[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2011-02-14 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

chris desjardins cddesjard...@gmail.com changed:

   What|Removed |Added

 Status|ASSIGNED|CLOSED
 Resolution||NOTABUG
Last Closed||2011-02-14 10:28:00

--- Comment #21 from chris desjardins cddesjard...@gmail.com 2011-02-14 
10:28:00 EST ---
Sorry I don't have time to do this anymore. Graduate school!!! So I have to
close this bug.

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-08-02 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

Martin Gieseking martin.giesek...@uos.de changed:

   What|Removed |Added

 Status|NEW |ASSIGNED
 AssignedTo|nob...@fedoraproject.org|martin.giesek...@uos.de
   Flag||fedora-review?

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-24 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #18 from chris desjardins cddesjard...@gmail.com 2010-06-24 
11:36:51 EDT ---
Updated:

SPEC URL: http://dl.dropbox.com/u/1501309/Fedora/JAGS/JAGS.spec
Source URL:
http://dl.dropbox.com/u/1501309/Fedora/JAGS/JAGS-2.1.0-7.fc13.src.rpm

The change from -6 to -7 is that I removed the patches for ltdl. The upstream
author informed that while JAGS ships with its own copy of ltdl if it detects a
system copy then it will automatically use that and not the version in the
sources. He said that I need to only add libtoool-ltdl-devel in the
BuildRequires. Therefore, I believed this rendered my patches unnecessary. This
is reflected in the new .src.rpm and .spec file. Also he thinks it's probably
fine to remove those two .la files.

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-24 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #19 from Martin Gieseking martin.giesek...@uos.de 2010-06-24 
13:26:39 EDT ---
(In reply to comment #18)
 He said that I need to only add libtoool-ltdl-devel in the
 BuildRequires. Therefore, I believed this rendered my patches unnecessary.

Hi Chris,

you should not rely on this. Since using bundled libraries is not permitted in
Fedora, you have to ensure that these are not linked. You usually do this by
removing the bundled libs. Thus, I suggest to revert to release 6.

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-24 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #20 from chris desjardins cddesjard...@gmail.com 2010-06-24 
15:11:12 EDT ---
OK reverting to release 6.

SPEC URL: http://dl.dropbox.com/u/1501309/Fedora/JAGS/JAGS.spec
Source URL:
http://dl.dropbox.com/u/1501309/Fedora/JAGS/JAGS-2.1.0-6.fc13.src.rpm

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-23 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

Martin Gieseking martin.giesek...@uos.de changed:

   What|Removed |Added

 CC||martin.giesek...@uos.de

--- Comment #9 from Martin Gieseking martin.giesek...@uos.de 2010-06-23 
06:13:52 EDT ---
Hi Chris,

.la files must not be packaged in Fedora according to the packaging guidelines.
I suggest to remove them in the %install section after make install, e.g.
with
find %{buildroot}%{_libdir} -name *.la -exec rm -f {} \;

Also, drop them in the %files section.

Here are some further comments:

- in the devel package, use a fully versioned dependency:
  Requires: %{name} = %{version}-%{release} 
  (rather than Requires: JAGS  = %{version})

- According to the source file headers, the license is GPLv2+ because 
  of the addition or (at your option) any later version.

- add file COPYING to the base package (as %doc)

- the Group of the devel package should be 'Development/Libraries'

- as a minor cosmetic addition, I suggest to append a slash to directory 
  names, e.g. %{_includedir}/JAGS/
  This way it's easier to recognize that a folder is added rather than a 
  single file

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-23 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #10 from Martin Gieseking martin.giesek...@uos.de 2010-06-23 
06:28:11 EDT ---
Some more comments:
- %setup -q should be sufficient in %prep
- add %{_smp_mflags} to the first 'make'
- replace %defattr(-,root,root) with %defattr(-,root,root,-)
- add AUTHORS, ChangeLog, NEWS and TODO as %doc to the base package

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-23 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #11 from chris desjardins cddesjard...@gmail.com 2010-06-23 
09:58:20 EDT ---
Hi Martin,
Thank you very much for reviewing this package! I am really excited about
hopefully getting this package into Fedora. 

I've updated my *.spec and *.src.rpm files to reflect all the changes that
you've mentioned above. Please let me know what else I can do. 

