On Tue, Jul 13, 2010 at 3:01 PM, Simon Urbanek
<simon.urba...@r-project.org>wrote:
> Thanks, Conrad,
>
> finally, I can give you some more targeted suggestions. I'll cover several
> issues (those will bite you later), not just the one that breaks.
>
> a) configure
> You have the order of check switched - you're first checking for the
> compiler (AC_LANG etc.) and only then setting the right one from R. The
> order should be reversed since you first need to find the compiler and only
> then check it.
>
Ahh, thanks - I'm still new to autotools.
> b) Brownie makefile
> The one is really hard-wired so it won't work since you have flags like
> -m32 in there so you end up with things like g++ -arch x86_64 -m32 .. which
> cannot work. Also compilation should not include $(LNK_OPTIONS) [you don't
> need them at all since you're not linking anything anyway]. In fact it would
> be much better to just take the flags from R since you are also missing PIC
> flags and they will be needed: although you are compiling a static library
> it will be linked into a dynamic object so it has to be PIC.
>
Great suggestion - I've been looking into using variables gleaned from R CMD
config instead of hardcoding it into the Brownie makefilestatic, that is
what you meant correct?
>
> c) Now, the real meat is in the linker flags in RBrownie - and the compiler
> actually tells you what the mistake is:
>
> ld: warning: path './brownie_src/libBrownie.a' following -L not a directory
>
> You didn't really mean to sdd the libBrownie.a directory to be the search
> path - you really meant to use the library so your configure should read
>
> AC_SUBST([LDFLAGS],["brownie_src/libBrownie.a ${LIBS} ${RCPP_LIB} "])
>
> ... and with that it works.
>
Thanks, I did make that change and got rid of the 'symbol not found' error.
After that though, I was back to getting the "Bus error: non-existent
memory address 0x0 ..." during the dyn.load call. After much painful trial
and error (and re-installing Rcpp), I figured out that if I used the linker
flag: -nostdlib, during the shared library building step that the R package
worked fine.
I originally tried this because I thought the macports and standard mac osx
libraries might not be compatible with each other, but I'm not fully sure
why it worked. Any thoughts would be great.
Thanks!
Conrad
>
> Cheers,
> Simon
>
>
> On Jul 13, 2010, at 2:05 PM, Conrad Stack wrote:
>
> > Ah, sorry about that. I'm working off of this branch:
> >
> > svn checkout http://brownie.googlecode.com/svn/branches/brownie_jcs
> > brownieTEST
> >
> > cd brownieTEST
> > chmod +x build_r
> > ./build_r
> >
> > That should start the build.
> >
> > Thanks!
> > Conrad
> >
> >
> > On Mon, Jul 12, 2010 at 3:58 PM, Simon Urbanek <
> simon.urba...@r-project.org> wrote:
> > Conrad,
> >
> > On Jul 12, 2010, at 4:57 PM, Conrad Stack wrote:
> >
> > > On Sun, Jul 11, 2010 at 12:56 PM, Simon Urbanek <
> simon.urba...@r-project.org
> > >> wrote:
> > >
> > >>
> > >> On Jul 10, 2010, at 4:55 PM, Conrad Stack wrote:
> > >>
> > >>> Hello fellows,
> > >>>
> > >>> I'm currently developing an R package and having some trouble getting
> it
> > >> to
> > >>> install on Mac OS (the build process works fine on Windows 7 and
> Ubuntu
> > >> 10).
> > >>> The little prototype that I'm trying to get working compiles a large
> > >> amount
> > >>> of C++ code which is connected to R via Rcpp (0.8.2). The C++ is
> > >> compiled
> > >>> using autoconfig scripts into a static library which is used in
> Makevars
> > >> (in
> > >>> the src directory). Here is the relevant Makevars line (where
> libBrownie
> > >> is
> > >>> the static library just compiled):
> > >>>
> > >>> PKG_LIBS=-s -L. -L./brownie_src -lBrownie -lR -lgsl -lgslcblas -lm
> > >>>> /opt/local/lib/R/library/Rcpp/lib/libRcpp.a
> > >>>
> > >>
> > >> That sounds like a lot of trouble in itself (you should not include
> any R
> > >> flags since that can break and -lR is not what's used on OS X; -s it
> bad as
> > >> well and static libraries are better linked using their name since
> they have
> > >> lower priority in -l). But it could be really anything including bugs
> in
> > >> your package, so without the actual package I fear we can't help you
> much.
