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Summary: Review Request: PyQuante - Python Quantum Chemistry
https://bugzilla.redhat.com/show_bug.cgi?id=468579
Summary: Review Request: PyQuante - Python Quantum Chemistry Product: Fedora Version: rawhide Platform: All OS/Version: Linux Status: NEW Severity: medium Priority: medium Component: Package Review AssignedTo: nobody@fedoraproject.org ReportedBy: jussi.lehtola@iki.fi QAContact: extras-qa@fedoraproject.org CC: notting@redhat.com, fedora-package-review@redhat.com Estimated Hours: 0.0 Classification: Fedora
Spec URL: http://theory.physics.helsinki.fi/~jzlehtol/rpms/PyQuante.spec SRPM URL: http://theory.physics.helsinki.fi/~jzlehtol/rpms/PyQuante-1.6.1-1.fc9.src.rp...
Description: PyQuante is an open-source suite of programs for developing quantum chemistry methods. The program is written in the Python programming language, but has many "rate-determining" modules also written in C for speed. The resulting code, though not as fast as Jaguar, NWChem, Gaussian, or GAMESS, is much easier to understand and modify. The goal of this software is not necessarily to provide a working quantum chemistry program (although it will hopefully do that), but rather to provide a well-engineered set of tools so that scientists can construct their own quantum chemistry programs without going through the tedium of having to write every low-level routine.
rpmlint output:
PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Minimizers.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/IO/XYZ.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/GridPoint.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/qmmd.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/pyints.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/PGBF.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/MINDO3_Parameters.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/DFunctionals.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/IO/Molf.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Constants.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Basis/Tools.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Atom.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/dft.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Molecule.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/leapfrog.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/OEP.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/EN2.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Lebedev.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/fermi_dirac.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/ThomasFermi.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/MINDO3.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/pressure.py 0644 PyQuante.x86_64: E: wrong-script-end-of-line-encoding /usr/lib64/python2.5/site-packages/PyQuante/pressure.py PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/DMP.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Bunch.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/IO/Cube.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/LA2.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Dynamics.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/IO/Jaguar.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/AnalyticDerivatives.py 0644 PyQuante.x86_64: E: wrong-script-end-of-line-encoding /usr/lib64/python2.5/site-packages/PyQuante/AnalyticDerivatives.py PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Wavefunction.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/force.py 0644 PyQuante.x86_64: E: wrong-script-end-of-line-encoding /usr/lib64/python2.5/site-packages/PyQuante/force.py PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/NumWrap.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/MolecularGrid.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/CGBF.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/IO/Matlab.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/CI.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Element.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/PyQuante2.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Convergence.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/NEB.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/AtomicGrid.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/DFunctionalsOld.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Slater.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Solvers.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/MP.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/HFGF.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/rys.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/hgp.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/hartree_fock.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Legendre.py 0644 PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/rohf.py 0644 PyQuante.x86_64: W: invalid-license Modified BSD PyQuante-debuginfo.x86_64: W: invalid-license Modified BSD 2 packages and 0 specfiles checked; 54 errors, 2 warnings.
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https://bugzilla.redhat.com/show_bug.cgi?id=468579
Fabian Affolter fabian@bernewireless.net changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |fabian@bernewireless.net
--- Comment #1 from Fabian Affolter fabian@bernewireless.net 2008-10-26 20:02:21 EDT --- Only some quick comment about the rpmlint output and your spec file...
Spec file:
Detail about packaging python stuff: https://fedoraproject.org/wiki/Packaging/Python
Name: PyQuante - The name of your package should be lower case https://fedoraproject.org/wiki/Packaging/NamingGuidelines#Case_Sensitivity
BuildRequires - 'BuildRequires: python' is missing
% files - Please follow the guidelines https://fedoraproject.org/wiki/Packaging/Python#System_Architecture
%changelog - E mail address is missing https://fedoraproject.org/wiki/Packaging/Guidelines#Changelogs
rpmlint output:
(In reply to comment #0)
PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Minimizers.py 0644
You can add something like 'find *.py -type f | xargs chmod a+x' to fix this.
PyQuante.x86_64: E: wrong-script-end-of-line-encoding /usr/lib64/python2.5/site-packages/PyQuante/pressure.py
If you have to remove DOS line endings in this file 'sed -i 's/\r$//' file.py'
PyQuante.x86_64: W: invalid-license Modified BSD PyQuante-debuginfo.x86_64: W: invalid-license Modified BSD
For a valid license for Fedora, please take a look at https://fedoraproject.org/wiki/Licensing
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--- Comment #2 from Fabian Affolter fabian@bernewireless.net 2008-11-13 08:13:25 EDT --- ping?
