[Rd] Mitigating Stalls Caused by Call Deparse on Error
brodie gaslam
brod|e@g@@|@m @end|ng |rom y@hoo@com
Sat Jul 13 19:31:44 CEST 2019
When large calls cause errors R may stall for extended periods. This
is particularly likely to happen with `do.call`, as in this example
with a 24 second stall:
x <- runif(1e7)
system.time(do.call(paste0, list(abs, x))) # intentional error
## Error in (function (..., collapse = NULL) :
## cannot coerce type 'builtin' to vector of type 'character'
## Calls: system.time -> do.call -> <Anonymous>
## Timing stopped at: 23.81 0.149 24.04
str(.Traceback)
## Dotted pair list of 3
## $ : chr [1:2500488] "(function (..., collapse = NULL) " ".Internal(paste0(list(...), collapse)))(.Primitive(\"abs\"), c(0.718117154669017, " "0.494785501621664, 0.1453434410505, 0.635028422810137, 0.0353180423844606, " "0.688418723642826, 0.889682895969599, 0.728154224809259, 0.292572240810841, " ...
## $ : chr "do.call(paste0, list(abs, x))"
## $ : chr "system.time(do.call(paste0, list(abs, x)))"
The first time I noticed this I thought my session had frozen/crashed
as the standard interrupt ^C does not work during the deparse. The
stall happens when on error the call stack is deparsed prior to being
saved to `.Traceback`. The deparsing is done by `deparse1m` in native
code, with the value of `getOption('deparse.max.lines')` which
defaults to all lines.
Since there is little value to seeing millions of lines of deparsed
objects in `traceback()`, a simple work-around is to change the
`deparse.max.lines` value:
options(deparse.max.lines=1)
system.time(do.call(paste0, list(abs, x)))
## Error in (function (..., collapse = NULL) :
## cannot coerce type 'builtin' to vector of type 'character'
## Calls: system.time -> do.call -> <Anonymous>
## Timing stopped at: 0 0 0
Unfortunately this will affect all `deparse` calls, and it seems
undesirable to pre-emptively enable it just for calls that might cause
large deparses on error.
An alternative is to store the actual calls instead of their deparsed
character equivalents in `.Traceback`. This defers the deparsing to
when `traceback()` is used. As per `?traceback`, it should be
relatively safe to modify `.Traceback` in this way:
> It is undocumented where .Traceback is stored nor that it is
> visible, and this is subject to change.
Deferring the deparsing to `traceback()` will give us the
opportunity to use a different `max.lines` setting as we do here
with the patch applied:
system.time(do.call(paste0, list(abs, x)))
## Error in (function (..., collapse = NULL) :
## cannot coerce type 'builtin' to vector of type 'character'
## Timing stopped at: 0.028 0 0.029
system.time(traceback(max.lines=3))
## 3: (function (..., collapse = NULL)
## .Internal(paste0(list(...), collapse)))(.Primitive("abs"), c(0.535468587651849,
## 0.0540027911774814, 0.732930393889546, 0.565360915614292, 0.544816034380347,
## ...
## 2: do.call(paste0, list(abs, x))
## 1: system.time(do.call(paste0, list(abs, x)))
## user system elapsed
## 0.000 0.000 0.003
More generally, it might be better to have a different smaller default
value for the lines to deparse when calls are _displayed_ as parts of
lists, as is the case with `traceback()`, or in `print(sys.calls())` and
similar.
I attach a patch that does this. I have run some basic tests
and `make check-devel` passes. I can file an issue on bugzilla
if that is a better place to have this conversation (assuming there
is interest in it).
Best,
Brodie
PS: for some reason my mail client is refusing to attach the patch so I paste it
starting on the next line.
