[BioC] Bioconductor-EBImage problem

[Wolfgang Huber]

Dear Xiushan,

the version of R and EBImage that you use are out of sync. I am not sure 
if that is the cause of your problem, but don't expect that there is 
much interest in excluding this possibility. So, before taking this any 
further, would you mind installing a more recent R (2.11.1), following 
e.g. the instructions on 
http://cran.r-project.org/bin/linux/ubuntu/README and making sure you 
include r-base-dev.

Then, try reinstalling ImageMagick and GTK+, following the instructions 
at http://www.bioconductor.org/packages/release/bioc/html/EBImage.html
--> EBImage installation. If the problem persists, please send the 
complete output of biocLite("EBImage"), including all the compiler etc. 
messages.

Best wishes
	Wolfgang

On 19/08/10 14:42, Xiushan Yin wrote:
> Dear All,
> I'm a beginner and learning R for microarray analysis.I'm using
> aroma.affymetrix.
> There is a problem when I installed the EBImage package.
> The installation is fine.
> *************************************
> ** R
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices ...
> * DONE (EBImage)
> **********************************
> But when I typed library(EBImage),then there are some information below.
> ****************************************
> Loading required package: abind
>
>   *** caught segfault ***
> address 0x2, 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")
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
> *******************************************
> By the way details are R2.10;  gtk+-2.20.0;  pkg-config-0.22;
>   ImageMagick-6.6.3-7 and EBImage 3.4.0
> My system is Ubuntu10.04.
> I searched it through google,somebody said for Ubuntu ,the GTK doesn't work
> well with ImageMagick.But the bug was in gcc4-2,and now it's changed.
> I think there might be something wrong about the GTK2.0 but I can't find
> out,Could anybody help me with this problem?Thanks a lot!

-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber