From simon.urbanek at r-project.org  Mon Feb  6 15:47:07 2012
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Mon, 6 Feb 2012 09:47:07 -0500
Subject: [Rd] Segfault on ".C" registration via R_CMethodDef according
	to 'Writing R Extensions'.
In-Reply-To: <1FB48665-E0BE-4956-A3BE-9B02038006B7@uni-goettingen.de>
References: <1FB48665-E0BE-4956-A3BE-9B02038006B7@uni-goettingen.de>
Message-ID: <EF93290B-D4D2-476C-8E35-698A5DA28721@r-project.org>

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
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> 



[Rd] Segfault on ".C" registration via R_CMethodDef according to 'Writing R Extensions'.
Simon Urbanek