[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2011-09-18 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

Jussi Lehtola jussi.leht...@iki.fi changed:

   What|Removed |Added

 Blocks|505154(FE-SCITECH)  |

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-07-15 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

Carl Byington c...@five-ten-sg.com changed:

   What|Removed |Added

 Status|ASSIGNED|CLOSED
 Resolution||CURRENTRELEASE

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-07-08 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

--- Comment #21 from Dominik 'Rathann' Mierzejewski r...@greysector.net 
2010-07-08 18:18:18 EDT ---
Just a small comment about the arch-independent data. If it's large (I haven't
checked) you could split it into a .noarch subpackage called -data.

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-07-08 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

--- Comment #22 from Carl Byington c...@five-ten-sg.com 2010-07-08 19:43:48 
EDT ---
708K installed, but it gzips down to 117K so that is presumably the size in the
.rpm file. I don't know what the normal limits are on noarch data before we
really need to make it a noarch data subpackage. I think that is just
repository size that it saves.

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-06-20 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

Carl Byington c...@five-ten-sg.com changed:

   What|Removed |Added

   Flag|fedora-cvs+ |fedora-cvs?

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-06-20 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

--- Comment #20 from Kevin Fenzi ke...@tummy.com 2010-06-20 21:53:36 EDT ---
CVS done (by process-cvs-requests.py).

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-05-10 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

Carl Byington c...@five-ten-sg.com changed:

   What|Removed |Added

   Flag||fedora-cvs+

--- Comment #19 from Carl Byington c...@five-ten-sg.com 2010-05-11 01:28:30 
EDT ---
New Package CVS Request
===
Package Name: libghemical
Short Description: Libraries for the Ghemical chemistry package
Owners: carllibpst
Branches: F-12 F-13
InitialCC:

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-05-09 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

Christian Krause c...@plauener.de changed:

   What|Removed |Added

   Flag|fedora-review?  |fedora-review+

--- Comment #18 from Christian Krause c...@plauener.de 2010-05-09 23:34:05 
EDT ---
Thanks for the new package. All mentioned issues were fixed.

- APPROVED

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-04-26 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

--- Comment #17 from Carl Byington c...@five-ten-sg.com 2010-04-26 18:45:40 
EDT ---
Oops, forgot to update the production web server from the staging server.

http://www.five-ten-sg.com/libghemical.spec
http://www.five-ten-sg.com/libghemical-2.99.1-15.fc12.src.rpm   
http://koji.fedoraproject.org/koji/taskinfo?taskID=2128853   

should be good now.

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-04-24 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

--- Comment #16 from Christian Krause c...@plauener.de 2010-04-24 12:38:20 
EDT ---
(In reply to comment #15)
 http://www.five-ten-sg.com/libghemical.spec
 http://www.five-ten-sg.com/libghemical-2.99.1-15.fc12.src.rpm   
 http://koji.fedoraproject.org/koji/taskinfo?taskID=2128853

Please can you check whether the files were correctly uploaded? The spec file
is  at release 14 and the src.rpm redirects to -14.fc12.src.rpm, too.

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-04-20 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

--- Comment #15 from Carl Byington c...@five-ten-sg.com 2010-04-20 16:10:28 
EDT ---
pkgconfig file patched.

http://www.five-ten-sg.com/libghemical.spec
http://www.five-ten-sg.com/libghemical-2.99.1-15.fc12.src.rpm   
http://koji.fedoraproject.org/koji/taskinfo?taskID=2128853

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-04-19 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

Tom spot Callaway tcall...@redhat.com changed:

   What|Removed |Added

 CC||tcall...@redhat.com
 Blocks|182235(FE-Legal)|

--- Comment #13 from Tom spot Callaway tcall...@redhat.com 2010-04-19 
13:01:17 EDT ---
The licensing on that data (Public Domain) looks acceptable to me. Lifting
FE-Legal.

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-04-19 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

--- Comment #14 from Christian Krause c...@plauener.de 2010-04-19 16:22:52 
EDT ---
(In reply to comment #13)
 The licensing on that data (Public Domain) looks acceptable to me. Lifting
 FE-Legal.

Thanks, spot!

So the only remaining issue is the change in the pkgconfig file - once this is
done, this review can be approved. ;-)

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-04-15 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

Christian Krause c...@plauener.de changed:

   What|Removed |Added

 Blocks||182235(FE-Legal)

--- Comment #12 from Christian Krause c...@plauener.de 2010-04-15 18:59:39 
EDT ---
Sorry for the late response.