Spec URL: http://dl.dropbox.com/u/1501309/Fedora/JAGS/JAGS.spec
Source URL:
http://dl.dropbox.com/u/1501309/Fedora/JAGS/JAGS-2.1.0-5.fc13.src.rpm

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-23 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #12 from Martin Gieseking martin.giesek...@uos.de 2010-06-23 
12:04:49 EDT ---
(In reply to comment #11)
 Thank you very much for reviewing this package! I am really excited about
 hopefully getting this package into Fedora. 

Hi Chris,

I'm not a sponsor, so I can't formally review this package. Nonetheless,
polishing the spec file will certainly help to find one. In addition, you
usually need to offer some more packages and comment on other packager's review
requests to show that you're familiar with the packaging guidelines.

Here are a couple of further remarks on your package:

- In Source0, replace JAGS-2.1.0.tar.gz with JAGS-%{version}.tar.gz or
  %{name}-%{version}.tar.gz. It simplifies future updates of the package

- I think, you can also add %{_smp_mflags} to make docs. It enables 
  parallel builds if possible, and thus speeds up the build process on 
  multi-processor systems.

- remove the trailing slash from %{_bindir}/jags/ because jags is not
  a directory here but a binary file

- you can drop jags_installation_manual.pdf as it's not of much use in 
  a binary package

- also adapt the %defattr parameters of the devel package as mentioned 
  in comment #10

- The tarball contains a copy of libltdl which should be removed in favor 
  of the package provided by Fedora (libtool-ltdl-devel).

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-23 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #13 from chris desjardins cddesjard...@gmail.com 2010-06-23 
13:53:03 EDT ---
Thanks. I will update the package once I get the libltdl situation figured out.
AI am not entirely sure that removing the *.la files is correct and I have
contacted the upstream author to verify this doesn't cripple the program. (It
doesn't appear to). 

Also, I wanted to mention I am seeking sponsorship for these packages as well:

https://bugzilla.redhat.com/show_bug.cgi?id=600529
https://bugzilla.redhat.com/show_bug.cgi?id=600517

I would like to maintain several R packages in Fedora beyond these (including
R-lme4 and R-MCMCglmm) but wanted to focus on these 3 first. Should I offer
more packages too?

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-23 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #14 from Martin Gieseking martin.giesek...@uos.de 2010-06-23 
14:27:48 EDT ---
(In reply to comment #13)
 AI am not entirely sure that removing the *.la files is correct and I have
 contacted the upstream author to verify this doesn't cripple the program. (It
 doesn't appear to). 

Removing the libtool archives isn't harmful at all. They are only used when
linking a library with libtool. Alternatively, you could also explicitly link
against the corresponding .a or .so files. Once the binary is built, the .la
files are not required any longer, especially since Fedora primarily
distributes shared libs which are linked via .so files. And the latter are part
of the devel package. 


 I would like to maintain several R packages in Fedora beyond these (including
 R-lme4 and R-MCMCglmm) but wanted to focus on these 3 first. Should I offer
 more packages too?

OK, that's fine. As far as I know, three packages should be enough, but this
decision is up to your sponsor.

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-23 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #15 from chris desjardins cddesjard...@gmail.com 2010-06-23 
14:38:25 EDT ---
Hi Martin,
Thanks for your speedy reply. Do you know how I would do this?

 - The tarball contains a copy of libltdl which should be removed in favor 
  of the package provided by Fedora (libtool-ltdl-devel).  

In the .spec file? I am unclear how to do this. Thanks!

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-23 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #16 from Martin Gieseking martin.giesek...@uos.de 2010-06-23 
15:11:20 EDT ---
I haven't had a deeper look into the tarball and the autotools scripts, but you
can probably do it this way:

- add BuildRequires: libtool-ltdl-devel autoconf automake

- in %prep: 
  * remove the libltdl directory
  * remove all references to this directory from configure.ac and Makefile.am 
by patching these files accordingly 
   (don't modify the files in the tarball but add .patch/.diff files
describing the changes to your package)
  * run 'autoreconf'

This is just the general idea. I haven't tried it, so there might be further
things to be addressed.

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-23 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #17 from chris desjardins cddesjard...@gmail.com 2010-06-23 
17:02:35 EDT ---
I have addressed all of the outstanding comments (#12 and #16) in the latest
version.

