Daniel,
the code you are using is probably not what you intended - since there is no
length information the compiler assumes you are filling the structure
sequentially and thus the expected value is that for R_NativePrimitiveArgType*
which has no length, so it can only be initialized with a scalar value, so you
are setting
R_NativePrimitiveArgType* types = REALSXP
which is wrong as you are casing an integer into a pointer. Also that's why you
get the warnings which are all valid:
ra.c:9: warning: braces around scalar initializer
-- because it is interpeted as {REALSXP} hence superfluous braces
ra.c:9: warning: initialization makes pointer from integer without a cast
-- because you're initializing R_NativePrimitiveArgType* with an integer
(REALSXP)
ra.c:9: warning: excess elements in scalar initializer
-- because INTSXP, ... must be ignored since "types" can only be initialized
with a scalar (pointer)
For what you intended, you're using variable-length array so you have to
specify its length:
{"myC", (DL_FUNC) &myC, 4, (R_NativePrimitiveArgType[4]) {REALSXP, INTSXP,
STRSXP, LGLSXP}}
which will allocate extra static object (it has to because "types" is a
pointer, not a fixed array) - so the effect is the same as using a static
object.
Cheers,
Simon
On Feb 6, 2012, at 8:27 AM, Daniel Adler wrote:
> Dear R List,
>
> I encountered a serious problem regarding the registration of ".C" when
> following the documentation "Writing R Extensions"
> that leads to a segmentation fault (tested on windows and mac os x).
>
> The registration mechanism for ".C" routines via R_registerRoutines and
> the R_CMethodDef structure has been enhanced recently with the
> addition of two fields, one for type specification and the other for
> the style (in, out, inout or irrelevant).
>
> According to the manual 'Writing R Extensions' of version 2.14.1
> an example is given that specifies to use the fourth field (type information)
> for definitions of C routines that use the ".C" calling convention:
>
> R_CMethodDef cMethods[] = {
> {"myC", (DL_FUNC) &myC, 4, {REALSXP, INTSXP, STRSXP, LGLSXP}}, /*
> segfault! */
> {NULL, NULL, 0}
> };
>
> If I follow this example I get compiler warnings or errors (whether I use C
> or C++, respectively) and
> a segmentation fault (in the case of C) when doing R CMD INSTALL, which seem
> to happen during testing.
> See build log at the end of this e-mail.
>
> When removing the last field in the initializer list in order to register .C
> routines in the old way the segfault goes away:
>
> R_CMethodDef cMethods[] = {
> {"myC", (DL_FUNC) &myC, 4}, /* works */
> {NULL, NULL, 0}
> };
>
> There are still warnings/segfault or an error when initializing the
> undocumented fifth entry (parameter passing style), e.g.
>
> R_CMethodDef cMethods[] = {
> {"myC", (DL_FUNC) &myC, 4, {REALSXP, INTSXP, STRSXP, LGLSXP},
> {R_ARG_IN, R_ARG_IN, R_ARG_IN, R_ARG_IN}, /* segfault! */
> {NULL, NULL, 0}
> };
>
> Using a C source, the warnings are:
>
> *** arch - i386
> gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386
> -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c reg.c -o reg.o
> reg.c:24: warning: braces around scalar initializer
> reg.c:24: warning: (near initialization for ‘cMethods[0].types’)
> reg.c:24: warning: initialization makes pointer from integer without a cast
> reg.c:24: warning: excess elements in scalar initializer
> reg.c:24: warning: (near initialization for ‘cMethods[0].types’)
> reg.c:24: warning: excess elements in scalar initializer
> reg.c:24: warning: (near initialization for ‘cMethods[0].types’)
> reg.c:24: warning: excess elements in scalar initializer
> reg.c:24: warning: (near initialization for ‘cMethods[0].types’)
>
>
> Using C++, protecting the init/unload function prototypes and structure
> declarations via 'extern "C" { }', I get the following error:
>
> *** arch - i386
> g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include
> -I/Library/Frameworks/R.framework/Resources/include/i386
> -I/usr/local/include -fPIC -g -O2 -c reg.cpp -o reg.o
> reg.cpp:30: error: braces around scalar initializer for type
> ‘R_NativePrimitiveArgType*’
>
> (line 24 is the point on the entry, while line 30 is the end of the overall
> array initialization list in C++).
