating the package to work with the most recent version of DataFrames. In any case:

• the master version of PhyloNetworks is fine, since upper bounds are in Project.toml, regardless of whether we update the package.
• the registered version is still causing issues for users (no upper bounds), but we can't register a new version until the current work in progress is in a better shape.