(In reply to comment #11)
 http://www.five-ten-sg.com/libghemical.spec
 http://www.five-ten-sg.com/libghemical-2.99.1-14.fc12.src.rpm   
 http://koji.fedoraproject.org/koji/taskinfo?taskID=2103279
 
 buildrequires gcc-gfortran, since it needs libgfortranbegin in the link.

Thanks for the new package and the bug fixes, here is the update of my review:

* spec file written in English and legible: OK
* BuildRequires: OK
* files section: OK

* compilation: TODO
Thanks for fixing the issue, the library looks now good. 
Probably it would be better to split the patch into two files: one for using
atlas and the 2nd one for fixing the compile issue.

There is one minor remaining issue: the pkg-config file still contains lots of
uneeded libraries and also references to the current compiler directory which
prevent compiling anything against libchemical just by using this pkg-config
file:

echo void main() {}  a.c  gcc `pkg-config --libs libghemical` -o a a.c

/tmp/ccZEt1Bd.o: In function `main':
a.c:(.text+0x0): multiple definition of `main'
/usr/lib/gcc/i686-redhat-linux/4.4.3/../../../libfl.a(libmain.o):(.text+0x0):
first defined here
/usr/lib/gcc/i686-redhat-linux/4.4.3/../../../libfl.a(libmain.o): In function
`main':
(.text+0x19): undefined reference to `yylex'
collect2: ld returned 1 exit status

If the Libs variable in libghemical.pc would only contain -L${libdir}
-lghemical everything would work fine.

* License  code vs. content: TODO
Thanks for asking upstream. I feel that there is no problem, but I don't think
I have the knowledge for the final decision. Let's get the final OK from
FE-LEGAL:

@spot: This package contains a number of data files which are needed for
chemical calculations of chemical bindings, etc.

On set of the files has the following license:
 The files in this directory were downloaded from:
http://www.amber.ucsf.edu/amber/dbase.html
At the download page there was the following copyright notice:

As has always been the case, the parameter information in the above file is
in the public domain, and may be redistributed or used in other programs. Any
such use should include proper citations, and any changes in the parameters
should be prominently noted.

and for the other one upstream gave the statement in comment #9. Based on these
statements and that other distributions (like Debian) have no issues, I assume
there is no problem.

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-04-08 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

--- Comment #11 from Carl Byington c...@five-ten-sg.com 2010-04-08 14:42:34 
EDT ---
fixed by patching configure.ac

http://www.five-ten-sg.com/libghemical.spec
http://www.five-ten-sg.com/libghemical-2.99.1-14.fc12.src.rpm   
http://koji.fedoraproject.org/koji/taskinfo?taskID=2103279

buildrequires gcc-gfortran, since it needs libgfortranbegin in the link.

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-04-07 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

Orcan 'oget' Ogetbil oget.fed...@gmail.com changed:

   What|Removed |Added

 CC||oget.fed...@gmail.com

--- Comment #10 from Orcan 'oget' Ogetbil oget.fed...@gmail.com 2010-04-07 
15:19:00 EDT ---
(In reply to comment #8)
 The upstream autoconf packaging does not seem to pickup the proper mpqc
 libraries, unless we override 'make LIBS=', which overrides everything. Unless
 we want to redo the whole autoconf package, overriding LIBS= seems to work.
 

Well, what you are doing is a workaround, not a fix. The proper fix is to
modify configure.ac (and his friends) accordingly, and rerun autoreconf. This
shouldn't be too hard. Just add the missing libraries using a similar scheme to
the exising ones. At the end of the day, you can submit the fix upstream, so
everyone, and not just Fedora users, can benefit from it.

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-04-06 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

--- Comment #9 from Carl Byington c...@five-ten-sg.com 2010-04-06 16:40:19 
EDT ---
data files license issue: upstream says:

I have myself typed the contents of the Tripos files from
a printed copy of an article printed in a scientific journal.
Therefore I assume the tripos data files and the rest of
libghemical are under the same license. The parameter
files other than Amber and Tripos are written my me
as well.

with Best Regards,

Tommi Hassinen

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-04-05 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

--- Comment #7 from Christian Krause c...@plauener.de 2010-04-05 12:15:10 EDT 
---
Thanks for the new package, here is now the full review:

* rpmlint: OK
rpmlint RPMS/i686/libghemical-* SRPMS/libghemical-2.99.1-12.fc13.src.rpm
SPECS/libghemical.spec
libghemical.i686: W: shared-lib-calls-exit /usr/lib/libghemical.so.5.0.0
e...@glibc_2.0
libghemical-devel.i686: W: no-documentation
4 packages and 1 specfiles checked; 0 errors, 2 warnings.

