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m-orton / Evolutionary-Rates-Analysis-Pipeline

The purpose of this repository is to develop software pipelines in R that can perform large scale phylogenetics comparisons of various taxa found on the Barcode of Life Database (BOLD) API.
GNU General Public License v3.0
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Error message when Sally running Annelida branch - line 869 - Nov 28 #9

Closed sadamowi closed 7 years ago

sadamowi commented 7 years ago

Hi Matt,

I am running the Annelida branch, using the Annelida workspace you sent me. I got the following error when I ran line 869 of the code.

noOutGroupCheck <- foreach(i=1:length(noOutGroupCheck)) %do% which(dfPairingResultsL1$bin_uri == noOutGroupCheck[[i]])

Error in which(dfPairingResultsL1$bin_uri == noOutGroupCheck[[i]]) : task 1 failed - "subscript out of bounds"

Have you seen this error before? Thanks.

Cheers, Sally

sadamowi commented 7 years ago

I reran the script again, starting from a fresh RStudio session. I got this error message a second time.

m-orton commented 7 years ago

So just to confirm, you are not getting any errors now?

sadamowi commented 7 years ago

I closed a couple of the other issues, as I didn't get those errors when I reran the script. However, I did get this error again and so am leaving this open for now.

m-orton commented 7 years ago

Ok I will look into this error today and get back to you.

sadamowi commented 7 years ago

Email from Matt on this issue:

"That nooutgroupcheck variable that gave you an error also gave me an error as well. I realized it was because the variable was empty for Annelida which is why we were getting the subscript out of bounds error. I encased the command in an if statement so it will only run if there are in fact pairings that dont have outgroups."

sadamowi commented 7 years ago

Thank you Matt. I no longer get this error and your solution looks good. Thank you. I will close this issue.