[R] Making R talk to Win/OpenBUGS in Linux (again)

[Uwe Ligges]

anuel Morales wrote:

> As far as I can figure out, the problem with running "LinBUGS" on FC5 is
> that support for linuxthreads was removed after being deprecated in FC4.
> 
> http://fedora.redhat.com/docs/release-notes/fc5/#id2887615
> 
> As a result, the LD_ASSUME_KERNEL workaround, which presumably forced
> the use of linuxthreads (see
> http://www.math.helsinki.fi/openbugs/phpBB2/viewtopic.php?t=4), doesn't
> work anymore.
> 
> Ideally, bugs.so / brugs.so would be compiled with support for NPTL
> instead of linuxthreads, but I don't think it's possible to do this as
> an end user. Unless changes are made by the OpenBUGS developers,
> OpenBUGS will not run natively in FC5.

The person who really knows is Andrew Thomas (CCing now). Why do people 
not ask him rather than speculating?

Uwe Ligges




> Manuel
> 
> On Mon, 2006-05-01 at 13:38 -0500, Paul Johnson wrote:
> 
>>Dear Jun:
>>
>>How about telling us which version of Linux you use and how you make
>>linbugs run?  As far as I can tell, the OpenBUGS people have
>>intentionally removed linbugs from their version 2.2.  That leaves us
>>with various scripts that people have posted & tried, none work for
>>me.  Fedora Core 5, I cannot get any of the linbugs scripts that are
>>floating around to work.
>>
>>I tried re-building the program thus:
>>
>>
>># gcc -o cbugs CBugs.c  -ldl
>>
>>That creates an executable cbugs, but there is no joy for me.
>>
>>$ ./cbugs
>>failed to install signal
>>32
>>failed to install signal
>>33
>>
>>****
>>* BlackBox
>>* illegal memory read [ad = 00000000]
>>- HostFiles.NewFileRef  (pc=00000D9B, fp=BFC73BE4)
>>- HostFiles.OpenFile  (pc=00000E0E, fp=BFC73BFC)
>>- HostFiles.Directory.Old  (pc=000029B2, fp=BFC73EA4)
>>- StdLoader.ThisObjFile  (pc=0000031D, fp=BFC744C0)
>>- StdLoader.ReadHeader  (pc=0000075F, fp=BFC746E0)
>>- StdLoader.LoadMod  (pc=0000107B, fp=BFC747F8)
>>- StdLoader.LoadMod  (pc=000011E0, fp=BFC74910)
>>- StdLoader.LoadMod  (pc=000011E0, fp=BFC74A28)
>>- StdLoader.Hook.ThisMod  (pc=00001355, fp=BFC74A3C)
>>- Kernel.ThisMod  (pc=00001224, fp=BFC74B58)
>>- Init.Init  (pc=0000004B, fp=BFC74B70)
>>- Init.$$  (pc=0000000A, fp=BFC74B80)
>>****
>>
>>
>>
>># export LD_ASSUME_KERNEL=2.4.1
>>
>>
>># ./cbugs
>>./cbugs: error while loading shared libraries: libdl.so.2: cannot open
>>shared object file: No such file or directory
>>
>>$ ldd ./cbugs
>>        linux-gate.so.1 =>  (0x00a2b000)
>>        libdl.so.2 => /lib/libdl.so.2 (0x00ba9000)
>>        libc.so.6 => /lib/libc.so.6 (0x00a4d000)
>>        /lib/ld-linux.so.2 (0x00a2c000)
>>
>>And after doing that LD_ASSUME_KERNEL thingie, nothing in the shell
>>works anymore...
>>
>>$ which cbugs
>>/usr/bin/which: error while loading shared libraries: libc.so.6:
>>cannot open shared object file: No such file or directory
>>
>>On 5/1/06, jun yan <jyan at stat.uiowa.edu> wrote:
>>
>>>I have used linbugs with the rbugs package for a recent work. It might be
>>>worthwhile trying.
>>>
>>> Jun