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--- Comment #3 from Jussi Lehtola jussi.lehtola@iki.fi 2008-11-13 08:46:23 EDT --- Sorry, I'll get right on it.
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--- Comment #4 from Jussi Lehtola jussi.lehtola@iki.fi 2008-11-13 09:13:27 EDT --- (In reply to comment #1)
Only some quick comment about the rpmlint output and your spec file...
Spec file:
Detail about packaging python stuff: https://fedoraproject.org/wiki/Packaging/Python
Name: PyQuante
- The name of your package should be lower case https://fedoraproject.org/wiki/Packaging/NamingGuidelines#Case_Sensitivity
The author refers to the software as PyQuante, also the python modules are called PyQuante. Refer to ORBit in Naming Guidelines.
BuildRequires
- 'BuildRequires: python' is missing
It is already required by python-setuptools-devel (and numpy too?).
% files
- Please follow the guidelines
https://fedoraproject.org/wiki/Packaging/Python#System_Architecture
Hmm, I thought I already was following them. I can't find anything wrong with using %{python_sitearch} as defined in the Python guidelines. PyQuante contains compiled C code in the modules..
PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Minimizers.py 0644
You can add something like 'find *.py -type f | xargs chmod a+x' to fix this.
If I do that then I get script-without-shebang errors. Besides, the files in site-packages don't need to be executable, since they just contain modules used by the frontend software.
Check your python-sitelib directory, only a small minority of the .py files are executable. rpmlint shouldn't complain about this.
PyQuante.x86_64: W: invalid-license Modified BSD PyQuante-debuginfo.x86_64: W: invalid-license Modified BSD
For a valid license for Fedora, please take a look at https://fedoraproject.org/wiki/Licensing
Yeah, but the license is not word-for-word BSD.
http://theory.physics.helsinki.fi/~jzlehtol/rpms/PyQuante.spec http://theory.physics.helsinki.fi/~jzlehtol/rpms/PyQuante-1.6.1-2.fc9.src.rp...
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--- Comment #5 from Fabian Affolter fabian@bernewireless.net 2008-11-14 06:20:59 EDT --- (In reply to comment #4)
(In reply to comment #1)
Name: PyQuante
- The name of your package should be lower case https://fedoraproject.org/wiki/Packaging/NamingGuidelines#Case_Sensitivity
The author refers to the software as PyQuante, also the python modules are called PyQuante. Refer to ORBit in Naming Guidelines.
OK
BuildRequires
- 'BuildRequires: python' is missing
It is already required by python-setuptools-devel (and numpy too?).
python is no longer in the default packageset. https://fedoraproject.org/wiki/Packaging/Python#BuildRequires
% files
- Please follow the guidelines
https://fedoraproject.org/wiki/Packaging/Python#System_Architecture
Hmm, I thought I already was following them. I can't find anything wrong with using %{python_sitearch} as defined in the Python guidelines. PyQuante contains compiled C code in the modules..
I guess that I have had %{python_sitearch}/* in my mind. But I can remember if I thought about %{python_sitearch}/modulename/*
PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Minimizers.py 0644
You can add something like 'find *.py -type f | xargs chmod a+x' to fix this.
If I do that then I get script-without-shebang errors. Besides, the files in site-packages don't need to be executable, since they just contain modules used by the frontend software.
Check your python-sitelib directory, only a small minority of the .py files are executable. rpmlint shouldn't complain about this.
I will take a look at it.
PyQuante.x86_64: W: invalid-license Modified BSD PyQuante-debuginfo.x86_64: W: invalid-license Modified BSD
For a valid license for Fedora, please take a look at https://fedoraproject.org/wiki/Licensing
Yeah, but the license is not word-for-word BSD.
The license looks like MIT 'Old Style with legal disclaimer 3' http://fedoraproject.org/wiki/Licensing/MIT
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--- Comment #6 from Jussi Lehtola jussi.lehtola@iki.fi 2008-11-21 09:45:39 EDT --- Fixed license tag to BSD (the license is almost the same as New BSD 3 clause license, only difference is
BSD: THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS AS IS
PyQuante: THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS AS IS
I don't think there's anything wrong with the %files section, since the package doesn't end up owning any directories or files it shouldn't.
http://theory.physics.helsinki.fi/~jzlehtol/rpms/PyQuante.spec http://theory.physics.helsinki.fi/~jzlehtol/rpms/PyQuante-1.6.1-3.fc9.src.rp...
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--- Comment #7 from Jussi Lehtola jussi.lehtola@iki.fi 2009-02-05 12:40:04 EDT --- Ping; Fabian, are you going to review the package?
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Fabian Affolter fabian@bernewireless.net changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED AssignedTo|nobody@fedoraproject.org |fabian@bernewireless.net Flag| |fedora-review?
