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Summary: Review Request: levmar - Levenberg-Marquardt nonlinear least squares optimization
https://bugzilla.redhat.com/show_bug.cgi?id=558061
Summary: Review Request: levmar - Levenberg-Marquardt nonlinear least squares optimization Product: Fedora Version: rawhide Platform: All OS/Version: Linux Status: NEW Severity: medium Priority: medium Component: Package Review AssignedTo: nobody@fedoraproject.org ReportedBy: eric@brouhaha.com QAContact: extras-qa@fedoraproject.org CC: notting@redhat.com, fedora-package-review@redhat.com Estimated Hours: 0.0 Classification: Fedora
This is my first package, so I'm seeking a sponsor.
Spec URL: http://www.brouhaha.com/~eric/software/fedora/f12/levmar/levmar.spec SRPM URL: http://www.brouhaha.com/~eric/software/fedora/f12/levmar/levmar-2.5-1.fc12.s... Description: levmar is a native ANSI C implementation of the Levenberg-Marquardt optimization algorithm. Both unconstrained and constrained (under linear equations, inequality and box constraints) Levenberg-Marquardt variants are included. The LM algorithm is an iterative technique that finds a local minimum of a function that is expressed as the sum of squares of nonlinear functions. It has become a standard technique for nonlinear least-squares problems and can be thought of as a combination of steepest descent and the Gauss-Newton method. When the current solution is far from the correct on, the algorithm behaves like a steepest descent method: slow, but guaranteed to converge. When the current solution is close to the correct solution, it becomes a Gauss-newton method.
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Eric Smith eric@brouhaha.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Blocks| |177841(FE-NEEDSPONSOR)
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Jussi Lehtola jussi.lehtola@iki.fi changed:
What |Removed |Added ---------------------------------------------------------------------------- CC| |jussi.lehtola@iki.fi
--- Comment #1 from Jussi Lehtola jussi.lehtola@iki.fi 2010-01-23 19:39:24 EST --- Hi,
go through the Fedora guidelines, most importantly http://fedoraproject.org/wiki/Packaging/Guidelines http://fedoraproject.org/wiki/Packaging/ReviewGuidelines Additionally to the Packaging Guidelines, there are a bunch of language / application specific guidelines that are linked to in the Packaging Guidelines.
Here are some tricks of the trade: http://fedoraproject.org/wiki/Packaging_tricks http://fedoraproject.org/wiki/Packaging/ScriptletSnippets http://fedoraproject.org/wiki/Common_Rpmlint_issues
***
A few notes:
- Drop the explicit requires, they're not necessary (and are in fact forbidden by the guidelines).
- Do the conversion dos2unix README.txt in %prep (after the %setup line), not in %build.
- Define macros for the major and minor revision, i.e. %global major 2 %global minor 2 and use for example ln -s liblevmar.so.%{major}.%{minor} %{buildroot}%{_libdir}/liblevmar.so.%{major}
- I suggest using the install command: instead of mkdir -p %{buildroot}%{_includedir} %{buildroot}%{_libdir} %{buildroot}%{_bindir} cp levmar.h %{buildroot}%{_includedir} cp sobj/liblevmar.so.2.2 %{buildroot}%{_libdir} cp lmdemo %{buildroot}%{_bindir} you can just run install -D -p -m 755 sobj/liblevmar.so.%{major}.%{minor} %{buildroot}%{_libdir}/liblevmar.so.%{major}.%{minor} install -D -p -m 644 levmar.h %{buildroot}%{_includedir}/levmar.h install -D -p -m 755 lmdemo %{buildroot}%{_bindir}/lmdemo which creates the necessary directores automatically, sets the correct permissions and also preserves time stamps (although this is not strictly necessary).
- Normally subpackages are declared at the beginning of the spec file, after the %description. Please move the declaration of the -devel package to the beginning (just before %prep).
- The -devel requirement should be Requires: liblevmar = %{version}-%{release}
- I'm not really sure if the demo should be in the main package; I think it would make more sense in -devel.
