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
This step seems to work fine and if I run the ./configure script which is
generated from the autoconfig file, 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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