That's the GTK I have installed in the framework path...but there's also a
GTK installation in /usr/local.
Otool of the Frameworks version gives:
/Library/Frameworks/GTK+.framework/Resources/lib/libpangoft2-1.0.0.dylib
(compatibility version 2601.0.0, current version 2601.1.0)
Which should be just fine according to EBImage; the usr/local/lib version,
on the other hand:
/usr/local/lib/libpangoft2-1.0.0.dylib (compatibility version 2106.0.0,
current version 2106.0.0)
Which made me realize I just needed to install with:
R CMD INSTALL EBImage_3.2.0.tar.gz
--libdir=/Library/Frameworks/GTK+.framework/Versions/2.18.X11/Resources/lib
--includedir=/Library/Frameworks/GTK+.framework/Versions/2.18.X11/Resources/include
And it worked; loads fine now.
Thanks,
Eric
On Mon, Feb 1, 2010 at 2:20 PM, Simon Urbanek
<simon.urba...@r-project.org>wrote:
>
> 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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>>
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>>
>>
>>
>
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