[R-SIG-Mac] EBImage segfault

[Simon Urbanek]

On Feb 1, 2010, at 13:51 , Eric Wooten wrote:

> 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?

My thoughts are that BioC have some issues with the binaries ;). 64- 
bit works only with the 64-bit GTK 2.18 builds:
http://r.research.att.com/libs/GTK+_2.18.5-X11-darwin9-bin3.tar.gz

(The previous 2.14 build does not contain 64-bit libraries)

The same applies to your attempt - you didn't give us any details, so  
there is not much I can help you with but I would expect it to work  
with the above.

Cheers,
Simon


> R
> 2.10.1, OSX 10.6.2, fresh R gtk library install.
> Thanks,
> Eric
>
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