Maybe more of a BioC forum question, but seemingly applicable here: after
compiling EBImage, I catch a segfault upon trying to load the library.
** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices ...
> * DONE (EBImage)
>
> > library(EBImage)
> Loading required package: abind
>
> *** caught segfault ***
> address 0x10, cause 'memory not mapped'
>
> 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)})
> 9: library(EBImage)
>
Why bother compiling my own, you ask? Because this is what you get from
trying the precompiled binary on my machine:
> library(EBImage)
> Loading required package: abind
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared library
> '/Library/Frameworks/R.framework/Resources/library/EBImage/libs/x86_64/EBImage.so':
>
> dlopen(/Library/Frameworks/R.framework/Resources/library/EBImage/libs/x86_64/EBImage.so,
> 6): Library not loaded:
> /Library/Frameworks/GTK+.framework/Versions/2.14.X11/Resources/lib/libpangoft2-1.0.0.dylib
> Referenced from:
> /Library/Frameworks/R.framework/Resources/library/EBImage/libs/x86_64/EBImage.so
> Reason: Incompatible library version: EBImage.so requires version
> 2201.0.0 or later, but libpangoft2-1.0.0.dylib provides version 1905.0.0
> Error: package/namespace load failed for 'EBImage'
>
Anyone out there have this library working or some thoughts on the matter? R
2.10.1, OSX 10.6.2, fresh R gtk library install.
Thanks,
Eric
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