[BioC] An importMAGEML problem in RMAGEML Package

[Haonan WU]

Hello,

I am trying to use the RMAGEML package to read in MAGE-ML files which I
had downloaded from the EBI ArrayExpress database. However, when I try and
use the importMAGEML()
function, I get this error:
--------------------------------------------
- Java Virtual Machine is running -
parsing MAGEML files

 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: .Call("getVoidArrayStr", "getBioSequenceID", mageOM,
..rmagemlJVM at jvmptr,     PACKAGE = "RMAGEML")
 2: getGnames(mageOM, arrayID = arrayID, DED = DED, db = db, package =
package)
 3: importMAGEML(directory = "/home/hwu/E-TABM-421/E-TABM-421_download",
  package = "marray", arrayID = "A-MEXP-931", DED = "none",     QTD =
"none", name.Rf = "QT:F635 Mean", name.Rb = "QT:B635 Median",     name.Gf
= "QT:F532 Mean", name.Gb = "QT:B532 Median")

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:
-------------------------------------------------------

Here are some descriptions on the structure of my data, it is a
MEGAML(.gz): E-TABM-421.mageml.tar.gz, and I un-ziped it at my local
directory in the folder:E-TABM-421_download, and imported it by its full
directory.(there are there files in it respectively:
E-TABM-421.xml,nrmzd_Sample_Probe_Profile.txt.proc, and
Sample_Probe_Profile.txt.proc.)

And the R cmd I used:
----------------------------------------------------
> library(RMAGEML)
Loading required package: marray
Loading required package: limma
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

> raw <- importMAGEML(directory =
"/home/hwu/E-TABM-421/E-TABM-421_download", package = "marray",arrayID =
"A-MEXP-931", DED = "none", QTD = "none", name.Rf = "QT:F635
Mean",name.Rb = "QT:B635 Median", name.Gf = "QT:F532 Mean",name.Gb =
"QT:B532 Median")
---------------------------------------------------------------

I am looking forward to your help and advices, Thanks in advance!

Haonan WU

Research Assistant, Department of Bioinformatics, Fraunhofer Institute for
Algorithms and Scientific Computing (SCAI),
Mobile: (+49) (0)163-2379046
E-mail:
wuh at cs.uni-bonn.com
haonan.wu at scai.fraunhofer.de