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--- Comment #2 from Eric Smith eric@brouhaha.com 2010-01-23 20:20:29 EST --- Hi! Thanks for the great advice! I'd read the packaging requirements but obviously managed to overlook a few things. I've updated the spec and SRPM based on your comments:
Spec URL: http://www.brouhaha.com/~eric/software/fedora/f12/levmar/levmar.spec SRPM URL: http://www.brouhaha.com/~eric/software/fedora/f12/levmar/levmar-2.5-2.fc12.s...
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--- Comment #3 from Eric Smith eric@brouhaha.com 2010-01-23 21:42:05 EST --- Koji scratch build: http://koji.fedoraproject.org/koji/taskinfo?taskID=1940699
Note to potential sponsors: I've done an unofficial package review of ByAIML, bug #557948.
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Jussi Lehtola jussi.lehtola@iki.fi changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED Blocks|177841(FE-NEEDSPONSOR) | AssignedTo|nobody@fedoraproject.org |jussi.lehtola@iki.fi Flag| |fedora-review?
--- Comment #4 from Jussi Lehtola jussi.lehtola@iki.fi 2010-01-24 04:27:50 EST --- I'm a sponsor, and will take this review.
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--- Comment #5 from Jussi Lehtola jussi.lehtola@iki.fi 2010-01-24 05:01:31 EST --- levmar.x86_64: W: shared-lib-calls-exit /usr/lib64/liblevmar.so.2.2 exit@GLIBC_2.2.5 levmar-debuginfo.x86_64: E: debuginfo-without-sources levmar-devel.x86_64: W: no-documentation 4 packages and 0 specfiles checked; 1 errors, 2 warnings.
The first warning is just a sign of unrefined coding (quite normal in scientific packages). The third one is OK.
The second one, however, needs to be fixed. The build is not using the Fedora optimization flags:
gcc -fPIC -ULINSOLVERS_RETAIN_MEMORY -O3 -funroll-loops -Wall -c lm.c -o sobj/lm.o gcc -fPIC -ULINSOLVERS_RETAIN_MEMORY -O3 -funroll-loops -Wall -c Axb.c -o sobj/Axb.o gcc -fPIC -ULINSOLVERS_RETAIN_MEMORY -O3 -funroll-loops -Wall -c misc.c -o sobj/misc.o gcc -fPIC -ULINSOLVERS_RETAIN_MEMORY -O3 -funroll-loops -Wall -c lmlec.c -o sobj/lmlec.o gcc -fPIC -ULINSOLVERS_RETAIN_MEMORY -O3 -funroll-loops -Wall -c lmbc.c -o sobj/lmbc.o gcc -fPIC -ULINSOLVERS_RETAIN_MEMORY -O3 -funroll-loops -Wall -c lmblec.c -o sobj/lmblec.o gcc -fPIC -ULINSOLVERS_RETAIN_MEMORY -O3 -funroll-loops -Wall -c lmbleic.c -o sobj/lmbleic.o gcc -fPIC -ULINSOLVERS_RETAIN_MEMORY -O3 -funroll-loops -Wall -c -o lmdemo.o lmdemo.c gcc -shared -Wl,-soname,liblevmar.so.2 -o sobj/liblevmar.so.2.2 sobj/lm.o sobj/Axb.o sobj/misc.o sobj/lmlec.o sobj/lmbc.o sobj/lmblec.o sobj/lmbleic.o #-llapack -lblas -lf2c ln -s liblevmar.so.2.2 sobj/liblevmar.so gcc lmdemo.o -o lmdemo -Lsobj -llevmar -llapack -lblas -lf2c -lm -u MAIN__
Just run make CFLAGS="%{optflags} -funroll-loops -fPIC" -f Makefile.so %{?_smp_mflags} to use the correct optimization flags.
**
You don't need f2c, it's not used anywhere (LAPACK is compiled with gfortran in Fedora). Drop the requirement from the spec file and drop the linking command from the Makefile.
**
I'd move the definitions of major and minor to the top of the spec file, and add a comment e.g.
