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Old 06-15-2011, 12:22 AM
Kevin Kofler
 
Default OpenBUGS program has a pre-compiled )S library from MS Windows. Any possibility to package it?

Paul Johnson wrote:
> First, the (now open) code for OpenBugs is written in Object Pascal
> and it requires a compiler framework called "Black Box" which is, as
> far as I can understand, available only for MS Windows. The OpenBUGS
> team compiles that library, and then for linux we use some accessor
> scripts to send jobs to it.
>
> This, of course, goes against the packaging policy that pre-compiled
> libraries are prohibited.
>
> I was wondering if there could be an exception here, since the code is
> actually available and open. This is more reasonable than
> re-packaging the closed Nvidia drivers, for example.

The code must be compilable with a Free compiler. If it is not (which seems
to be the case here, unfortunately), it must be fixed (ported) to be.

In this case, the most obvious candidates would probably be
FreePascal/Lazarus and GPC, but porting to a completely different, more
commonly used language (I'd suggest C++) might also be worth considering for
upstream (depending on how hard it is to port to a Free Pascal compiler).

> Second, there is a little packaging problem for 64 bit systems. The
> library that is provided is only 32 bit, and to build it for a 64 bit
> system, there is a somewhat confusing situation. The library itself
> gets put into /usr/lib, which is supposed to be for 64 bit libraries.
> And to make the whole thing package up in a workable way, the arch
> ends up saying the packge is x86_64, even though it is only 32 bit.

This is entirely unacceptable (and yet another reason why prebuilt binaries
are unacceptable).

If a package cannot be built as 64-bit, it must be ExcludeArch: x86_64 and
then it can be put on the multilib whitelist. But really, it needs to be
fixed to be buildable natively instead! That mostly means getting it to
compile with a Free compiler, then fixing 64-bit issues, if any, becomes
rather easy in my experience.

> To run OpenBUGS on a 64 bit system, one h as to install the 32bit libc
> packages.

That's exactly why such 32-bit stuff doesn't belong into an x86_64 package.
In fact, Koji will not let you build 32-bit binaries in an x86_64 package,
almost all 32-bit multilibs are explicitly blacklisted in the x86_64
repository configuration to prevent you from doing exactly that.

> In the current Fedora framework, I can't understand if that is
> supposed to happen.

No. 32-bit binaries are not allowed in x86_64 packages.

Kevin Kofler

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Old 06-15-2011, 12:41 AM
Kevin Kofler
 
Default OpenBUGS program has a pre-compiled )S library from MS Windows. Any possibility to package it?

PS:

Paul Johnson wrote:
> I was wondering if there could be an exception here, since the code is
> actually available and open.

Have you even looked at that "source code"? I just have:

1. They refer to the Window$ download for the code. That's a .EXE file
created with some proprietary installer generator (probably something that's
part of that "Black Box" crap), 7z cannot do anything with it (and it can
unpack at least self extractors and NSIS installers). Rather than running
that EXE in WINE to get at the .odc files, I decided to look elsewhere, and
in fact found their repository, but:

2. Here's the "source code":
http://openbugs.svn.sourceforge.net/viewvc/openbugs/openbugs/trunk/
Try to look at such a .odc file. You'll notice that ViewVC refuses to show
you the file because it's a binary! Look at it, you'll see some Pascal code
mixed with some opaque binary data which probably only "Black Box" (nomen
est omen…) can interpret.

I don't see this as being "open" source code at all.

I guess the binary metadata is an essential part of the code.

Kevin Kofler

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Old 06-15-2011, 12:57 AM
Kevin Kofler
 
Default OpenBUGS program has a pre-compiled )S library from MS Windows. Any possibility to package it?

Kevin Kofler wrote:
> In this case, the most obvious candidates would probably be
> FreePascal/Lazarus and GPC, but porting to a completely different, more
> commonly used language (I'd suggest C++) might also be worth considering
> for upstream (depending on how hard it is to port to a Free Pascal
> compiler).

Actually, maybe this can help: http://cp-dev.sourceforge.net/ (but it's 32-
bit-x86-only and it might not be complete enough to build OpenBUGS yet, plus
I still wonder why the .obc source files contain that binary metadata in
addition to the Pascal-like code).

Kevin Kofler

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Old 06-15-2011, 03:34 PM
Paul Johnson
 
Default OpenBUGS program has a pre-compiled )S library from MS Windows. Any possibility to package it?

