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
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