# SOlib major and minor version %global major 2 %global minor 2
**
Use %{version} on the Source-line: Source0: http://www.ics.forth.gr/~lourakis/levmar/levmar-%%7Bversion%7D.tgz
**
Your patch is missing its comment from the spec file: # Patch to fix compilation of the shared library and compile the demo program Patch0: levmar-makefile.patch
Patches aren't normally compressed in Fedora, as they will be stored in CVS which is only reasonable for text files. Don't compress patch0.
**
More than half of the patch is junk: diff -uNr levmar-2.5.orig/Makefile.so~ levmar-2.5/Makefile.so~
I suggest you create patches with gendiff $ cd levmar-2.5 $ cp -a Makefile{,.orig} (edit Makefile to suit your needs) $ cd .. $ gendiff levmar-2.5 .orig > levmar-2.5-makefile.patch
which doesn't give you such complications.
**
I'm not sure what -P 0 does in the %patch, as it's not documented on the patch man page. I believe you can drop it.
You may want to add "-b .makefile" to the patch line, though, so that patch creates backups before applying the patch. If you need to refine your patches later on, then you just edit the patched file and create a new patch with gendiff.
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--- Comment #6 from Jussi Lehtola jussi.lehtola@iki.fi 2010-01-24 05:03:36 EST --- Oh and one more thing: you're using ${RPM_BUILD_ROOT} in %clean, but elsewhere %{buildroot}. Mixing of styles ${RPM_BUILD_ROOT} & ${RPM_OPT_FLAGS} vs. %{buildroot} & %{optflags} is forbidden in Fedora.
Please be consistent and use only %{buildroot}.
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--- Comment #7 from Jussi Lehtola jussi.lehtola@iki.fi 2010-01-24 05:25:31 EST --- Convince me that you know the packaging guidelines by doing another package submission and another informal review (go through what you missed in bug #557948), and I will sponsor you.
Please review only packages *not* marked with FE-NEEDSPONSOR. I will have to do the full formal review after you to check that you have got everything correctly. Once I have sponsored you you will be able to do formal reviews of your own.
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--- Comment #8 from Eric Smith eric@brouhaha.com 2010-01-24 23:40:20 EST --- Thanks for all of the advice, and the sponsorship offer.
"-P 0" selects patch 0; earlier I had multiple patches, but the others proved to be unnecessary. I've removed it, and made the other changes you've recommended. Here are the updated spec and SPRM:
Spec URL: http://www.brouhaha.com/~eric/software/fedora/f12/levmar/levmar.spec SRPM URL: http://www.brouhaha.com/~eric/software/fedora/f12/levmar/levmar-2.5-3.fc12.s... Koji scratch build: http://koji.fedoraproject.org/koji/taskinfo?taskID=1942076
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--- Comment #9 from Jussi Lehtola jussi.lehtola@iki.fi 2010-01-25 02:15:03 EST --- (In reply to comment #8)
"-P 0" selects patch 0; earlier I had multiple patches, but the others proved to be unnecessary. I've removed it, and made the other changes you've recommended. Here are the updated spec and SPRM:
Oh, right. But you can also do it with just %patch0
You're losing the time stamp of README.txt in the conversion. Add the -k switch to the dos2unix command, or use the sed command in
http://fedoraproject.org/wiki/Packaging_tricks#Remove_DOS_line_endings
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--- Comment #10 from Jussi Lehtola jussi.lehtola@iki.fi 2010-01-25 02:18:05 EST --- I'll do the full review once you have made another submission and another informal review.
If you're looking for something to package, you could find e.g. PRNG useful, which doesn't seem to be currently in Fedora. http://statmath.wu.ac.at/prng/
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--- Comment #11 from Eric Smith eric@brouhaha.com 2010-01-27 03:06:45 EST --- I've submitted an RPM of lcdtest. The review request is bug #559117.
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--- Comment #12 from Jussi Lehtola jussi.lehtola@iki.fi 2010-01-28 14:28:48 EST --- rpmlint output: levmar.x86_64: W: shared-lib-calls-exit /usr/lib64/liblevmar.so.2.2 exit@GLIBC_2.2.5 levmar-devel.x86_64: W: no-documentation 4 packages and 0 specfiles checked; 0 errors, 2 warnings.