According to rpmlint's help the usage of exit in libraries is discouraged since
the calling application can not handle the error. However, in this case it
seems to be a design decisions of the upstream evelopers. This will not block
the review. But depending on your involvement with upstream it would probably
be worth to ask them for the reasons and/or explain them why its discouraged.

The no-documentation for the -devel package is also a false positive, it seems
that there is no API documentation available.

* naming: OK
- name matches upstream
- spec file name matches package name

* sources: OK
- md5sum: d2dae2d7d786d3cba335cb29d85033ea  libghemical-2.99.1.tar.gz
- sources matches upstream
- Source0 tag ok
- spectool -g  works

* License: TODO
- License in spec file matches the actual license (of the sources)
- License GPLv2+ acceptable
- However, for most of the data files the license is not 100% clear. A few of
the data files use the following license:
The files in this directory were downloaded from:
http://www.amber.ucsf.edu/amber/dbase.html
At the download page there was the following copyright notice:
'As has always been the case, the parameter information in the above file is
in the public domain, and may be redistributed or used in other programs. Any
such use should include proper citations, and any changes in the parameters
should be prominently noted.'

- Please can you ask upstream for a statement about the licenses of all of the
data files?

* spec file written in English and legible: TODO
Please can you enhance the description of the main package a little bit to
include some information what is the purpose of libghemical?

* compilation: TODO
- supports parallel build
- RPM_OPT_FLAGS are correctly used
- builds in koji: F14
- However, in the %build section the LIBS variable generated by %configure is
fully overwritten by the custom LIBS make parameter. 

If you call rpmlint libghemical on a system having the library installed,
there will be some warnings:


libghemical.i686: W: undefined-non-weak-symbol /usr/lib/libghemical.so.5.0.0
dlopen
libghemical.i686: W: undefined-non-weak-symbol /usr/lib/libghemical.so.5.0.0
lm7_set_plots_orbital_index
libghemical.i686: W: undefined-non-weak-symbol /usr/lib/libghemical.so.5.0.0
getorb_
...

The warnings show that the library uses symbols but does not link the
appropriate libraris.

Additionally there are warnings like:

libghemical.i686: W: unused-direct-shlib-dependency
/usr/lib/libghemical.so.5.0.0 /usr/lib/libSCmbptr12.so.7
libghemical.i686: W: unused-direct-shlib-dependency
/usr/lib/libghemical.so.5.0.0 /usr/lib/libSCoint3.so.7
...

These warnings show that a couple of the manually added libraries are not
needed on the other hand (this is not that critical as the previous warnings).

Sure, I don't know upstream's intention, but IMHO it should be rather done like
this:

1. don't overwrite the LIBS in the spec file
2. ensure, that libghemical is linked against all libraries from which
libghemical uses any symbols
- this should be changed probably in the Makefile.am's of the package
- finally there should be no undefined non-weak symbols

Some more information can be found here:
https://fedoraproject.org/wiki/Features/ChangeInImplicitDSOLinking

Additionally the Libs variable in the pkg-config file looks rather strange. In
general Libs should only contain the library itself. 


* BuildRequires: TODO
It looks like that the following BuildRequirements are not needed:
BuildRequires:  gcc-gfortran
BuildRequires:  openbabel-devel = 2.2

* locales handling: OK

* ldconfig in %post and %postun: OK

* package owns all directories that it creates: OK

* %files section: TODO (minor)
Please add a / at the line
%{_datadir}/%{name}
in the %files section to explicit state that this is a directory.

* no files listed twice in %files: OK

* file permissions: OK
- %defattr used
- actual permissions in packages OK

* %clean section: OK

* macro usage: TODO (minor)
please use %{_includedir}/%{name} for consistency

* code vs. content: TODO
This package contains content (the various data files). Let's wait for
upstream's feedback regarding the Licenses and ask then Fedora Legal...

* main package should not contain development related parts: OK

* large documentation into subpackage: OK (n/a)

* header files in -devel subpackage: OK

* static 

[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-04-05 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=542765

--- Comment #8 from Carl Byington c...@five-ten-sg.com 2010-04-05 16:58:51 
EDT ---
exit in library - yes, that seems to be the way they wrote the code, and I
don't see that changing since there are a LOT of such calls.

data files license - the amber and tripos data files are public domain, and
used in a many other chemistry packages. I will check with upstream, but I
doubt there is a more explicit license.

