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e1ba71f |
%global packname rtracklayer
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e1ba71f |
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4d90641 |
%global __suggests_exclude ^R\\((BSgenome\\.Hsapiens\\.UCSC\\.hg19|GenomicFeatures|TxDb\\.Hsapiens\\.UCSC\\.hg19\\.knownGene|genefilter|hgu133plus2\\.db|humanStemCell|limma|microRNA|org\\.Hs\\.eg\\.db)\\)
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4d90641 |
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e1ba71f |
Name: R-%{packname}
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d1c0167 |
Version: 1.56.1
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032012c |
Release: 4%{dist}
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e1ba71f |
Summary: R interface to genome browsers and their annotation tracks
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e1ba71f |
License: Artistic 2.0 and BSD
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e1ba71f |
URL: http://www.bioconductor.org/packages/release/bioc/html/rtracklayer.html
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1f67813 |
Source0: http://www.bioconductor.org/packages/release/bioc/src/contrib/%{packname}_%{version}.tar.gz
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e1ba71f |
Source1: rtracklayer_jimkent_license.txt
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dc2a214 |
Requires: texlive-latex
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1f67813 |
BuildRequires: R-devel >= 3.3.0, R-methods, R-RCurl >= 1.4.2, R-XML >= 1.98.0
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a8f2f62 |
BuildRequires: R-IRanges-devel >= 2.13.13, R-GenomicRanges >= 1.37.2, R-Biostrings-devel >= 2.47.6
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add5b12 |
BuildRequires: R-Rsamtools-devel >= 1.31.2, zlib-devel
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94f7aa2 |
BuildRequires: R-XVector-devel >= 0.19.7, R-BiocGenerics >= 0.35.3, R-S4Vectors-devel >= 0.23.18
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add5b12 |
BuildRequires: R-GenomeInfoDb >= 1.15.2, R-GenomicAlignments >= 1.15.6, R-tools
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bde1ad3 |
BuildRequires: openssl-devel
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398ba68 |
BuildRequires: R-BiocIO, R-restfulr >= 0.0.13
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e1ba71f |
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e1ba71f |
%description
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a8f2f62 |
Extensible framework for interacting with multiple genome browsers (currently
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a8f2f62 |
UCSC built-in) and manipulating annotation tracks in various formats
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e1ba71f |
(currently GFF, BED, bedGraph, BED15, WIG, and BigWig built-in). The user may
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a8f2f62 |
export/import tracks to/from the supported browsers, as well as query and
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e1ba71f |
modify the browser state, such as the current viewport.
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e1ba71f |
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e1ba71f |
%prep
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e1ba71f |
%setup -c -q -n %{packname}
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c5659b4 |
sed -i -e 's|zlibbioc,||' rtracklayer/DESCRIPTION
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c5659b4 |
sed -i -e 's|import(zlibbioc)||' rtracklayer/NAMESPACE
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c5659b4 |
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a8f2f62 |
# This email confirms that we have permission to use the Jim Kent
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e1ba71f |
# copyrighted files under the BSD license.
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e1ba71f |
cp %{SOURCE1} .
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e1ba71f |
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e1ba71f |
%build
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e1ba71f |
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e1ba71f |
%install
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e1ba71f |
mkdir -p %{buildroot}%{_libdir}/R/library
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a8f2f62 |
%{_bindir}/R CMD INSTALL %{packname} -l %{buildroot}%{_libdir}/R/library
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e1ba71f |
# Clean up in advance of check
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e1ba71f |
test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
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e1ba71f |
rm -rf %{buildroot}%{_libdir}/R/library/R.css
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e1ba71f |
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e1ba71f |
# Zero file
|
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e1ba71f |
rm -rf %{buildroot}%{_libdir}/R/library/%{packname}/tests/quickload/T_species_Oct_2011/bedGraphData.bw
