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EBImage segfault
3 messages · Eric Wooten, 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 [[alternative HTML version deleted]]
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