Problems with Maaslin2

[Bruno Gabriel Andrade]

Dear Maaslin developers, Maaslin2 is returning an annoying error that I can identify:

"2019-04-04 14:41:23 INFO::Plotting data for metadata number 1, Diet

2019-04-04 14:41:23 INFO::Creating boxplot for catgorical data, Diet vs ASV_2

Error in if (nchar(msg) > 8192) { : argument with zero length

Calls: Maaslin2 ... <Anonymous> -> .levellog -> <Anonymous> -> composer_f"

Does anyone here know what is going on?

[samantha...@gmail.com]

I have recently run into the same problem. The description file says I am using version 0.2. 

It seems to fit the model per feature appropriately, but breaks during the creation of the boxplots. My error had additional lines though:

...
2019-04-12 11:19:45 INFO::Creating boxplot for catgorical data, Day vs UniRef90_R9KU54
Error in if (nchar(msg) > 8192) { : argument is of length zero

Calls: Maaslin2 ... <Anonymous> -> .levellog -> <Anonymous> -> composer_f

In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

When I went in and looked in my log file (which I will attach) after each attempt for a boxplot there is a debug error:

2019-04-12 11:19:45 DEBUG::notch went outside hinges. Try setting notch=FALSE.

I went back and looked at the help options for Maaslin2 (Maaslin2.R -h) and I don't see an option for notch. Could someone explain what notch is and how I set it to false? What what the underlying problem with the data seems to be?

Thanks,
Samantha

[Jeremy Wilkinson]

Try installing the newest version of MaAsLin2 (ref="0.2.3") and see if that makes it run smoothly. It's still having small tweaks made to it, so the versions are being updated occasionally. 

-Jeremy

[samantha...@gmail.com]

After many R version errors I finally got version 0.2.3 installed!  

It seems to have worked! My only remaining question is whether there's a finished message? Meaning the last line of code output to the log file is this:

2019-04-15 16:46:53 INFO::Creating boxplot for catgorical data, Treatment vs UniRef90_UPI0004289577

Is that/something similar the expected last line or is something missing?

Thanks,

Samantha