On Tue, Jun 14, 2011 at 7:57 PM, Kevin Kofler <kevin.kofler@chello.at> wrote:
> Kevin Kofler wrote:
>> In this case, the most obvious candidates would probably be
>> FreePascal/Lazarus and GPC, but porting to a completely different, more
>> commonly used language (I'd suggest C++) might also be worth considering
>> for upstream (depending on how hard it is to port to a Free Pascal
>> compiler).
>
> Actually, maybe this can help: http://cp-dev.sourceforge.net/ (but it's 32-
> bit-x86-only and it might not be complete enough to build OpenBUGS yet, plus
> I still wonder why the .obc source files contain that binary metadata in
> addition to the Pascal-like code).
>
> * * * *Kevin Kofler
>

Thanks for the link. I did not know about that project yet, but it
does point over to the OpenBUGS site.

I agree with you it is a bit weird that the BUGS source code is
wrapped into those binary odc files. The most favorable
interpretation I can give this is that it is a form of literate
programming, where the code is wrapped into documentation and so
forth.

To the ODC haters: I agree, but...

This *is* an open source project, if you have the right editor. I ran
the free BlackBox program inside Wine just now. Putting code into ODC
files is not conceptually different from wrapping a CPP program into
LaTeX source code, or wrapping R code into an Rnw file. The fact that
the code is not just a flat ascii file you can read with Emacs does
not make it less open.

I will try to find out the historical reasons for relying on BlackBox.
That decision was made in 1996 or so, and if you remember the state
of the world then, the g++ did not work very well and there were
competing/incomplete versions of the standard template library. Java
did not exist, and Pascal was just about as widely used as C (moreso
in the classroom). A lot of the bigger scientific programming
projects of that era avoided C++. The other project with which I was
intimately familiar is Swarm, which adopted Objective-C as its
language, mostly for the same reasons.

pj



> --



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Old 06-16-2011, 11:53 AM
"Richard W.M. Jones"
 
Default OpenBUGS program has a pre-compiled )S library from MS Windows. Any possibility to package it?

On Wed, Jun 15, 2011 at 10:34:46AM -0500, Paul Johnson wrote:
> On Tue, Jun 14, 2011 at 7:57 PM, Kevin Kofler <kevin.kofler@chello.at> wrote:
> > Kevin Kofler wrote:
> >> In this case, the most obvious candidates would probably be
> >> FreePascal/Lazarus and GPC, but porting to a completely different, more
> >> commonly used language (I'd suggest C++) might also be worth considering
> >> for upstream (depending on how hard it is to port to a Free Pascal
> >> compiler).
> >
> > Actually, maybe this can help: http://cp-dev.sourceforge.net/ (but it's 32-
> > bit-x86-only and it might not be complete enough to build OpenBUGS yet, plus
> > I still wonder why the .obc source files contain that binary metadata in
> > addition to the Pascal-like code).
> >
> > * * * *Kevin Kofler
> >
>
> Thanks for the link. I did not know about that project yet, but it
> does point over to the OpenBUGS site.
>
> I agree with you it is a bit weird that the BUGS source code is
> wrapped into those binary odc files. The most favorable
> interpretation I can give this is that it is a form of literate
> programming, where the code is wrapped into documentation and so
> forth.
>
> To the ODC haters: I agree, but...
>
> This *is* an open source project, if you have the right editor. I ran
> the free BlackBox program inside Wine just now. Putting code into ODC
> files is not conceptually different from wrapping a CPP program into
> LaTeX source code, or wrapping R code into an Rnw file. The fact that
> the code is not just a flat ascii file you can read with Emacs does
> not make it less open.

Is there any editor on Fedora that can handle these files? I
tried libreoffice but it appeared to crash.

Rich.

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Old 08-26-2011, 05:13 PM
Michael Ekstrand
 
Default OpenBUGS program has a pre-compiled )S library from MS Windows. Any possibility to package it?

