I am working with one of our researchers who is doing
multiple sequence alignment. 

She has 200,000+ sequences in a file. Her code is basically the following:

library("msa")
mySeq <- readAAStringSet("myData.fa")

myFirstAlignment <- msa(mySeq)
msaPrettyPrint(MyFirstAlignment, output=c("pdf", "tex", "dvi", "asis"))

But, R is crashing during the msa function, with the following error message:

 *** caught segfault ***
address 0x7f5ace31d0d0, cause 'memory not mapped'

Traceback:
 1: .Call("RClustalW", inputSeqs, cluster, abs(gapOpening), abs(gapExtension),     maxiters, substitutionMatrix, type, verbose, params, PACKAGE = "msa")

We are running R 3.4.3.  I have uninstalled and reinstalled the msa package and its dependencies.

Is there anything else we could try, or is this a limitation due to the size of the data?

Thank you for your response.  We will try ClustalOmega.

Thanks for reporting this issue! As far as I can see, my suspicion is indeed the vast amount of data. Actually, ClustalW is not made for such excessive amounts of data. I would rather suggest to use ClustalOmega instead. If that does not work via 'msa' either, maybe the last resort is to use stand-alone ClustalOmega. Sorry that I cannot be more helpful.