SPEC URL: http://dl.dropbox.com/u/1501309/Fedora/JAGS/JAGS.spec
Source URL:
http://dl.dropbox.com/u/1501309/Fedora/JAGS/JAGS-2.1.0-6.fc13.src.rpm

I have patched configure.ac and Makefile.am as per Martin's requests. Also, I
removed ChangeLog as it is empty. The binary installs fine and works.

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-09 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

Randall Berry randyn3...@gmail.com changed:

   What|Removed |Added

 Blocks||600529

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-08 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

chris desjardins cddesjard...@gmail.com changed:

   What|Removed |Added

  Alias||FE-NEEDSPONSER

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-08 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

chris desjardins cddesjard...@gmail.com changed:

   What|Removed |Added

 Blocks|177841(FE-NEEDSPONSOR)  |505154(FE-SCITECH)

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-08 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

Steve Traylen steve.tray...@cern.ch changed:

   What|Removed |Added

 CC||steve.tray...@cern.ch

--- Comment #4 from Steve Traylen steve.tray...@cern.ch 2010-06-08 14:18:24 
EDT ---
This is an informal review, as I understand from a mail you are
seeking sponsership and should block this bug on FE-NEEDSPONSER accordingly.

Just looking at the .spec file for now 

1) The .la should be removed somehow.

See:
http://fedoraproject.org/wiki/PackagingGuidelines#Packaging_Static_Libraries

2) Your release tag is 2.1 which is odd, it typically starts at 1. :-)

See: http://fedoraproject.org/wiki/Packaging:NamingGuidelines#Package_Version
In a nutshell it's the number of .spec file modifications or builds in fact
since the Version was last update.

3) Not important I would say but in principal packages take the name of 
the tar ball so JAGS but I would never not approve based on that.
http://fedoraproject.org/wiki/Packaging:NamingGuidelines

4) BuildRequires: gcc-c++ certainly is not needed, see
http://fedoraproject.org/wiki/PackagingGuidelines#Exceptions_2

5) I see you have a .tex file in your docs have you considered converting
   it to something more readable such as ps or pdf.

 Steve.

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-08 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

chris desjardins cddesjard...@gmail.com changed:

   What|Removed |Added

 Blocks|505154(FE-SCITECH)  |177841(FE-NEEDSPONSOR)

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-08 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

chris desjardins cddesjard...@gmail.com changed:

   What|Removed |Added

  Alias|FE-NEEDSPONSER  |

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-08 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

chris desjardins cddesjard...@gmail.com changed:

   What|Removed |Added

 Blocks||177841(FE-NEEDSPONSOR)

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-08 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #5 from chris desjardins cddesjard...@gmail.com 2010-06-08 
17:09:33 EDT ---
Hi Steve,
Thanks for for taking a quick look at this. Regarding:

1) I am really not sure how to deal with this one. I tried to configure it w/
--disable-static but those two *.la files still showed up. The two *.la files:

libjags.la
libjrmath.la

are JAGS specific I believe and looking here:
http://fedoraproject.org/wiki/PackagingGuidelines#Packaging_Static_Libraries

I can't determine exactly what I should do. Create a *-static package, contact
upstream or something else. Help with this would be very useful!

2) I know. I didn't realize that until after I uploaded it. This should be
fixed now.

3) and 4)  Fixed in JAGS-2.1.0-3.fc13.src.rpm[1]

5) I haven't really given this much consideration. It would be a good idea ...
but what format? http://fedoraproject.org/wiki/Packaging:Guidelines doesn't
seem to provide any real guidance.

[1] Updated Spec and Source URL
Spec URL: http://dl.dropbox.com/u/1501309/Fedora/JAGS.spec
Source URL: http://dl.dropbox.com/u/1501309/Fedora/JAGS-2.1.0-3.fc13.src.rpm

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-08 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #6 from Steve Traylen steve.tray...@cern.ch 2010-06-08 17:47:25 
EDT ---
(In reply to comment #5)
 Hi Steve,
 Thanks for for taking a quick look at this. Regarding:
 
 1) I am really not sure how to deal with this one. I tried to configure it w/
 --disable-static but those two *.la files still showed up. The two *.la files:
 
 libjags.la
 libjrmath.la
 
 are JAGS specific I believe and looking here:
 http://fedoraproject.org/wiki/PackagingGuidelines#Packaging_Static_Libraries
 
 I can't determine exactly what I should do. Create a *-static package, contact
 upstream or something else. Help with this would be very useful!