On 06/14/2011 07:41 PM, Kevin Kofler wrote:
> PS:
>
> Paul Johnson wrote:
>> I was wondering if there could be an exception here, since the code is
>> actually available and open.
>
> Have you even looked at that "source code"? I just have:
>
> 1. They refer to the Window$ download for the code. That's a .EXE file
> created with some proprietary installer generator (probably something that's
> part of that "Black Box" crap), 7z cannot do anything with it (and it can
> unpack at least self extractors and NSIS installers). Rather than running
> that EXE in WINE to get at the .odc files, I decided to look elsewhere, and
> in fact found their repository, but:

I'm wanting to use BUGS myself, so I've spent some time today poking
around at it. Here's a report on what I've found; it might help in
future analysis or further work on making this software usable and
available.

They use Inno Setup for their installer, so it is "proprietary" in the
sense that the format is not standardized, but Inno Setup is open
source. Its source code has been used to write innounp[1], an unpacker
for Inno Setup files.

Unfortunately, Inno Setup and innounp are written in Delphi, so the
usefulness diminishes at that point. However, it should be possible to
construct a portable unpacker using the innounp sources as a reference,
and it may even be possble to build them with FreePascal, depending on
how much Delphi-specific stuff they use.

Also, there is the cp-dev project[2] for building Component Pascal
programs on Linux, but it seems to want plain text input (.cp rather
than .odc) and also seems to require Black Box to bootstrap. I do not
know if it is self-hosting after the initial bootstrap.

So, a from-source build is still a ways off, but not necessarily
entirely unfeasible. If cp-dev is self-hosting, license-clean[3], and
capable of building OpenBUGS, is there a way to get it in to Fedora? It
seems it would require running an initial pre-compiled binary,
bootstrapped with Black Box, to then be able to recompile cp-dev from
SRPMs and use the recompiled version to keep it up to date.

There is still the issue of the lack of a free software viewer and
editor for the .odc files, but that seems to be a separate issue from
that of being able to re-build OpenBUGS with a completely free toolchain.

It could be that OpenBUGS will forever need to live in third-party
repositories.

- Michael

1. http://innounp.sourceforge.net/
2. http://cp-dev.sourceforge.net
3. cp-dev seems to not only use Black Box to bootstrap, but it also
seems to use Black Box sources as a part of itself. I have not yet
investigated whether this is true and, if true, how the relevant sources
are licensed.

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Old 08-26-2011, 06:50 PM
Michael Ekstrand
 
Default OpenBUGS program has a pre-compiled )S library from MS Windows. Any possibility to package it?

On 08/26/2011 12:13 PM, Michael Ekstrand wrote:
> 3. cp-dev seems to not only use Black Box to bootstrap, but it also
> seems to use Black Box sources as a part of itself. I have not yet
> investigated whether this is true and, if true, how the relevant sources
> are licensed.

BlackBox Component Builder's installation includes lots of source code
and is licensed under what looks like the Sleepycat license (BSD +
copyleft).

So it looks like the build and packaging toolchain for OpenBUGS does
consist of open source software, but this software is built for Windows,
may depend on GUIs for launching and controlling the build, and has a
nontrivial bootstrap process.

- Michael

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Old 08-27-2011, 11:33 PM
Jonathan Underwood
 
Default OpenBUGS program has a pre-compiled )S library from MS Windows. Any possibility to package it?

On 26 August 2011 19:50, Michael Ekstrand <michael@elehack.net> wrote:
> On 08/26/2011 12:13 PM, Michael Ekstrand wrote:
>> 3. cp-dev seems to not only use Black Box to bootstrap, but it also
>> seems to use Black Box sources as a part of itself. *I have not yet
>> investigated whether this is true and, if true, how the relevant sources
>> are licensed.
>
> BlackBox Component Builder's installation includes lots of source code
> and is licensed under what looks like the Sleepycat license (BSD +
> copyleft).
>
> So it looks like the build and packaging toolchain for OpenBUGS does
> consist of open source software, but this software is built for Windows,
> may depend on GUIs for launching and controlling the build, and has a
> nontrivial bootstrap process.

Perhaps JAGS is a better option for Fedora:

http://en.wikipedia.org/wiki/Just_another_Gibbs_sampler

"Its main advantage in comparison to the members of the original BUGS
family (WinBUGS and OpenBUGS) is its platform independence. It is
written in C++, while the BUGS family is written Component Pascal
which is only available for Windows.[1][2] Therefore it is already
part of many repositories of Linux distributions like Ubuntu. It can
also be compiled as a 64-bits application on 64-bits platforms, thus
making all the addressable space available to BUGS models."

J.
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