hi dirk---look, it's a fickle bus segfault. if you read my email in full,
you will note that even eliminating an irrelevant print(head()) statement
makes it go away. we are lucky it is reproducible and thus easy to track
down for whoever wrote the code, given my code AND the data, of course.
(maybe it could do with me trying to create data that are random, maybe
not. but there is no point to me doing so. if we have the bug
reproducible, we should chase it down when we know it appears.) I know
that you cannot reproduce it from what I have posted. I also wrote that I
will bring the tarball (with the files) into my office tomorrow to see if I
can make it remotely available to simon or you, if you are interested.
I am trying to help...it did take me a day to reduce the code to figure out
what went wrong,, and an hour to get it to this point where it is easily
understandable, reproducible, and digestable by you.
regards,
/iaw
----
Ivo Welch (ivo.we...@gmail.com)
On Sun, Jul 14, 2013 at 9:20 AM, Dirk Eddelbuettel <e...@debian.org> wrote:
>
> On 14 July 2013 at 09:04, ivo welch wrote:
> | thanks, simon. it's replicable even on
> |
> | R version 3.0.1 Patched (2013-07-13 r63293) -- "Good Sport"
> |
> | (I presume that it is loading its own updated dynamic libraries when I
> | installed it in a temporary directory and am invoking it as
> | "temp/R-patched/bin/R", and not the system-wide unpatched version.) the
>
> It "should" stay within its own tree. I call my r-devel builds with a
> two-line shell script wrapper to make sure its bin/ directory is prefixed
> to
> the $PATH.
>
> | program that causes it is small enough to be displayable
> |
> | if (interactive()) options(error=recover)
> | year <- 1982
> |
> | for (yr in (year-6):year) {
> | ifname <- paste0("dbetas/dbetas-",yr, ".Rdata")
>
> That is obviously NOT reproducible as we do not have your files.
>
> If possible, please create a _self-contained reproducible script_ as it
> ought
> to be possible to create such data matrices with random data.
>
> Dirk
>
> | load(ifname)
> | print(head(dbetas,2)) ## if you remove this, then the core dump goes
> | away
> | dm <- if (!exists("dm")) dbetas else rbind(dm, dbetas)
> | cat("[Loaded ", yr,"]\n")
> | }
> | cat("\n[", now(), "Loaded All Data]\n")
> |
> |
> | Reproducing the error,
> |
> | # r-devel/R-patched/bin/R --vanilla
> |
> | R version 3.0.1 Patched (2013-07-13 r63293) -- "Good Sport"
> | Copyright (C) 2013 The R Foundation for Statistical Computing
> | Platform: x86_64-unknown-linux-gnu (64-bit)
> |
> | R is free software and comes with ABSOLUTELY NO WARRANTY.
> | You are welcome to redistribute it under certain conditions.
> | Type 'license()' or 'licence()' for distribution details.
> |
> | Natural language support but running in an English locale
> |
> | R is a collaborative project with many contributors.
> | Type 'contributors()' for more information and
> | 'citation()' on how to cite R or R packages in publications.
> |
> | Type 'demo()' for some demos, 'help()' for on-line help, or
> | 'help.start()' for an HTML browser interface to help.
> | Type 'q()' to quit R.
> |
> | > source("coredump.R")
> | permno yyyymmdd lagmval beta
> | 31303 10006 19760102 219450 -0.81162794
> | 31304 10006 19760105 218025 -0.01280477
> | [Loaded 1976 ]
> | permno yyyymmdd lagmval beta
> | 31556 10006 19770103 304709.4 4.5770379
> | 31557 10006 19770104 301456.2 -0.3810519
> | [Loaded 1977 ]
> | permno yyyymmdd lagmval beta
> | 31808 10006 19780103 301219.5 1.277823
> | 31809 10006 19780104 296854.0 2.671327
> | [Loaded 1978 ]
> | permno yyyymmdd lagmval beta
> | 32060 10006 19790102 269308.5 -0.06000999
> | 32061 10006 19790103 269308.5 -0.83697042
> | [Loaded 1979 ]
> | permno yyyymmdd lagmval beta
> | 32313 10006 19800102 303420.8 -0.3768525
> | 32314 10006 19800103 305635.5 2.2475787
> | Error in rbind(deparse.level, ...) :
> | 'pairlist' object cannot be coerced to type 'double'
> |
> | Enter a frame number, or 0 to exit
> |
> | 1: source("coredump.R")
> | 2: withVisible(eval(ei, envir))
> | 3: eval(ei, envir)
> | 4: eval(expr, envir, enclos)
> | 5: coredump.R#8: rbind(dm, dbetas)
> | 6: rbind(deparse.level, ...)