If --disable-static does not work, just delete them
in the %build section after your build. i.e

rm %{_builddir}%{_libdir}/*.la

 
 2) I know. I didn't realize that until after I uploaded it. This should be
 fixed now.
 
 3) and 4)  Fixed in JAGS-2.1.0-3.fc13.src.rpm[1]
 
 5) I haven't really given this much consideration. It would be a good idea ...
 but what format? http://fedoraproject.org/wiki/Packaging:Guidelines doesn't
 seem to provide any real guidance.

Your choice even if it to do it or not , I would probably convert to
pdf , of course you will need to pull in pdflatex as build dependencies
if you choose to do this.
 
 [1] Updated Spec and Source URL
 Spec URL: http://dl.dropbox.com/u/1501309/Fedora/JAGS.spec
 Source URL: http://dl.dropbox.com/u/1501309/Fedora/JAGS-2.1.0-3.fc13.src.rpm  
   

Will look after the next iteration.

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-08 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #8 from chris desjardins cddesjard...@gmail.com 2010-06-08 
19:14:40 EDT ---
Oh the difference between -3 and -4 is that I now build the .tex files into PDF
and some other subtle differences.

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-08 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #7 from chris desjardins cddesjard...@gmail.com 2010-06-08 
19:11:30 EDT ---
Updated.
SPEC URL: http://dl.dropbox.com/u/1501309/Fedora/JAGS.spec
Source URL: http://dl.dropbox.com/u/1501309/Fedora/JAGS-2.1.0-4.fc13.src.rpm

However, I still wasn't able to get:

rm %{_builddir}%{_libdir}/*.la


to work no matter where I put it. Also are all files that end in .la static?
Are they all problematic? If so there are several files in JAGS that have .la
in them.

[r...@goddard x86_64]# rpm -ql JAGS | grep la
/usr/lib64/JAGS/modules-2.1.0/basemod.la
/usr/lib64/JAGS/modules-2.1.0/bugs.la
/usr/lib64/JAGS/modules-2.1.0/dic.la
/usr/lib64/JAGS/modules-2.1.0/glm.la
/usr/lib64/JAGS/modules-2.1.0/lecuyer.la
/usr/lib64/JAGS/modules-2.1.0/mix.la
/usr/lib64/JAGS/modules-2.1.0/msm.la
/usr/lib64/libjags.la
/usr/lib64/libjrmath.la

To be honest, I am a little stumped and unsure about how to deal with this. I
looked at the Debian package and it had these .la files in there too. Any
further help you can give me is greatly appreciated!

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-07 Thread bugzilla
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comments should be made in the comments box of this bug.


https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #3 from chris desjardins cddesjard...@gmail.com 2010-06-07 
14:47:27 EDT ---
I've updated the SRPM and the spec file. 
Spec URL: http://dl.dropbox.com/u/1501309/jags.spec
Source URL: http://dl.dropbox.com/u/1501309/Fedora/jags-2.1.0-2.fc13.src.rpm

This addresses the issues with the man page and an explanation of the exit()
warning from the upstream author (see the Changelog). The man page will be
included in newer releases.

Additionally, the upstream author believes that the final outstanding rpmlint
warning associated with hidden files has to do with libtool and not JAGS.

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-04 Thread bugzilla
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comments should be made in the comments box of this bug.


https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #1 from chris desjardins cddesjard...@gmail.com 2010-06-04 
15:08:21 EDT ---
Also, I've sent my rpmlint warnings to the developer upstream re: the absence
of a manpage and exit().

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[Bug 600467] Review Request: jags - Just Another Gibbs Sampler

2010-06-04 Thread bugzilla
Please do not reply directly to this email. All additional
comments should be made in the comments box of this bug.


https://bugzilla.redhat.com/show_bug.cgi?id=600467

--- Comment #2 from chris desjardins cddesjard...@gmail.com 2010-06-04 
18:59:57 EDT ---
Also this is my first package so I need a sponsor. I've also submitted 2 other
packages allowing a user to interact from R with JAGS. These review requests
are 

https://bugzilla.redhat.com/show_bug.cgi?id=600517
https://bugzilla.redhat.com/show_bug.cgi?id=600529

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