>
> If I put the type and style (unsigned int and enum) arrays separately,
> the build process works just fine. E.g.
>
> R_NativePrimitiveArgType types[] = {REALSXP, INTSXP, STRSXP, LGLSXP};
> R_NativeArgStyle styles[] = { R_ARG_IN, R_ARG_IN, R_ARG_IN, R_ARG_IN };
>
> R_CMethodDef cMethods[] = {
> {"myC", (DL_FUNC) &myC, 4, types, NULL}, /* works */
> {"myC2", (DL_FUNC) &myC, 4, types, style}, /* works */
> {NULL, NULL, 0}
> };
>
> (Though I haven't tested the runtime behaviour yet.. but at least no segfault
> during R CMD INSTALL..)
>
> I wonder what is wrong with the static initializer lists?!
>
> I could imagine it has something to do with the standard compilance of the
> C/C++
> compiler (due to the different behaviour warning or error during compilation).
>
> Anyway, going with the manual right now, the ordinary user will get warnings
> and
> errors - at least on the systems that I have tested (recent version of
> Rtools/Windows 7
> and Mac OS X 10.6 with gcc 4.2.1).
> On Windows instead of a trace output, a window pops up during install to tell
> about a process crash.
>
> - Daniel
>
> PS: If it helps, I could put up a test package online for further debugging.
>
> --- build log:
> ----------------------------------------------------------------
>
> ** testing if installed package can be loaded
> *** arch - i386
>
> *** caught bus error ***
> address 0xe, cause 'non-existent physical address'
>
> Traceback:
> 1: dyn.load(file, DLLpath = DLLpath, ...)
> 2: library.dynam(lib, package, package.lib)
> 3: loadNamespace(package, c(which.lib.loc, lib.loc))
> 4: doTryCatch(return(expr), name, parentenv, handler)
> 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 6: tryCatchList(expr, classes, parentenv, handlers)
> 7: 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 <- paste(prefix, "\n ",
> sep = "") } else prefix <- "Error : " msg <- paste(prefix,
> conditionMessage(e), "\n", sep = "") .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))})
> 8: try({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc))
> dataPath <- file.path(which.lib.loc, package, "data") env <-
> attachNamespace(ns, pos = pos, dataPath = dataPath, deps)})
> 9: library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return =
> TRUE)
> 10: withCallingHandlers(expr, packageStartupMessage = function(c)
> invokeRestart("muffleMessage"))
> 11: suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
> character.only = TRUE, logical.return = TRUE))
> 12: doTryCatch(return(expr), name, parentenv, handler)
> 13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 14: tryCatchList(expr, classes, parentenv, handlers)
> 15: 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 <- paste(prefix, "\n ",
> sep = "") } else prefix <- "Error : " msg <- paste(prefix,
> conditionMessage(e), "\n", sep = "") .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))})
> 16: try(suppressPackageStartupMessages(library(pkg_name, lib.loc = lib,
> character.only = TRUE, logical.return = TRUE)))
> 17: tools:::.test_load_package("mylib",
> "/Users/dadler/Library/R/2.14/library")
> aborting ...
> sh: line 1: 75200 Bus error
> '/Library/Frameworks/R.framework/Resources/bin/R' --arch=i386 --no-save
> --slave <
> /var/folders/Lr/Lrh7GWILEqCwHkyF1MdauE+++TI/-Tmp-//RtmpDqusSN/file1259d93ec2eb
> *** arch - x86_64
>
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>
>
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