Thanks -- fixed in R-devel and R_patched.
luke
On Sun, 3 Mar 2013, Martin Morgan wrote:
The Bioconductor build for a package DirichletMultinomial on
R Under development (unstable) (2013-02-26 r62077) -- "Unsuffered
Consequences"
at
http://bioconductor.org/checkResults/devel/bioc-LATEST/DirichletMultinomial/george2-buildsrc.html
shows
* creating vignettes ... ERROR
...
Error: processing vignette ‘DirichletMultinomial.Rnw’ failed with
diagnostics:
chunk 21 (label = ROC-dmngroup)
Error in mapply(FUN = f, ..., SIMPLIFY = FALSE) :
invalid primitive operation given for dispatch
Execution halted
I have not been able to reproduce this on other systems, but the basic
approach to a simpler reproducible example is to install the
DirichletMultinomial Bioconductor package and then
tools::buildVignettes(dir="DirichletMultinomial")
where the 'dir' argument points to the uncompressed tarball. There is C code
in the package, but not reached by this code chunk. Attempts to simplify the
code generally results in the error disappearing.
R -d valgrind -e "tools::buildVignettes(dir="DirichletMultinomial")"
does not reveal anything. The error does not occur with gctorture(TRUE);
tools::buildVignettes(dir="DirichletMultinomial").
By setting a breakpoint at Rf_error and creating a back-trace
(gdb) bt
#0 Rf_error (
format=0x7ffff7a7cef8 "invalid primitive operation given for dispatch")
at /home/biocbuild/src/R-3.0.r62077/src/main/errors.c:741
#1 0x00007ffff793a7ed in R_possible_dispatch (call=0x164d5c0, op=0x4d772a0,
args=0x53325d0, rho=0x5334428, promisedArgs=TRUE)
at /home/biocbuild/src/R-3.0.r62077/src/main/objects.c:1414
#2 0x00007ffff7908463 in Rf_DispatchOrEval (call=0x164d5c0, op=0x4d772a0,
generic=0x7ffff7a8b0ef "length", args=0x53325d0, rho=0x5334428,
ans=0x7ffffffe45a0, dropmissing=0, argsevald=1)
at /home/biocbuild/src/R-3.0.r62077/src/main/eval.c:2413
#3 0x00007ffff792c318 in do_mapply (call=0x164d5c0, op=<optimized out>,
args=<optimized out>, rho=0x5334428)
at /home/biocbuild/src/R-3.0.r62077/src/main/mapply.c:49
...
we get to
(gdb) l mapply.c:49
44 /* Cache the .Primitive: unclear caching is worthwhile.
*/
45 static SEXP length_op = NULL;
46 if (length_op == NULL) length_op = R_Primitive("length");
47 // DispatchOrEval() needs 'args' to be a pairlist
48 SEXP ans, tmp2 = PROTECT(list1(tmp1));
49 if (DispatchOrEval(call, length_op, "length", tmp2, rho,
&ans, 0, 1))
50 lengths[i] = (R_xlen_t) (TYPEOF(ans) == REALSXP ?
51 REAL(ans)[0] :
asInteger(ans));
52 UNPROTECT(1);
53 }
and it seems like length_op is somehow incorrect. Starting again with a
breakpoint at mapply.c:46, and watching the memory location of length_op,
once assigned, for a write at the address of length_op
(gdb) b mapply.c:46
(gdb) r
...
(gdb) p length_op
$11 = (SEXP) 0x4d772a0
(gdb) watch *0x4d772a0
(gdb) c
leads to
(gdb) c
Continuing.
Hardware watchpoint 4: *0x4d772a0
Old value = 8
New value = 0
Rf_allocSExp (t=<optimized out>)
at /home/biocbuild/src/R-3.0.r62077/src/main/memory.c:2056
2056 TYPEOF(s) = t;
which is R writing a new SEXP to the length_op location, as though this
location had been garbage collected.
Asking for R_Primitive("length") in mapply.c gets us to dstruct.c:60, where
we end up at
if (result == R_NilValue) {
result = allocSExp(type);
SET_PRIMOFFSET(result, offset);
}
...
return result;
which looks like the allocated SEXP is not added to the PrimCache vector, and
hence available for garbage collection. Perhaps a patch is along the lines of
Index: dstruct.c
===================================================================
--- dstruct.c (revision 62113)
+++ dstruct.c (working copy)
@@ -59,6 +59,7 @@
if (result == R_NilValue) {
result = allocSExp(type);
SET_PRIMOFFSET(result, offset);
+ SET_VECTOR_ELT(PrimCache, offset, result);
}
else if (TYPEOF(result) != type)
error("requested primitive type is not consistent with cached
value");
Martin
--
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics and Fax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: luke-tier...@uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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