> |
> | Selection: 6
> | Called from: eval(substitute(browser(skipCalls = skip), list(skip = 7 -
> | which)),
> | envir = sys.frame(which))
> | Browse[1]> head(dm)
> | permno yyyymmdd lagmval beta
> | 31303 10006 19760102 219450 -0.81162794
> | 31304 10006 19760105 218025 -0.01280477
> | 31305 10006 19760106 218025 7.26041268
> | 31306 10006 19760107 236550 -1.23044474
> | 31307 10006 19760108 235125 3.02461687
> | 31308 10006 19760109 239400 2.04868169
> | Browse[1]> head(rbind(dm,dbetas))
> |
> | *** caught segfault ***
> | address 0x10, cause 'memory not mapped'
> |
> | Traceback:
> | 1: rbind(deparse.level, ...)
> | 2: rbind(dm, dbetas)
> | 3: head(rbind(dm, dbetas))
> | 4: eval(expr, envir, enclos)
> | 5: eval(substitute(browser(skipCalls = skip), list(skip = 7 - which)),
> | envir = sys.frame(which))
> | 6: (function () { if (.isMethodsDispatchOn()) { tState <-
> | tracingState(FALSE) on.exit(tracingState(tState)) } calls <-
> | sys.calls() from <- 0L n <- length(calls) if
> | (identical(sys.function(n), recover)) n <- n - 1L for (i in
> | rev(seq_len(n))) { calli <- calls[[i]] fname <- calli[[1L]]
> | if (!is.na(match(deparse(fname)[1L], c("methods::.doTrace",
> | ".doTrace")))) { from <- i - 1L break }
> }
> | if (from == 0L) for (i in rev(seq_len(n))) { calli
> <-
> | calls[[i]] fname <- calli[[1L]] if (!is.name
> (fname)
> | || is.na(match(as.character(fname), c("recover", "stop",
> | "Stop")))) { from <- i break }
> | } if (from > 0L) { if (!interactive()) {
> | try(dump.frames()) cat(gettext("recover called
> | non-interactively; frames dumped, use debugger() to view\n"))
> | return(NULL) } else if
> | (identical(getOption("show.error.messages"), FALSE))
> | return(NULL) calls <- limitedLabels(calls[1L:from])
> repeat
> | { which <- menu(calls, title = "\nEnter a frame number, or 0
> to
> | exit ") if (which)
> | eval(substitute(browser(skipCalls = skip), list(skip = 7 -
> | which)), envir = sys.frame(which)) else break } }
> | else cat(gettext("No suitable frames for recover()\n"))})()
> | 7: rbind(deparse.level, ...)
> | 8: rbind(dm, dbetas)
> | 9: eval(expr, envir, enclos)
> | 10: eval(ei, envir)
> | 11: withVisible(eval(ei, envir))
> | 12: source("coredump.R")
> |
> | Possible actions:
> | 1: abort (with core dump, if enabled)
> | 2: normal R exit
> | 3: exit R without saving workspace
> | 4: exit R saving workspace
> | Selection:
> |
> |
> | the data files used are about 60mb. this is all happening on a home
> | machine, which is not easy to ssh into. however, I can bring it into the
> | office and see if I can replicate it there, too. if I can, I could put
> it
> | up and give you an account on my machine. or I can tar it up incl the
> data
> | and put it somewhere for download. whatever you prefer.
> |
> | regards,
> |
> | /iaw
> | ----
> | Ivo Welch (ivo.we...@gmail.com)
> |
> | [[alternative HTML version deleted]]
> |
> | ______________________________________________
> | R-devel@r-project.org mailing list
> | https://stat.ethz.ch/mailman/listinfo/r-devel
>
> --
> Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com
>
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