[Rd] Missing PROTECT in mkPRIMSXP ?
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=0x77a7cef8 "invalid primitive operation given for dispatch")
at /home/biocbuild/src/R-3.0.r62077/src/main/errors.c:741
#1 0x7793a7ed 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 0x77908463 in Rf_DispatchOrEval (call=0x164d5c0, op=0x4d772a0,
generic=0x77a8b0ef "length", args=0x53325d0, rho=0x5334428,
ans=0x7ffe45a0, dropmissing=0, argsevald=1)
at /home/biocbuild/src/R-3.0.r62077/src/main/eval.c:2413
#3 0x7792c318 in do_mapply (call=0x164d5c0, op=,
args=, 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=)
at /home/biocbuild/src/R-3.0.r62077/src/main/memory.c:2056
2056TYPEOF(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
--
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Missing PROTECT in mkPRIMSXP ?
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=0x77a7cef8 "invalid primitive operation given for dispatch")
at /home/biocbuild/src/R-3.0.r62077/src/main/errors.c:741
#1 0x7793a7ed 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 0x77908463 in Rf_DispatchOrEval (call=0x164d5c0, op=0x4d772a0,
generic=0x77a8b0ef "length", args=0x53325d0, rho=0x5334428,
ans=0x7ffe45a0, dropmissing=0, argsevald=1)
at /home/biocbuild/src/R-3.0.r62077/src/main/eval.c:2413
#3 0x7792c318 in do_mapply (call=0x164d5c0, op=,
args=, 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=)
at /home/biocbuild/src/R-3.0.r62077/src/main/memory.c:2056
2056TYPEOF(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 andFax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: luke-tier...@uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Missing PROTECT in mkPRIMSXP ?
On Mar 3, 2013, at 19:55 ,
wrote:
> Thanks -- fixed in R-devel and R_patched.
However, notice that the change in R-patched is not likely to make it into a
public release since 2.15.3 is officially final and we branch for 3.0.x on
Wednesday. (It will be present in the 3.x.y series, of course.)
If this bug bites someone who for whatever reason wants to stay on 2.15.3,
they'll have to dig the patch out from SVN.
Peter
>
> 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=0x77a7cef8 "invalid primitive operation given for dispatch")
>> at /home/biocbuild/src/R-3.0.r62077/src/main/errors.c:741
>> #1 0x7793a7ed 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 0x77908463 in Rf_DispatchOrEval (call=0x164d5c0, op=0x4d772a0,
>> generic=0x77a8b0ef "length", args=0x53325d0, rho=0x5334428,
>> ans=0x7ffe45a0, dropmissing=0, argsevald=1)
>> at /home/biocbuild/src/R-3.0.r62077/src/main/eval.c:2413
>> #3 0x7792c318 in do_mapply (call=0x164d5c0, op=,
>> args=, 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=)
>> at /home/biocbuild/src/R-3.0.r62077/src/main/memory.c:2056
>> 2056TYPEOF(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,