I added a bit of description for the libghemical package. 

Removed unnecessary build-requires.

rpmlint undefined-non-weak-symbol vs. unused-direct-shlib-dependency : for an
example, if we don't add -ldl, then we get dlopen as an
undefined-non-weak-symbol. If we do add -ldl, we get
unused-direct-shlib-dependency for dlopen.so. I have opted to prevent the
undefined-non-weak-symbol errors.

The upstream autoconf packaging does not seem to pickup the proper mpqc
libraries, unless we override 'make LIBS=', which overrides everything. Unless
we want to redo the whole autoconf package, overriding LIBS= seems to work.

http://www.five-ten-sg.com/libghemical.spec
http://www.five-ten-sg.com/libghemical-2.99.1-13.fc12.src.rpm   
http://koji.fedoraproject.org/koji/taskinfo?taskID=2096296

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-03-30 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

--- Comment #5 from Christian Krause c...@plauener.de 2010-03-30 03:49:19 EDT 
---
(In reply to comment #4)
 Sorry about the delay - I now have some time to work on these packages.
 
 naming - I thought there was some fedora requirement that .so objects be in
 -lib subpackages.
 
 data - as a separate package, that is arch-independent, which we lose if 
 placed
 in the main package.

No, this is not necessary and not intended:

- if the package contains only a library, then the *.so.* files go into the
base package which name matches the upstream tarball

- exception: if the package contains a library and e.g. a binary which uses the
library and if this library may be also used by other packages then it is
justified to create a -libs package (see e.g. tcp_wrappers, tcp_wrappers-libs)

- if the arch-independent data is needed for the base package, then it should
not be separated (and for sure the COPYING file should never be separated from
the binaries)

- in general: separate files into sub-packages only in case it is necessary,
reasons could be:
* the situation with the libraries as described above
* very large documentation
* additional data which is not really needed for the base package (e.g.
additional levels for a game)
* -devel

The main reasons is to save same disk space for people who don't need the
additional files.

So in case of this package, all files should go into the base package (no
-libs, no -data) besides the devel files which are already correct in the
-devel package.

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-03-29 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

--- Comment #4 from Carl Byington c...@five-ten-sg.com 2010-03-29 18:06:26 
EDT ---
Sorry about the delay - I now have some time to work on these packages.

naming - I thought there was some fedora requirement that .so objects be in
-lib subpackages.

data - as a separate package, that is arch-independent, which we lose if placed
in the main package.

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-03-29 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

Bug 542765 depends on bug 542759, which changed state.

Bug 542759 Summary: Review Request: mpqc - Ab-initio chemistry program
https://bugzilla.redhat.com/show_bug.cgi?id=542759

   What|Old Value   |New Value

 Status|ASSIGNED|CLOSED
 Resolution||CURRENTRELEASE

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-03-07 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

Christian Krause c...@plauener.de changed:

   What|Removed |Added

 Status|NEW |ASSIGNED
 CC||c...@plauener.de
 AssignedTo|nob...@fedoraproject.org|c...@plauener.de
   Flag||fedora-review?

--- Comment #3 from Christian Krause c...@plauener.de 2010-03-07 16:03:31 EST 
---
Since all dependent packages are now available (it looks like that BZ #542759
can be closed now) I'll review this package.

Here are two questions:

Naming of the packages: since the basename of this pacakge is already
libghemical I think it would be better to omit the sub-package
libghemical-libs and put the library directly in the base package.

Data package: What is the purpose of the data files in the -data sub-package?
If the library won't work without it, I would rather omit this sub-package as
well and put everything into the base package.

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-01-23 Thread bugzilla
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https://bugzilla.redhat.com/show_bug.cgi?id=542765

Dominik 'Rathann' Mierzejewski r...@greysector.net changed:

   What|Removed |Added

 CC||r...@greysector.net

Bug 542765 depends on bug 542760, which changed state.

Bug 542760 Summary: Review Request: mopac7 - Semi-empirical quantum mechanics 
suite
https://bugzilla.redhat.com/show_bug.cgi?id=542760

   What|Old Value   |New Value

 Status|ON_QA   |CLOSED
 Resolution||ERRATA

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[Bug 542765] Review Request: libghemical - Libraries for the Ghemical chemistry package

2010-01-23 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=542765

Dominik 'Rathann' Mierzejewski r...@greysector.net changed:

   What|Removed |Added

 Blocks||505154(FE-SCITECH)

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