These are OK. However, by installing the library and running rpmlint on it I get
levmar.x86_64: W: shared-lib-calls-exit /usr/lib64/liblevmar.so.2.2 exit@GLIBC_2.2.5 levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 spotf2_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 sqrt levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 spotrs_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 sgeqrf_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 dgemm_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 dgeqp3_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 ssytrs_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 sqrtf levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 dtrtrs_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 sgeqp3_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 dpotf2_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 dtrtri_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 dgetrf_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 sgesvd_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 ssytrf_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 sgemm_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 sgetrs_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 dorgqr_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 spotrf_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 sgetrf_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 dpotrf_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 dsytrf_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 dsytrs_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 dgeqrf_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 pow levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 strtrs_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 dpotrs_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 strtri_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 sorgqr_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 dgesvd_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 log10 levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 dgetrs_ levmar.x86_64: W: undefined-non-weak-symbol /usr/lib64/liblevmar.so.2.2 log10f 1 packages and 0 specfiles checked; 0 errors, 34 warnings.
so it actually seems that -lm -llapack is missing from the library link command.
As the library itself uses LAPACK, I recommend that you change BuildRequires: lapack-devel to BuildRequires: atlas-devel the library from "-llapack" to "-L%{_libdir}/atlas -llapack" and the blas library from "-lblas" to "-L%{_libdir}/atlas -lf77blas -latlas" since ATLAS is a lot faster than reference BLAS and LAPACK.
MUST: The package does not yet exist in Fedora. The Review Request is not a duplicate. OK MUST: The spec file for the package is legible and macros are used consistently. OK MUST: The package must be named according to the Package Naming Guidelines. OK MUST: The spec file name must match the base package %{name}. OK MUST: The package must be licensed with a Fedora approved license and meet the Licensing Guidelines. OK MUST: The License field in the package spec file must match the actual license. OK MUST: The sources used to build the package must match the upstream source, as provided in the spec URL. OK MUST: The package MUST successfully compile and build into binary rpms. OK MUST: The spec file MUST handle locales properly. N/A
MUST: Optflags are used and time stamps preserved. NEEDSWORK - Time stamp is lost in %prep phase.
MUST: Packages containing shared library files must call ldconfig. OK MUST: A package must own all directories that it creates or require the package that owns the directory. OK MUST: Files only listed once in %files listings. OK MUST: Debuginfo package is complete. OK MUST: Permissions on files must be set properly. OK MUST: Clean section exists. OK MUST: Large documentation files must go in a -doc subpackage. N/A MUST: All relevant items are included in %doc. Items in %doc do not affect runtime of application. OK MUST: Header files must be in a -devel package. OK MUST: Static libraries must be in a -static package. N/A MUST: Packages containing pkgconfig(.pc) files must 'Requires: pkgconfig'. N/A MUST: If a package contains library files with a suffix then library files ending in .so must go in a -devel package. OK MUST: In the vast majority of cases, devel packages must require the base package using a fully versioned dependency. OK MUST: Packages does not contain any .la libtool archives. N/A MUST: Desktop files are installed properly. N/A
MUST: No file conflicts with other packages and no general names. ~OK - I don't know about "lmdemo", I really would name it to "levmardemo". - Currently there doesn't seem to be any package providing /usr/bin/lmdemo. Still, I'd contact upstream to ask for a rename in the next release.
MUST: Buildroot cleaned before install. OK SHOULD: %{?dist} tag is used in release. OK SHOULD: If the package does not include license text(s) as separate files from upstream, the packager should query upstream to include it. OK SHOULD: The package builds in mock. OK
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--- Comment #13 from Eric Smith eric@brouhaha.com 2010-01-28 15:57:02 EST --- I'm reluctant to replace lapack with Atlas due to my lack of experience with the latter. I'd rather stick with lapack for now, and consider switching to Atlas at some later date. (I'll be more enthusiastic about switching if anyone using the Fedora levmar package requests the switch, and even more so if they try it and report that it works well and is noticably faster for their application.)