> > >>
> > >>
> > > Thanks Simon, linking the static library using it's name directly and
> > > removing the -lR and -s flags fixed the bus error. Unfortunately, I'm
> now
> > > getting another error when the package tries to load:
> > >
> > > Error in dyn.load("RBrownie.so") :
> > >
> > > unable to load shared library
> > >> '/Users/conrad/brownie/RBrownie/src/RBrownie.so':
> > >
> > > dlopen(/Users/conrad/brownie/RBrownie/src/RBrownie.so, 6): Symbol not
> > >> found: __ZTV16NewickTreeWriter
> > >
> > > Referenced from: /Users/conrad/brownie/RBrownie/src/RBrownie.so
> > >
> > > Expected in: dynamic lookup
> > >
> > >
> > > Where that function is from the static library (libBrownie.a) which was
> not
> > > being linked properly from before. I think this is a fairly standard
> C++
> > > error, but any help would be appreciated. I do know enough to run
> these
> > > commands:
> > > (from the static library)
> > > nm libBrownie.a | grep __ZTV16NewickTreeWriter:
> > > U __ZTV16NewickTreeWriter
> > > 0000f7a0 S __ZTV16NewickTreeWriter
> > >
> > > (from the shared library which R builds):
> > > nm libBrownie.a | grep __ZTV16NewickTreeWriter
> > > U __ZTV16NewickTreeWriter
> > >
> >
> > Unfortunately http://code.google.com/p/brownie/source/checkout doesn't
> even compile so I don't think we can help you any further. From experience I
> would still bet on the package flags being wrong (it's a bit tedious to
> debug since symbols are only resolved at load time, not at link time) but we
> can't tell without the package.
> >
> > Cheers,
> > Simon
> >
> >
> > > Thanks!
> > >
> > >
> > >>> This step seems to work fine and if I run the ./configure script
> which is
> > >> generated from the autoconfig file,
> > >>
> > >> More trouble - you should never run configure by hand because it will
> > >> likely use wrong settings (unless it is written such that it attempts
> to
> > >> find R and run it to get flags) - R CMD INSTALL is what you need to
> use so
> > >> the correct architecture, compilers and flags are setup.
> > >>
> > >
> > > Yes, my config script uses R to supply the flags, so running configure
> seems
> > > to run okay....
> > >
> > >
> > >>
> > >> Cheers,
> > >> Simon
> > >>
> > >>
> > >>
> > >
> > >
> > >>
> > >>> the library builds properly on Mac OS.
> > >>> The problem manifests when installing the package:
> > >>>
> > >>> ** testing if installed package can be loaded
> > >>>
> > >>>
> > >>>> *** caught bus error ***
> > >>>
> > >>> address 0x0, 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), keep.source =
> > >>> keep.source)
> > >>>
> > >>> 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"))})
> > >>>
> > >>> 8: try({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc),
> > >>> keep.source = keep.source) 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"))})
> > >>>
> > >>> 16: try(suppressPackageStartupMessages(library(pkg_name, lib.loc =
> lib,
> > >>> character.only = TRUE, logical.return = TRUE)))
> > >>>
> > >>> 17: do_install_source(pkg_name, instdir, pkg, desc)
> > >>>
> > >>> 18: do_install(pkg)
> > >>>
> > >>> 19: tools:::.install_packages()
> > >>>
> > >>> aborting ...
> > >>>
> > >>> /opt/local/lib/R/bin/INSTALL: line 34: 1357 Done
> echo
> > >>> 'tools:::.install_packages()'
> > >>>
> > >>> 1358 Bus error | R_DEFAULT_PACKAGES= LC_COLLATE=C
> > >>> "${R_HOME}/bin/R" $myArgs --slave --args ${args}
> > >>>
> > >>> I'm not really familiar with Mac OS at all so any direction would be
> > >> great.
> > >>> Thanks!
> > >>> Conrad
> > >>>
> > >>> --
> > >>> Conrad Stack
> > >>> -----------------------
> > >>> PSU Department of Biology
> > >>> 208 Mueller Lab
> > >>> University Park, PA 16802
> > >>> cell: 814.409.8310
> > >>> email: conrad.st...@gmail.com
> > >>>
> > >>> [[alternative HTML version deleted]]
> > >>>
> > >>> _______________________________________________
> > >>> R-SIG-Mac mailing list
> > >>> R-SIG-Mac@stat.math.ethz.ch
> > >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> > >>>
> > >>>
> > >>
> > >>
> > >>
> > >
> > >
> > > --
> > > Conrad Stack
> > > -----------------------
> > > PSU Department of Biology
> > > 208 Mueller Lab
> > > University Park, PA 16802
> > > cell: 814.409.8310
> > > email: conrad.st...@gmail.com
> > >
> > >
> > >
> > > --
> > > Conrad Stack
> > > -----------------------
> > > PSU Department of Biology
> > > 208 Mueller Lab
> > > University Park, PA 16802
> > > cell: 814.409.8310
> > > email: conrad.st...@gmail.com
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > R-SIG-Mac mailing list
> > > R-SIG-Mac@stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> > >
> > >
> >
> >
> >
> >
> >
> > --
> > Conrad Stack
> > -----------------------
> > PSU Department of Biology
> > 208 Mueller Lab
> > University Park, PA 16802
> > cell: 814.409.8310
> > email: conrad.st...@gmail.com
>
>
>
--
Conrad Stack
-----------------------
PSU Department of Biology
208 Mueller Lab
University Park, PA 16802
cell: 814.409.8310
email: conrad.st...@gmail.com
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