Index: src/gnuwin32/Rdll.hide
===================================================================
--- src/gnuwin32/Rdll.hide (revision 76827)
+++ src/gnuwin32/Rdll.hide (working copy)
@@ -94,6 +94,7 @@
R_GetMaxNSize
R_GetMaxVSize
R_GetTraceback
+ R_GetTracebackParsed
R_GetVarLocSymbol
R_GetVarLocValue
R_HandlerStack
Index: src/include/Defn.h
===================================================================
--- src/include/Defn.h (revision 76827)
+++ src/include/Defn.h (working copy)
@@ -1296,6 +1296,7 @@
void NORET ErrorMessage(SEXP, int, ...);
void WarningMessage(SEXP, R_WARNING, ...);
SEXP R_GetTraceback(int);
+SEXP R_GetTracebackParsed(int);
R_size_t R_GetMaxVSize(void);
void R_SetMaxVSize(R_size_t);
Index: src/library/base/R/traceback.R
===================================================================
--- src/library/base/R/traceback.R (revision 76827)
+++ src/library/base/R/traceback.R (working copy)
@@ -16,9 +16,19 @@
# A copy of the GNU General Public License is available at
# https://www.R-project.org/Licenses/
-.traceback <- function(x = NULL) {
- if(is.null(x) && !is.null(x <- get0(".Traceback", envir = baseenv())))
- {}
+.traceback <- function(x = NULL, max.lines=getOption("deparse.max.lines")) {
+ if(!(is.numeric(max.lines) && !is.na(max.lines) &&
+ as.integer(max.lines) > 0L)
+ ) {
+ max.lines <- -1L
+ }
+ if(is.null(x) && !is.null(x <- get0(".Traceback", envir = baseenv()))) {
+ for(i in seq_along(x)) {
+ srcref <- attr(x[[i]], 'srcref')
+ x[[i]] <- deparse(x[[i]], nlines=max.lines)
+ attr(x[[i]], 'srcref') <- srcref
+ }
+ }
else if (is.numeric(x))
x <- .Internal(traceback(x))
x
@@ -26,7 +36,16 @@
traceback <- function(x = NULL, max.lines = getOption("deparse.max.lines"))
{
- n <- length(x <- .traceback(x))
+ valid.max.lines <- is.numeric(max.lines) && !is.na(max.lines) &&
+ as.integer(max.lines) > 0L
+
+ if(valid.max.lines) {
+ # max.lines + 1L so we can know that output was truncated by .traceback
+ max.lines.2 <- as.integer(max.lines) + 1L
+ } else {
+ max.lines.2 <- -1L
+ }
+ n <- length(x <- .traceback(x, max.lines=max.lines.2))
if(n == 0L)
cat(gettext("No traceback available"), "\n")
else {
@@ -40,7 +59,7 @@
paste0(" at ", basename(srcfile$filename), "#", srcref[1L])
}
## Truncate deparsed code (destroys attributes of xi)
- if(is.numeric(max.lines) && max.lines > 0L && max.lines < m) {
+ if(valid.max.lines && max.lines < m) {
xi <- c(xi[seq_len(max.lines)], " ...")
m <- length(xi)
}
Index: src/library/base/man/traceback.Rd
===================================================================
--- src/library/base/man/traceback.Rd (revision 76827)
+++ src/library/base/man/traceback.Rd (working copy)
@@ -21,7 +21,7 @@
}
\usage{
traceback(x = NULL, max.lines = getOption("deparse.max.lines"))
-.traceback(x = NULL)
+.traceback(x = NULL, max.lines = getOption("deparse.max.lines"))
}
\arguments{
\item{x}{\code{NULL} (default, meaning \code{.Traceback}), or an
Index: src/main/errors.c
===================================================================
--- src/main/errors.c (revision 76827)
+++ src/main/errors.c (working copy)
@@ -1008,7 +1008,7 @@
(which should not happen) */
if (traceback && inError < 2 && inError == oldInError) {
inError = 2;
- PROTECT(s = R_GetTraceback(0));
+ PROTECT(s = R_GetTracebackParsed(0));
SET_SYMVALUE(install(".Traceback"), s);
/* should have been defineVar
setVar(install(".Traceback"), s, R_GlobalEnv); */
@@ -1440,9 +1440,11 @@
PrintWarnings();
}
}
-
+/*
+ * Return the traceback without deparsing the calls
+ */
attribute_hidden
-SEXP R_GetTraceback(int skip)
+SEXP R_GetTracebackParsed(int skip)
{
int nback = 0, ns;
RCNTXT *c;
@@ -1467,7 +1469,9 @@
if (skip > 0)
skip--;
else {
- SETCAR(t, deparse1m(c->call, 0, DEFAULTDEPARSE));
+ // Extra paranoid PROTECTS
+ SETCAR(t, PROTECT(duplicate(c->call)));
+ UNPROTECT(1);
if (c->srcref && !isNull(c->srcref)) {
SEXP sref;
if (c->srcref == R_InBCInterpreter)
@@ -1482,7 +1486,26 @@
UNPROTECT(1);
return s;
}
+/*
+ * Return the traceback with calls deparsed
+ */
+attribute_hidden
+SEXP R_GetTraceback(int skip)
+{
+ int nback = 0;
+ SEXP s, t, u, v;
+ s = PROTECT(R_GetTracebackParsed(skip));
+ for(t = s; t != R_NilValue; t = CDR(t)) nback++;
+ u = v = PROTECT(allocList(nback));
+ for(t = s; t != R_NilValue; t = CDR(t), v=CDR(v)) {
+ SETCAR(v, PROTECT(deparse1m(CAR(t), 0, DEFAULTDEPARSE)));
+ UNPROTECT(1);
+ }
+ UNPROTECT(1);
+ return u;
+}
+
SEXP attribute_hidden do_traceback(SEXP call, SEXP op, SEXP args, SEXP rho)
{
int skip;
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