Error in ncol(snps.ori) : object 'snps.ori' not found

[Tonny-zhou]

Dear author,

Thank you very much for this great gwas tool! I am sorry for bothering you... When I was running the sample data, I encountered an error. Can you help me solve it ?

>data(snps)
>data(phen)
>data(tree)
>treeWAS(snps = snps,phen = phen,tree = tree,seed = 1)

1414 snps columns are over 50% NAs.
            You may want to consider removing these columns as they are unlikely to be significant
            and can generate inappropriate inferences during ancestral state reconstruction.Note: Updating n.snps.sim to match 10x the number of real loci after data cleaning.
                Input: 200030 -->
                Updated: 184510
[1] "treeWAS snps sim done @ 2022-11-08 18:27:18"
Error in ncol(snps.ori) : object 'snps.ori' not found

[myoungblom]

I am having the same error (not with sample data but real data). I have used treeWAS previously (~2020) and didn't have this issue so I believe it is being caused by a more recent change. Hoping it will be a simple fix! :)

[caitiecollins]

Oh dear, must be a bug! I'll try to get it fixed by tomorrow.

[caitiecollins]

Thanks for your patience.
The error should be fixed now!
Please let me know how it goes.

#bugHaiku

[Estellaknight]

Thanks for your patience. The error should be fixed now! Please let me know how it goes.

#bugHaiku

I re-installed the package after the bug fixed, but still got the same error messages with the sample data. Is there any suggestion for it? Many thx!

[caitiecollins]

The snps.ori error or the other warning messages or both?

[Estellaknight]

The snps.ori error or the other warning messages or both?

Thx for the quick reply! It was the snps.ori error. Exactly like this one:"Error in ncol(snps.ori) : object 'snps.ori' not found".

[ruutmdlv]

I found the same error! ("Error in ncol(snps.ori) : object 'snps.ori' not found"). I also reinstalled and continue having the same problem.

[caitiecollins]

I'll take another look at it today. Thanks for letting me know.

[caitiecollins]

I'm struggling to reproduce the snps.ori error with the most recent version installed.
Could anyone still getting the snps.ori error please run these lines and tell me what it returns:

pi <- package_info()
pi[pi$package=="treeWAS",]

Thank you.

[ruutmdlv]

Restarted my pc and now works great. Thanks a lot for the fast fixing!

[caitiecollins]

Huzzah! Glad to hear it.

[Estellaknight]

Huzzah! Glad to hear it.

I just restarted the Mac and it can work normally now. Really appreciate your effort and following ups!