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--- Comment #8 from Fabian Affolter fabian@bernewireless.net 2009-02-23 18:18:13 EDT --- - '%{!?python_sitelib: ...' is not needed at the top of the spec file. - Source URL should be http://downloads.sourceforge.net/pyquante/%%7Bname%7D-%%7Bversion%7D.tar.gz
- (In reply to comment #5)
(In reply to comment #4)
(In reply to comment #1)
PyQuante.x86_64: E: non-executable-script /usr/lib64/python2.5/site-packages/PyQuante/Minimizers.py 0644
You can add something like 'find *.py -type f | xargs chmod a+x' to fix this.
If I do that then I get script-without-shebang errors. Besides, the files in site-packages don't need to be executable, since they just contain modules used by the frontend software.
Check your python-sitelib directory, only a small minority of the .py files are executable. rpmlint shouldn't complain about this.
Will upstream fix this? If the modules only are used by the frontend then the shebang can be removed (and then the rpmlint errors will disappear, I guess)
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--- Comment #9 from Fabian Affolter fabian@bernewireless.net 2009-02-23 18:21:26 EDT --- Is the line encodings fixing not better be done in the %prep section?
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--- Comment #10 from Jussi Lehtola jussi.lehtola@iki.fi 2009-02-24 06:46:13 EDT --- Okay, I've removed the shebangs, and the package still works. rpmlint output is now clean.
http://theory.physics.helsinki.fi/~jzlehtol/rpms/PyQuante.spec http://theory.physics.helsinki.fi/~jzlehtol/rpms/PyQuante-1.6.1-4.fc10.src.r...
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--- Comment #11 from Jussi Lehtola jussi.lehtola@iki.fi 2009-02-24 13:54:10 EDT --- Added tests directory.
http://theory.physics.helsinki.fi/~jzlehtol/rpms/PyQuante.spec http://theory.physics.helsinki.fi/~jzlehtol/rpms/PyQuante-1.6.1-5.fc10.src.r...
Also, I've contacted upstream about the shebangs; they will be removed in the next release.
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--- Comment #12 from Jussi Lehtola jussi.lehtola@iki.fi 2009-02-25 15:30:56 EDT --- Coordinated fixes with upstream. Rpmlint output is now clean.
http://theory.physics.helsinki.fi/~jzlehtol/rpms/PyQuante.spec http://theory.physics.helsinki.fi/~jzlehtol/rpms/PyQuante-1.6.3-1.fc10.src.r...
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Fabian Affolter fabian@bernewireless.net changed:
What |Removed |Added ---------------------------------------------------------------------------- Flag|fedora-review? |fedora-review+
--- Comment #13 from Fabian Affolter fabian@bernewireless.net 2009-03-07 06:51:16 EDT --- Package Review ==============
Package:
Key: - = N/A x = Check ! = Problem ? = Not evaluated
=== REQUIRED ITEMS === [x] Package is named according to the Package Naming Guidelines. [x] Spec file name must match the base package %{name}, in the format %{name}.spec. [x] Package meets the Packaging Guidelines [x] Package successfully compiles and builds into binary RPMs on at least one supported architecture. Tested on: F10/i386 [x] Rpmlint output: Source RPM: [fab@laptop24 SRPMS]$ rpmlint PyQuante-1.6.3-1.fc10.src.rpm 1 packages and 0 specfiles checked; 0 errors, 0 warnings. Binary RPM(s): [fab@laptop24 i386]$ rpmlint PyQuante-1.6.3-1.fc10.i386.rpm 1 packages and 0 specfiles checked; 0 errors, 0 warnings. [x] Package is not relocatable. [x] Buildroot is correct master : %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) spec file: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) [x] Package is licensed with an open-source compatible license and meets other legal requirements as defined in the legal section of Packaging Guidelines. [x] License field in the package spec file matches the actual license. License type: BSD [x] If (and only if) the source package includes the text of the license(s) in its own file, then that file, containing the text of the license(s) for the package is included in %doc.
[x] Spec file is legible and written in American English. [x] Sources used to build the package matches the upstream source, as provided in the spec URL. Upstream source: 5e44d1e67a4f62da69ade7e26e53ab7b Build source: 5e44d1e67a4f62da69ade7e26e53ab7b [x] Package is not known to require ExcludeArch. [x] All build dependencies are listed in BuildRequires, except for any that are listed in the exceptions section of Packaging Guidelines. [-] The spec file handles locales properly. %find_lang used for locales. [-] %{optflags} or RPM_OPT_FLAGS are honoured. [-] ldconfig called in %post and %postun if required. [x] %install starts with rm -rf %{buildroot} or $RPM_BUILD_ROOT. [x] Package must own all directories that it creates. [x] Package requires other packages for directories it uses. [x] Package does not own files or directories owned by other packages. [x] Package does not contain duplicates in %files. [x] Permissions on files are set properly. %defattr(-,root,root,-) is in every %files section. [x] Package uses nothing in %doc for runtime. [x] Package has a %clean section, which contains rm -rf %{buildroot} or $RPM_BUILD_ROOT. [x] Package consistently uses macros. [x] Package contains code, or permissable content.