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e1ba71f |
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e1ba71f |
%check
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e1ba71f |
# All sorts of missing Suggests prevents this from working.
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e1ba71f |
# %%{_bindir}/R CMD check %%{packname}
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e1ba71f |
|
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e1ba71f |
%files
|
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|
e1ba71f |
%dir %{_libdir}/R/library/%{packname}
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e1ba71f |
%doc %{_libdir}/R/library/%{packname}/html
|
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|
c10330c |
%doc %{_libdir}/R/library/%{packname}/CITATION
|
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|
e1ba71f |
%doc %{_libdir}/R/library/%{packname}/DESCRIPTION
|
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|
c10330c |
%doc %{_libdir}/R/library/%{packname}/NEWS
|
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e1ba71f |
%doc %{_libdir}/R/library/%{packname}/doc/
|
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|
1f67813 |
%license rtracklayer_jimkent_license.txt
|
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|
1f67813 |
%license %{_libdir}/R/library/%{packname}/LICENSE
|
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|
e1ba71f |
%{_libdir}/R/library/%{packname}/INDEX
|
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|
e1ba71f |
%{_libdir}/R/library/%{packname}/NAMESPACE
|
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|
e1ba71f |
%{_libdir}/R/library/%{packname}/Meta
|
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|
e1ba71f |
%{_libdir}/R/library/%{packname}/R
|
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|
e1ba71f |
%{_libdir}/R/library/%{packname}/data/
|
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|
f3ae07c |
%{_libdir}/R/library/%{packname}/extdata/
|
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|
e1ba71f |
%{_libdir}/R/library/%{packname}/demo/
|
|
|
e1ba71f |
%{_libdir}/R/library/%{packname}/help
|
|
|
e1ba71f |
%{_libdir}/R/library/%{packname}/libs/
|
|
|
e1ba71f |
%{_libdir}/R/library/%{packname}/notes/
|
|
|
e1ba71f |
%{_libdir}/R/library/%{packname}/scripts/
|
|
|
e1ba71f |
%{_libdir}/R/library/%{packname}/tests/
|
|
|
c10330c |
%{_libdir}/R/library/%{packname}/unitTests/
|
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|
e1ba71f |
|
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|
e1ba71f |
%changelog
|
|
|
032012c |
* Wed Jul 19 2023 Fedora Release Engineering <releng@fedoraproject.org> - 1.56.1-4
|
|
|
032012c |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild
|
|
|
032012c |
|
|
|
2015379 |
* Fri Apr 21 2023 Iñaki Úcar <iucar@fedoraproject.org> - 1.56.1-3
|
|
|
2015379 |
- R-maint-sig mass rebuild
|
|
|
2015379 |
|
|
|
5b4886c |
* Wed Jan 18 2023 Fedora Release Engineering <releng@fedoraproject.org> - 1.56.1-2
|
|
|
5b4886c |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild
|
|
|
5b4886c |
|
|
|
d1c0167 |
* Sun Sep 04 2022 Iñaki Úcar <iucar@fedoraproject.org> - 1.56.1-1
|
|
|
d1c0167 |
- R 4.2.1, update to 1.56.1
|
|
|
d1c0167 |
|
|
|
3461e4b |
* Wed Jul 20 2022 Fedora Release Engineering <releng@fedoraproject.org> - 1.52.0-5
|
|
|
3461e4b |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild
