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.
> 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.
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
>
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>
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