[-] Large documentation files are in a -doc subpackage, if required. [-] Header files in -devel subpackage, if present. [-] Fully versioned dependency in subpackage, if present. [-] Static libraries in -devel subpackage, if present. [-] Package requires pkgconfig, if .pc files are present. [-] Development .so files in -devel subpackage, if present. [-] Package does not contain any libtool archives (.la). [x] -debuginfo subpackage is present and looks complete. [-] Package contains a properly installed %{name}.desktop file if it is a GUI application.
=== SUGGESTED ITEMS === [-] Timestamps preserved with cp and install. [-] Uses parallel make (%{?_smp_mflags}) [x] Latest version is packaged. [-] Package does not include license text files separate from upstream. [-] Description and summary sections in the package spec file contains translations for supported Non-English languages, if available. [x] Reviewer should test that the package builds in mock. Tested on: F10/i386 [x] Package should compile and build into binary RPMs on all supported architectures. Tested: http://koji.fedoraproject.org/koji/taskinfo?taskID=1228388 [x] Package functions as described. [-] Scriptlets must be sane, if used. [-] The placement of pkgconfig(.pc) files is correct. [-] File based requires are sane. [x] Changelog in allowed format
I see no further blocker, package APPROVED
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Jussi Lehtola jussi.lehtola@iki.fi changed:
What |Removed |Added ---------------------------------------------------------------------------- Flag| |fedora-cvs?
--- Comment #14 from Jussi Lehtola jussi.lehtola@iki.fi 2009-03-07 08:10:53 EDT --- Thanks for the review.
New Package CVS Request ======================= Package Name: PyQuante Short Description: Python Quantum Chemistry Owners: jussilehtola Branches: F-9 F-10 InitialCC:
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Kevin Fenzi kevin@tummy.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flag|fedora-cvs? |fedora-cvs+
--- Comment #15 from Kevin Fenzi kevin@tummy.com 2009-03-07 12:10:29 EDT --- cvs done.
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Jussi Lehtola jussi.lehtola@iki.fi changed:
What |Removed |Added ---------------------------------------------------------------------------- Flag|fedora-cvs+ |fedora-cvs?
--- Comment #16 from Jussi Lehtola jussi.lehtola@iki.fi 2009-03-07 18:37:06 EDT --- Oh, I need EPEL branches, too. Sorry.
Package Change Request ====================== Package Name: PyQuante New Branches: EL-5 Owners: jussilehtola
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--- Comment #17 from Fedora Update System updates@fedoraproject.org 2009-03-07 19:05:36 EDT --- PyQuante-1.6.3-1.fc10 has been submitted as an update for Fedora 10. http://admin.fedoraproject.org/updates/PyQuante-1.6.3-1.fc10
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--- Comment #18 from Fedora Update System updates@fedoraproject.org 2009-03-07 19:06:21 EDT --- PyQuante-1.6.3-1.fc9 has been submitted as an update for Fedora 9. http://admin.fedoraproject.org/updates/PyQuante-1.6.3-1.fc9
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https://bugzilla.redhat.com/show_bug.cgi?id=468579
Kevin Fenzi kevin@tummy.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flag|fedora-cvs? |fedora-cvs+
--- Comment #19 from Kevin Fenzi kevin@tummy.com 2009-03-07 19:12:46 EDT --- cvs done.
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https://bugzilla.redhat.com/show_bug.cgi?id=468579
--- Comment #20 from Fedora Update System updates@fedoraproject.org 2009-03-09 18:44:14 EDT --- PyQuante-1.6.3-1.fc10 has been pushed to the Fedora 10 stable repository. If problems still persist, please make note of it in this bug report.
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https://bugzilla.redhat.com/show_bug.cgi?id=468579
Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |CLOSED Fixed In Version| |1.6.3-1.fc10 Resolution| |NEXTRELEASE
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https://bugzilla.redhat.com/show_bug.cgi?id=468579
--- Comment #21 from Fedora Update System updates@fedoraproject.org 2009-03-09 19:11:07 EDT --- PyQuante-1.6.3-1.fc9 has been pushed to the Fedora 9 stable repository. If problems still persist, please make note of it in this bug report.
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