[R-SIG-Mac] Problems loading Java libraries in R 2.2.1 OS X 10.4.5, Java 1.5.0 rev 3

[Marc Saric]

Hi list,

I have a PowerMac G5 running OS X 10.4.5 and Java 1.5.0 rev_3 together
with the precompiled R Version 2.2.1  (2005-12-20 r36812) from CRAN.

I tried to install a Bioconductor package called RMAGEML which depends
on an external Java-tool for data parsing and loading.

Compilation went fine after some configuration issues but the program
crashes with a "Bus error" while parsing testdata with the Java-module,
see below.

Debugging gave the following error message:

snip-------------------------------------------

dragonfish-g5:~/data/R/testing_RMAGEML saric$ R -d gdb
GNU gdb 6.1-20040303 (Apple version gdb-384) (Mon Mar 21 00:05:26 GMT 2005)
[...]
(gdb) run
Starting program:
/Library/Frameworks/R.framework/Versions/2.2/Resources/bin/exec/R
Reading symbols for shared libraries ..........+ done

R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.2.1  (2005-12-20 r36812)
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Reading symbols for shared libraries
.............................................................. done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
> library(RMAGEML)
Loading required package: marray
Loading required package: limma
Loading required package: limma
Loading required package: Biobase
Loading required package: tools
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done

Welcome to Bioconductor

        Vignettes contain introductory material.
        To view, simply type 'openVignette()' or start with
'help(Biobase)'.
        For details on reading vignettes, see the openVignette help page.

Reading symbols for shared libraries .. done
> datadir <- system.file("MAGEMLdata", package = "RMAGEML")
> raw <- importMAGEML(directory = datadir, package = "marray",
+ arrayID = "A-MEXP-14", DED = "DED:707", QTD = "QTD:707",
+ name.Rf = "QT:F635 Mean", name.Rb = "QT:B635 Median", name.Gf =
"QT:F532 Mean",
+ name.Gb = "QT:B532 Median")
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
Reading symbols for shared libraries . done
- Java Virtual Machine is running -
parsing MAGEML files

Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_PROTECTION_FAILURE at address: 0x00000000
0x94bfafa0 in JNI_GetDefaultJavaVMInitArgs_Impl ()
(gdb) info program
macosx_debug_inferior_status: current status:
              inferior task: 0x313
                [SIGNAL THREAD]
macosx_debug_inferior_status: information on debugger task:
macosx_debug_inferior_status: information on inferior task:
macosx_debug_inferior_status: information on debugger threads:
  thread: 0x117
  thread: 0x1003
  thread: 0x1303
macosx_debug_inferior_status: information on inferior threads:
  thread: 0xf03
  thread: 0x1603
  thread: 0x1743
  thread: 0x1803
  thread: 0x1903
  thread: 0x1a03
  thread: 0x1b03
  thread: 0x1c03
Program stopped at 0x94bfafa0.
It stopped with signal EXC_BAD_ACCESS, Could not access memory.
(gdb) info symbol 0x94bfafa0
JNI_GetDefaultJavaVMInitArgs_Impl + 5084 in section
LC_SEGMENT.__TEXT.__text of
/System/Library/Frameworks/JavaVM.framework/Versions/1.3.1/Libraries/libhotspot.dylib
(gdb)

snip-------------------------------------------

To me this looks like it uses the wrong library (1.3.1 instead of
/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Libraries/libhotspot.dylib)
but I have no clue how to change that.

I have set the preferences for Java apps to 1.4.2>1.5.0, so it should
not use 1.3.1 at all I think.

Software had to be compiled with gcc 3 via

dragonfish-g5:~ saric$ sudo gcc_select 3.3
Password:
Default compiler has been set to:
gcc version 3.3 20030304 (Apple Computer, Inc. build 1809)

Any idea?

Thanks in advance.


-- 
Bye,

Marc Saric