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sherman5 / RVS

Computes estimates of the probability of related individuals sharing a rare variant.
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multipleVariantPValue function stopped working and Error in sort.int #4

Closed klmartinez closed 5 years ago

klmartinez commented 5 years ago

I was able to successfully run RVS and the multipleVariantPValuefunction on a set of 2 exome families a few days ago.

Yesterday I tried running the same script and received the following errors:

> resultB <- multipleVariantPValue(fam27_28$genotypes, fam27_28$fam, sharingProbs, filter='bonferroni', alpha=0.05) 
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 'x' must be atomic 
> traceback() 
5: stop("'x' must be atomic") 
4: sort.int(x, na.last = na.last, decreasing = decreasing, ...) 
3: sort.default(unname(pot_pvals)) 
2: sort(unname(pot_pvals)) 
1: multipleVariantPValue(fam27_28$genotypes, fam27_28$fam, sharingProbs, filter = "bonferroni", alpha = 0.05)

My inputs haven't changed so I am not sure what I am doing wrong. My understanding of the error is that one of the inputs isn't formatted correctly, but this was all running successfully only a few days ago. The only inconsistency is that my version of RVS stopped working, and I had to re-install the updated "sherman5/RVS" version. What could I be doing wrong?

sherman5 commented 5 years ago

We haven't changed RVS recently, but a new version of Bioconductor came out a month ago, as well as a new version of R (3.6.0). My only guess is one of these version changes affected a dependency in RVS. As of now, we're still seeing clean builds - so I'm not sure what exactly the problem was. Is everything working ok now that you reinstalled?

klmartinez commented 5 years ago

I am having the same error after re-installing. I can try re-installing the older versions of Bioconductor and R.

sherman5 commented 5 years ago

What are your current versions of Bioconductor, R, and RVS?

klmartinez commented 5 years ago

R 3.6.0 RVS 1.5.4 BiocManager 1.30.4

klmartinez commented 5 years ago

One new thing I did notice is that instead of using BiocManager::install("sherman5/RVS") to install RVS, I have to now install using remotes::install_github("sherman5/RVS")...

klmartinez commented 5 years ago

I forgot to update with the solution that worked for me. I use these specific versions to successfully run RVS:

R 3.5.2 RVS 1.5.4 BiocManager 3.8