[R-sig-Debian] Debian packaging and openblas related crash when profiling in R

[Paul Johnson]

Hello R-sig-debian and (hopefully) Dirk:

On Debian wheezy, I have the R packaging that CRAN (you) provide.  I
run into a little trouble while trying to fiddle with alternative
BLAS.

I know you and I went around on this last year and I think perhaps
I've found something wrong in the framework, or I've just done
something wrong.

I installed the packages openblas-base and openblas-dev, and they do
the "update alternatives" thing so that their shared library is at the
right spot. I can't tell if R runs any faster, but it does run, which
is encouraging.

Now here's the problem I see. Using Rprof causes R to crash, but only
when openblas stuff is in the picture. I wondered what you think?

Here's the code to reproduce this:

datM <- read.csv("http://pj.freefaculty.org/scraps/profile/missingDat.csv")
library(Amelia)
set.seed(12345)
Rprof("Amelia-1.out")
impA <- amelia(datM, m = 5, idvars="group")
Rprof(NULL)
summaryRprof("Amelia-1.out")


Here's the crashed session

> datM <- read.csv("http://pj.freefaculty.org/scraps/profile/missingDat.csv")
> library(Amelia)
Loading required package: foreign
##
## Amelia II: Multiple Imputation
## (Version 1.6.3, built: 2012-06-21)
## Copyright (C) 2005-2012 James Honaker, Gary King and Matthew Blackwell
## Refer to http://gking.harvard.edu/amelia/ for more information
##
> set.seed(12345)
> Rprof("Amelia-1.out")
> impA <- amelia(datM, m = 5, idvars="group")
-- Imputation 1 --

 1
 *** caught segfault ***
address 0x11000088, cause 'memory not mapped'
Warning: stack imbalance in 'length', 121 then 122
Warning: stack imbalance in '==', 120 then 121
Warning: stack imbalance in 'if', 118 then 119
Warning: stack imbalance in '<-', 120 then 124
Warning: stack imbalance in '<-', 97 then 94
Warning: stack imbalance in 'min', 117 then 116
Warning: stack imbalance in 'min', 117 then 118

Traceback:
 1: am.inv(a = g11)
 2: doTryCatch(return(expr), name, parentenv, handler)
 3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 4: tryCatchList(expr, classes, parentenv, handlers)
 5: tryCatch(expr, error = function(e) {    call <- conditionCall(e)
 if (!is.null(call)) {        if (identical(call[[1L]],
quote(doTryCatch)))             call <- sys.call(-4L)        dcall <-
deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")
  LONG <- 75L        msg <- conditionMessage(e)        sm <-
strsplit(msg, "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") +
nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L +
nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")
     if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }
 else prefix <- "Error : "    msg <- paste0(prefix,
conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if
(!silent && identical(getOption("show.error.messages"),         TRUE))
{        cat(msg, file = stderr())
.Internal(printDeferredWarnings())    }    invisible(structure(msg,
class = "try-error", condition = e))})
 6: try(am.inv(a = g11), silent = TRUE)
 7: amsweep(thetareal, c(FALSE, o[ss, ]))
 8: emfred(x, thetaold, indx$o, indx$m, indx$ivector, indx$icap,
indx$AMr1, indx$AMr2, AM1stln = AM1stln, returntype = "theta",
priors = priors, empri = empri, collect = collect)
 9: emarch(x.stacked$x, p2s = p2s, thetaold = NULL, tolerance =
tolerance,     startvals = startvals, x.stacked$priors, empri = empri,
frontend = frontend,     collect = collect, autopri = prepped$autopri,
emburn = emburn)
10: amelia.default(datM, m = 5, idvars = "group")
11: amelia(datM, m = 5, idvars = "group")
Warning: stack imbalance in '<-', 108 then 110

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: 3

Process R exited abnormally with code 70 at Tue Dec 11 10:36:51 2012

I double-checked /etc/alternatives and as you can see it does now
point to openbas

pauljohn at pjlap-124:alternatives$ ls -la libblas.*
lrwxrwxrwx 1 root root 36 Dec 11 10:34 libblas.a ->
/usr/lib/openblas-base/libopenblas.a
lrwxrwxrwx 1 root root 37 Dec 11 10:34 libblas.so ->
/usr/lib/openblas-base/libopenblas.so
lrwxrwxrwx 1 root root 39 Dec 11 10:34 libblas.so.3 ->
/usr/lib/openblas-base/libopenblas.so.0
lrwxrwxrwx 1 root root 39 Dec 11 10:34 libblas.so.3gf ->
/usr/lib/openblas-base/libopenblas.so.0

-- 
Paul E. Johnson
Professor, Political Science      Assoc. Director
1541 Lilac Lane, Room 504      Center for Research Methods
University of Kansas                 University of Kansas
http://pj.freefaculty.org               http://quant.ku.edu