I’m using macOS Sierra (10.12.6) on a Macbook Pro. RStudio Version 1.1.423. I just installed rcpp and rstan from source. xtools has been updated today as well.
I am repeatedly getting a segfault (output below) but only when I run my Rnw (knitr) file. When I run the code chunk by chunk, it all works fine. If I run the stan model separately from the Rnw file and just try to save the fitted model and then load it into the Rnw file using load (i.e., I try to avoid fitting the model at all within the Rnw), I still get the same segfault. Weirdly, if I now move all my code into an Rmd file and run that file (with all the stan models in it), it works fine!
Here is the segfault message:
*** caught segfault ***
address 0x1126e4198, cause ‘memory not mapped’
Traceback:
1: .Call(list(name = “CppObject__finalize”, address = <pointer: 0x7f951081f7b0>, dll = list(name = “Rcpp”, path = “/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/libs/Rcpp.so”, dynamicLookup = TRUE, handle = <pointer: 0x7f9510831fb0>, info = <pointer: 0x1067ee1e0>), numParameters = 2L), <pointer: 0x7f950de12360>, .pointer)
2: x$.self$finalize()
3: (function (x) x$.self$finalize())()
An irrecoverable exception occurred. R is aborting now …
That is weird. I am going to guess that the background R process that does the knitting is finding a different version of some package than when you do it in an interactive session. Try
ip <- installed.packages()
dupes <- duplicated(ip)
if(any(dupes)) rownames(ip)[dupes]
to see if there are any packages you have installed multiple times in different directories.
I think this problem is only happening for one particular set of Rnw files. If I compile some other paper in another directory, all Stan models run fine. Makes me think that maybe I have a .Rhistory or .Rdata or something hiding somewhere. But I don’t see any hidden files anywhere.
to see hidden files. You might also have an outdated .rda file that is getting picked up. Or perhaps you have cache = TRUE in your chunk options and the cache is corrupted somehow.
I think I have come closer to isolating the problem. I compiled the Rnw from the command line using Rscript, and everything compiles fine. This means it’s a problem with RStudio. But I couldn’t figure out why RStudio and rstan work fine when I compile some other document, but not the one I am working on. I restarted in a fresh directory, incrementally building up my document, but I still get the error. My problematic document is a book draft.
So essentially I am giving up and will just compile from the command line. I guess I should have written a Makefile in the first place, should stop using RStudio anyway and go back to emacs.
I’m so sorry to hear that. Config issues like this are even more frustrating than programming issues.
If I understand correctly, your knitr document works OK running R from the command line, but not through RStudio.
P.S. My advice for debugging this kind of thing is to divide-and-conquer (I would say that as a computer scientist). Take the header of your doc and see if it works with just a title and some dummy text. Then insert things bit by bit until it breaks. You can also just keep cutting it in half until you get a minimal example that fails.
Yes, I agree this is a good strategy. This is what I tried, and this is how I lost a day or so. I figured out where the problems begin but not why. I guess if I spend enough time on it I will work it out, but it just doesn’t seem worth the effort any more. I have more important things to do so I just by-passed this by compiling from the command line. I’m at Henrik’s fifth stage of software development, the highest stage there is!
That’s just level one. Then there’s C++. We regularly spend days trying to debug things that fail for one one compiler on one platform. Daniel and I would regularly go days without being able to get over compiler bugs.