|
|
|
3461e4b |
|
|
|
3bf5555 |
* Wed Jan 19 2022 Fedora Release Engineering <releng@fedoraproject.org> - 1.52.0-4
|
|
|
3bf5555 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild
|
|
|
3bf5555 |
|
|
|
484ed45 |
* Tue Sep 14 2021 Sahana Prasad <sahana@redhat.com> - 1.52.0-3
|
|
|
484ed45 |
- Rebuilt with OpenSSL 3.0.0
|
|
|
484ed45 |
|
|
|
3d5f801 |
* Wed Jul 21 2021 Fedora Release Engineering <releng@fedoraproject.org> - 1.52.0-2
|
|
|
3d5f801 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild
|
|
|
3d5f801 |
|
|
|
398ba68 |
* Thu Jun 17 2021 Tom Callaway <spot@fedoraproject.org> - 1.52.0-1
|
|
|
398ba68 |
- update to 1.52.0
|
|
|
398ba68 |
- Rebuilt for R 4.1.0
|
|
|
398ba68 |
|
|
|
94f7aa2 |
* Thu Feb 4 2021 Tom Callaway <spot@fedoraproject.org> - 1.50.0-1
|
|
|
94f7aa2 |
- update to 1.50.0
|
|
|
94f7aa2 |
|
|
|
274ca13 |
* Mon Jan 25 2021 Fedora Release Engineering <releng@fedoraproject.org> - 1.48.0-4
|
|
|
274ca13 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild
|
|
|
274ca13 |
|
|
|
21d1353 |
* Sat Aug 01 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.48.0-3
|
|
|
21d1353 |
- Second attempt - Rebuilt for
|
|
|
21d1353 |
https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
|
|
|
21d1353 |
|
|
|
774111d |
* Mon Jul 27 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.48.0-2
|
|
|
774111d |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
|
|
|
774111d |
|
|
|
83193c5 |
* Mon Jun 8 2020 Tom Callaway <spot@fedoraproject.org> - 1.48.0-1
|
|
|
83193c5 |
- update to 1.48.0
|
|
|
83193c5 |
- rebuild for R 4
|
|
|
83193c5 |
|
|
|
62da8ac |
* Tue Jan 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.46.0-3
|
|
|
62da8ac |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
|
|
|
62da8ac |
|
|
|
4d90641 |
* Thu Nov 21 2019 Elliott Sales de Andrade <quantum.analyst@gmail.com> - 1.46.0-2
|
|
|
4d90641 |
- Exclude Suggests for unavailable packages
|
|
|
4d90641 |
|
|
|
a8f2f62 |
* Wed Nov 6 2019 Tom Callaway <spot@fedoraproject.org> - 1.46.0-1
|
|
|
a8f2f62 |
- update to 1.46.0
|
|
|
a8f2f62 |
|
|
|
dc2a214 |
* Mon Aug 12 2019 Elliott Sales de Andrade <quantum.analyst@gmail.com> - 1.44.0-3
|
|
|
dc2a214 |
- Remove explicit dependencies provided by automatic dependency generator
|
|
|
dc2a214 |
|
|
|
5c10024 |
* Wed Jul 24 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.44.0-2
|
|
|
5c10024 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild
|
|
|
5c10024 |
|
|
|
bde1ad3 |
* Fri Jun 7 2019 Tom Callaway <spot@fedoraproject.org> - 1.44.0-1
|
|
|
bde1ad3 |
- update to 1.44.0
|
|
|
bde1ad3 |
|
|
|
c430b60 |
* Thu Jan 31 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.40.2-3
|
|
|
c430b60 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild
|
|
|
c430b60 |
|
|
|
1f3bbb9 |
* Thu Jul 12 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.40.2-2
|
|
|
1f3bbb9 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild
|
|
|
1f3bbb9 |
|
|
|
add5b12 |
* Fri May 18 2018 Tom Callaway <spot@fedoraproject.org> - 1.40.2-1
|
|
|
add5b12 |
- update to 1.40.2
|
|
|
add5b12 |
|
|
|
3be4ac3 |
* Fri Mar 23 2018 Tom Callaway <spot@fedoraproject.org> - 1.38.3-1
|
|
|
3be4ac3 |
- update to 1.38.3
|
|
|
3be4ac3 |
|
|
|
f0ce968 |
* Wed Feb 07 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.36.3-4
|
|
|
f0ce968 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild
|
|
|
f0ce968 |
|
|
|
db3d48c |
