[R-SIG-Mac] plier source compilation error related to dylib

[S Kong]

Dear Simon

Does  "/Users/skong/libR.dylib" (file not found).  mean that there's  
missing symbolic link to libR.dylib ?

Thank you very much,
-S

[Quad:~] skong% R64 -d gdb
GNU gdb 6.1-20040303 (Apple version gdb-437) (Sun Dec 25 08:31:29 GMT  
2005)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and  
you are
welcome to change it and/or distribute copies of it under certain  
conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for  
details.
This GDB was configured as "powerpc-apple-darwin"...
warning: Unable to read symbols for "/Users/skong/libR.dylib" (file  
not found).
Reading symbols for shared libraries ... done

(gdb) run
Starting program: /usr/local/lib64/R/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
 > dyn.load("/Research/GEO_CEL/pliersrc/affyplier.so")

Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_INVALID_ADDRESS at address: 0x00000000646c6fc0
0x000000008fe1adc0 in __dyld___cxa_end_catch ()
(gdb) bt
#0  0x000000008fe1adc0 in __dyld___cxa_end_catch ()
#1  0x000000008fe0aa60 in __dyld_dlopen ()
#2  0x00000000008da7c0 in dlopen ()
#3  0x0000000000657680 in loadLibrary ()
#4  0x0000000000408ca0 in AddDLL ()
#5  0x0000000000409dc0 in do_dynload ()
#6  0x000000000050807c in do_internal ()
#7  0x00000000004b3d18 in Rf_eval ()
#8  0x00000000004b47dc in Rf_applyClosure ()
#9  0x00000000004b4114 in Rf_eval ()
#10 0x00000000004eba48 in Rf_ReplIteration ()
#11 0x00000000004ebc80 in R_ReplConsole ()
#12 0x00000000004ecc58 in run_Rmainloop ()
#13 0x00000000004ecc90 in Rf_mainloop ()
#14 0x0000000000001e74 in main ()
(gdb)

------------------------------------------------------------------------ 
--------------------------------------------


On Apr 21, 2006, at 3:00 PM, Simon Urbanek wrote:

>
> On Apr 21, 2006, at 2:43 PM, S Kong wrote:
>
>> Dear Simon
>>
>> It seems there is the affyplier.so in the directory.
>
> I thought so - what you saw were just warnings, not errors -  
> nothing really wrong with that.
>
>> When I start R64 and try to dyn.load
>> > dyn.load("/Research/GEO_CEL/pliersrc/affyplier.so")
>> Segmentation fault
>>
>
> Ah, that's more interesting - chances are that it's a problem in  
> the package itself. Please run
> R64 -d gdb
> in gdb type "run", then load the library to see what happens
> once you have the crash, type "bt" to see where is crashed.
>
> Cheers,
> Simon
>