Recurring warning after using functions that permute data

[Hunterefs]

Hello,

I've been using vegan to analyze a set of gene expression data - I have lots of columns so I have been using rda() and metaMDS() to permute my dataset. Often after doing so I encounter this warning:

x <- rda(data) Warning messages: 1: Unknown or uninitialised column: loadings. 2: Unknown or uninitialised column: loadings.

Once this warning message appears, it does not disappear until I clear my environment or start a new session. Strangely, R will produce this warning when I attempt to run unrelated code - even comment lines will trigger it. It is also variable in how many times it produces this warning, it can range from 1 to 20+ identical warnings. Reloading a workspace image that this warning occurred in will continue to give warning - it seems like the data needs to be totally cleared. Also, I'm not sure if it is relevant or not, but my dataset includes negative values.

This is the first time I have submitted a ticket, so please let me know if I can include anything more that might help with this!

Thanks,

• Hunter

[gavinsimpson]

It sounds like the output raising the warning is being buffered.

You could turn warnings into errors and then do a traceback() when you hit the warning (now error) to see what causing it, and post that traceback() output if you need more help tracking it down.

op <- options(warn = 3)

If you want to turn this off again, do

options(op)

Also make sure you are loading a hidden .RData file on startup.

[Hunterefs]

Hi Gavin, I tried that options() line and the warning stopped popping up so I couldn't trace it back. I'll try to code as much as I can with that options() line turned on.

What do you mean by loading a hidden .RData file? Just prior to submitting this ticket I actually went and deleted the hidden .RData file my workspace kept loading from, since it would reload whatever was causing the warning.