* Wed Aug 02 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.36.3-3
|
|
|
db3d48c |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild
|
|
|
db3d48c |
|
|
|
72f7dd7 |
* Wed Jul 26 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.36.3-2
|
|
|
72f7dd7 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild
|
|
|
72f7dd7 |
|
|
|
1f67813 |
* Wed May 31 2017 Tom Callaway <spot@fedoraproject.org> - 1.36.3-1
|
|
|
1f67813 |
- update to 1.36.3
|
|
|
1f67813 |
|
|
|
661aac0 |
* Fri Feb 10 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.30.2-2
|
|
|
661aac0 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild
|
|
|
661aac0 |
|
|
|
f5028fe |
* Thu Feb 11 2016 pingou <pingou@pingoured.fr> 1.30.2-1
|
|
|
f5028fe |
- Update to version 1.30.2
|
|
|
f5028fe |
|
|
|
bdaa4f1 |
* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 1.28.6-2
|
|
|
bdaa4f1 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild
|
|
|
bdaa4f1 |
|
|
|
28afc59 |
* Fri Jul 03 2015 pingou <pingou@pingoured.fr> 1.28.6-1
|
|
|
28afc59 |
- Update to version 1.28.6
|
|
|
28afc59 |
|
|
|
275f793 |
* Tue Jun 16 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.22.3-6
|
|
|
275f793 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild
|
|
|
275f793 |
|
|
|
8d95ff1 |
* Fri Aug 15 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.22.3-5
|
|
|
8d95ff1 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
|
|
|
8d95ff1 |
|
|
Yaakov Selkowitz |
080be86 |
* Thu Jul 31 2014 Yaakov Selkowitz <yselkowi@redhat.com> - 1.22.3-4
|
|
Yaakov Selkowitz |
080be86 |
- Add missing BR: R-XVector-devel (#1105923)
|
|
Yaakov Selkowitz |
080be86 |
|
|
|
c5659b4 |
* Thu Jul 03 2014 Pierre-Yves Chibon <pingou@pingoured.fr> - 1.22.3-3
|
|
|
c5659b4 |
- Drop the patch fixing the zlibbioc import/dependency in favor of a couple of
|
|
|
c5659b4 |
sed commands
|
|
|
c5659b4 |
|
|
|
47b81e8 |
* Fri Jun 06 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.22.3-2
|
|
|
47b81e8 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
|
|
|
47b81e8 |
|
|
|
76069fb |
* Mon Feb 3 2014 Tom Callaway <spot@fedoraproject.org> - 1.22.3-1
|
|
|
76069fb |
- update to 1.22.3
|
|
|
76069fb |
|
|
|
0a80b55 |
* Fri Aug 02 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.20.0-2
|
|
|
0a80b55 |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild
|
|
|
0a80b55 |
|
|
|
f3ae07c |
* Thu Apr 11 2013 Tom Callaway <spot@fedoraproject.org> - 1.20.0-1
|
|
|
f3ae07c |
- update to 1.20.0
|
|
|
f3ae07c |
|
|
|
c10330c |
* Fri Feb 22 2013 Tom Callaway <spot@fedoraproject.org> - 1.18.2-1
|
|
|
c10330c |
- update to 1.18.2
|
|
|
c10330c |
|
|
|
d6b1cad |
* Wed Feb 13 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.14.1-5
|
|
|
d6b1cad |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild
|
|
|
d6b1cad |
|
|
|
ba4cacd |
* Wed Jul 18 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.14.1-4
|
|
|
ba4cacd |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild
|
|
|
ba4cacd |
|
|
|
d2d7d6d |
* Thu Jan 12 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.14.1-3
|
|
|
d2d7d6d |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild
|
|
|
d2d7d6d |
|
|
|
e1ba71f |
* Mon Nov 14 2011 Tom Callaway <spot@fedoraproject.org> 1.14.1-2
|
|
|
e1ba71f |
- update licensing with clarification from Jim Kent
|
|
|
e1ba71f |
|
|
|
e1ba71f |
* Thu Nov 10 2011 Tom "spot" Callaway <tcallawa@redhat.com> 1.14.1-1
|
|
|
e1ba71f |
- initial package for Fedora
|