I found and fixed two more problems in the upstream Makefile.so and have corrected them in my patch. I have notified the upstream author and provided the patch, a description of all of the problems I've found in Makefile.so, and also about adding building the lmdemo program to it, and mentioning your request to change the name lmdemo to levmardemo.
Here's the updated package that fixes the link and preserves the README timestamp.
Spec URL: http://www.brouhaha.com/~eric/software/fedora/f12/levmar/levmar.spec SRPM URL: http://www.brouhaha.com/~eric/software/fedora/f12/levmar/levmar-2.5-4.fc12.s... Koji scratch build: http://koji.fedoraproject.org/koji/taskinfo?taskID=1950603
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--- Comment #14 from Jussi Lehtola jussi.lehtola@iki.fi 2010-01-28 16:32:11 EST --- (In reply to comment #13)
I'm reluctant to replace lapack with Atlas due to my lack of experience with the latter. I'd rather stick with lapack for now, and consider switching to Atlas at some later date. (I'll be more enthusiastic about switching if anyone using the Fedora levmar package requests the switch, and even more so if they try it and report that it works well and is noticably faster for their application.)
ATLAS is just another implementation of the same routines (and it actually uses LAPACK itself for many things). For instance in Octave we have just changed to ATLAS, which results in speedups of an order of magnitude or so. So there really is a huge difference.
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Jussi Lehtola jussi.lehtola@iki.fi changed:
What |Removed |Added ---------------------------------------------------------------------------- Flag|fedora-review? |fedora-review+
--- Comment #15 from Jussi Lehtola jussi.lehtola@iki.fi 2010-01-28 16:55:10 EST --- You can change to atlas by changing lapack-devel -> atlas-devel and defining LAPACKLIBS="-L%{_libdir}/atlas -llapack" in the make.
**
All issues have been fixed, so this package is
APPROVED
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--- Comment #16 from Eric Smith eric@brouhaha.com 2010-01-28 17:47:01 EST --- New Package CVS Request ======================= Package Name: levmar Short Description: Levenberg-Marquardt nonlinear least squares algorithm Owners: brouhaha Branches: F-12 InitialCC:
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Eric Smith eric@brouhaha.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flag| |fedora-cvs?
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--- Comment #17 from Kevin Fenzi kevin@tummy.com 2010-01-31 13:55:56 EST --- CVS done (by process-cvs-requests.py).
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--- Comment #18 from Fedora Update System updates@fedoraproject.org 2010-01-31 20:35:43 EST --- levmar-2.5-4.fc12 has been submitted as an update for Fedora 12. http://admin.fedoraproject.org/updates/levmar-2.5-4.fc12
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--- Comment #19 from Fedora Update System updates@fedoraproject.org 2010-02-01 20:14:57 EST --- levmar-2.5-4.fc12 has been pushed to the Fedora 12 stable repository. If problems still persist, please make note of it in this bug report.
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Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |CLOSED Fixed In Version| |2.5-4.fc12 Resolution| |ERRATA
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Eric Smith eric@brouhaha.com changed:
What |Removed |Added ---------------------------------------------------------------------------- Flag|fedora-cvs+ |fedora-cvs?
--- Comment #20 from Eric Smith eric@brouhaha.com 2012-03-11 03:24:36 EDT --- Package Change Request ====================== Package Name: levmar New Branches: el6 Owners: brouhaha
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--- Comment #21 from Jon Ciesla limburgher@gmail.com 2012-03-12 08:01:15 EDT --- Git done (by process-git-requests).
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--- Comment #22 from Fedora Update System updates@fedoraproject.org 2012-03-12 15:21:06 EDT --- levmar-2.5-6.el6 has been submitted as an update for Fedora EPEL 6. https://admin.fedoraproject.org/updates/levmar-2.5-6.el6
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Fedora Update System updates@fedoraproject.org changed:
What |Removed |Added ---------------------------------------------------------------------------- Fixed In Version|2.5-4.fc12 |levmar-2.5-6.el6
--- Comment #23 from Fedora Update System updates@fedoraproject.org 2012-03-28 16:39:50 EDT --- levmar-2.5-6.el6 has been pushed to the Fedora EPEL 6 stable repository.
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