%global packname  rtracklayer

%global __suggests_exclude ^R\\((BSgenome\\.Hsapiens\\.UCSC\\.hg19|GenomicFeatures|TxDb\\.Hsapiens\\.UCSC\\.hg19\\.knownGene|genefilter|hgu133plus2\\.db|humanStemCell|limma|microRNA|org\\.Hs\\.eg\\.db)\\)

Name:             R-%{packname}

Version:          1.44.0

Release:          4%{dist}

Summary:          R interface to genome browsers and their annotation tracks

License:          Artistic 2.0 and BSD

URL:              http://www.bioconductor.org/packages/release/bioc/html/rtracklayer.html

Source0:          http://www.bioconductor.org/packages/release/bioc/src/contrib/%{packname}_%{version}.tar.gz

Source1:          rtracklayer_jimkent_license.txt

Requires:         texlive-latex

BuildRequires:    R-devel >= 3.3.0, R-methods, R-RCurl >= 1.4.2, R-XML >= 1.98.0

BuildRequires:    R-IRanges-devel >= 2.13.13, R-GenomicRanges >= 1.31.8, R-Biostrings-devel >= 2.47.6

BuildRequires:    R-Rsamtools-devel >= 1.31.2, zlib-devel

BuildRequires:    R-XVector-devel >= 0.19.7, R-BiocGenerics >= 0.25.1, R-S4Vectors-devel >= 0.19.22

BuildRequires:    R-GenomeInfoDb >= 1.15.2, R-GenomicAlignments >= 1.15.6, R-tools

BuildRequires:    openssl-devel

%description

Extensible framework for interacting with multiple genome browsers (currently 

UCSC built-in) and manipulating annotation tracks in various formats 

(currently GFF, BED, bedGraph, BED15, WIG, and BigWig built-in). The user may

export/import tracks to/from the supported browsers, as well as query and 

modify the browser state, such as the current viewport.

%prep

%setup -c -q -n %{packname}

sed -i -e 's|zlibbioc,||' rtracklayer/DESCRIPTION

sed -i -e 's|import(zlibbioc)||' rtracklayer/NAMESPACE

# This email confirms that we have permission to use the Jim Kent 

# copyrighted files under the BSD license.

cp %{SOURCE1} .

%build

%install

mkdir -p %{buildroot}%{_libdir}/R/library

%{_bindir}/R CMD INSTALL %{packname} -l %{buildroot}%{_libdir}/R/library 

# Clean up in advance of check

test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)

rm -rf %{buildroot}%{_libdir}/R/library/R.css

# Zero file

rm -rf %{buildroot}%{_libdir}/R/library/%{packname}/tests/quickload/T_species_Oct_2011/bedGraphData.bw

%check

# All sorts of missing Suggests prevents this from working.

# %%{_bindir}/R CMD check %%{packname}

%files

%dir %{_libdir}/R/library/%{packname}

%doc %{_libdir}/R/library/%{packname}/html

%doc %{_libdir}/R/library/%{packname}/CITATION

%doc %{_libdir}/R/library/%{packname}/DESCRIPTION

%doc %{_libdir}/R/library/%{packname}/NEWS

%doc %{_libdir}/R/library/%{packname}/doc/

%license rtracklayer_jimkent_license.txt

%license %{_libdir}/R/library/%{packname}/LICENSE

%{_libdir}/R/library/%{packname}/INDEX

%{_libdir}/R/library/%{packname}/NAMESPACE

%{_libdir}/R/library/%{packname}/Meta

%{_libdir}/R/library/%{packname}/R

%{_libdir}/R/library/%{packname}/data/

%{_libdir}/R/library/%{packname}/extdata/

%{_libdir}/R/library/%{packname}/demo/

%{_libdir}/R/library/%{packname}/help

%{_libdir}/R/library/%{packname}/libs/

%{_libdir}/R/library/%{packname}/notes/

%{_libdir}/R/library/%{packname}/scripts/

%{_libdir}/R/library/%{packname}/tests/

%{_libdir}/R/library/%{packname}/unitTests/

%changelog

* Thu Nov 21 2019 Elliott Sales de Andrade <quantum.analyst@gmail.com> - 1.44.0-4

- Exclude Suggests for unavailable packages

* Mon Aug 12 2019 Elliott Sales de Andrade <quantum.analyst@gmail.com> - 1.44.0-3

- Remove explicit dependencies provided by automatic dependency generator

* Wed Jul 24 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.44.0-2

- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild

* Fri Jun  7 2019 Tom Callaway <spot@fedoraproject.org> - 1.44.0-1

- update to 1.44.0

* Thu Jan 31 2019 Fedora Release Engineering <releng@fedoraproject.org> - 1.40.2-3

- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild

* Thu Jul 12 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.40.2-2

- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild

* Fri May 18 2018 Tom Callaway <spot@fedoraproject.org> - 1.40.2-1

- update to 1.40.2

* Fri Mar 23 2018 Tom Callaway <spot@fedoraproject.org> - 1.38.3-1

- update to 1.38.3

* Wed Feb 07 2018 Fedora Release Engineering <releng@fedoraproject.org> - 1.36.3-4

- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild

* Wed Aug 02 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.36.3-3

- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild

* Wed Jul 26 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.36.3-2

- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild

* Wed May 31 2017 Tom Callaway <spot@fedoraproject.org> - 1.36.3-1

- update to 1.36.3

* Fri Feb 10 2017 Fedora Release Engineering <releng@fedoraproject.org> - 1.30.2-2

- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild

* Thu Feb 11 2016 pingou <pingou@pingoured.fr> 1.30.2-1

- Update to version 1.30.2

* Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 1.28.6-2

- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild

* Fri Jul 03 2015 pingou <pingou@pingoured.fr> 1.28.6-1

- Update to version 1.28.6

* Tue Jun 16 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.22.3-6

- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild

* Fri Aug 15 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.22.3-5

- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild

* Thu Jul 31 2014 Yaakov Selkowitz <yselkowi@redhat.com> - 1.22.3-4

- Add missing BR: R-XVector-devel (#1105923)

* Thu Jul 03 2014 Pierre-Yves Chibon <pingou@pingoured.fr> - 1.22.3-3

- Drop the patch fixing the zlibbioc import/dependency in favor of a couple of

  sed commands

* Fri Jun 06 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.22.3-2

- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild

* Mon Feb  3 2014 Tom Callaway <spot@fedoraproject.org> - 1.22.3-1

- update to 1.22.3

* Fri Aug 02 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.20.0-2

- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild

* Thu Apr 11 2013 Tom Callaway <spot@fedoraproject.org> - 1.20.0-1

- update to 1.20.0

* Fri Feb 22 2013 Tom Callaway <spot@fedoraproject.org> - 1.18.2-1

- update to 1.18.2

* Wed Feb 13 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.14.1-5

- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild

* Wed Jul 18 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.14.1-4

- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild

* Thu Jan 12 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 1.14.1-3

- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild

* Mon Nov 14 2011 Tom Callaway <spot@fedoraproject.org> 1.14.1-2

- update licensing with clarification from Jim Kent

* Thu Nov 10 2011 Tom "spot" Callaway <tcallawa@redhat.com> 1.14.1-1

- initial package for Fedora